Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and Engineering

ABSTRACT The field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de novo protein design. This review consolidates and critiques a comprehensive range of modern computational resources, offering a unique focus on...

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Vydáno v:Engineering reports (Hoboken, N.J.) Ročník 7; číslo 2
Hlavní autoři: Mia, Md. Mojnu, Sultana, Habiba, Amin, Md. Al, Hossain, Md. Sakhawat, Imam, Hasan, Mohiuddin, A. K. M., Mahmud, Shahin
Médium: Journal Article
Jazyk:angličtina
Vydáno: Hoboken, USA John Wiley & Sons, Inc 01.02.2025
Wiley
Témata:
Accuracy
Algorithms
Amino acids
Artificial intelligence
Bioinformatics
Biomedical materials
Datasets
Design
Energy
Engineering
Machine learning
Mutagenesis
Mutation
Neural networks
NMR
Nuclear magnetic resonance
protein computational resources
protein design
protein engineering
protein engineering tools
Proteins
Research methodology
Software
Stability
ISSN:2577-8196, 2577-8196
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Abstract ABSTRACT The field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de novo protein design. This review consolidates and critiques a comprehensive range of modern computational resources, offering a unique focus on their applications across diverse domains, including protein stability prediction, posttranslational modification analysis, and mutation effect evaluation. Key contributions include a detailed examination of tools integrating machine learning and artificial intelligence to enhance predictive accuracy and streamline protein engineering workflows. By highlighting underexplored tools and novel methodologies, such as advanced protein–ligand interaction predictors and neural network–based stability assessment models, this study establishes itself as a unique reference for researchers aiming to develop tailored proteins for therapeutic, industrial, and biomedical applications. Illustration of modern computational approaches in protein engineering, encompassing mutation analysis, protein dynamics, high‐throughput screening, and enzyme optimization to enhance de novo protein design and functional understanding
AbstractList The field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de novo protein design. This review consolidates and critiques a comprehensive range of modern computational resources, offering a unique focus on their applications across diverse domains, including protein stability prediction, posttranslational modification analysis, and mutation effect evaluation. Key contributions include a detailed examination of tools integrating machine learning and artificial intelligence to enhance predictive accuracy and streamline protein engineering workflows. By highlighting underexplored tools and novel methodologies, such as advanced protein–ligand interaction predictors and neural network–based stability assessment models, this study establishes itself as a unique reference for researchers aiming to develop tailored proteins for therapeutic, industrial, and biomedical applications.
ABSTRACT The field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de novo protein design. This review consolidates and critiques a comprehensive range of modern computational resources, offering a unique focus on their applications across diverse domains, including protein stability prediction, posttranslational modification analysis, and mutation effect evaluation. Key contributions include a detailed examination of tools integrating machine learning and artificial intelligence to enhance predictive accuracy and streamline protein engineering workflows. By highlighting underexplored tools and novel methodologies, such as advanced protein–ligand interaction predictors and neural network–based stability assessment models, this study establishes itself as a unique reference for researchers aiming to develop tailored proteins for therapeutic, industrial, and biomedical applications.
ABSTRACT The field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de novo protein design. This review consolidates and critiques a comprehensive range of modern computational resources, offering a unique focus on their applications across diverse domains, including protein stability prediction, posttranslational modification analysis, and mutation effect evaluation. Key contributions include a detailed examination of tools integrating machine learning and artificial intelligence to enhance predictive accuracy and streamline protein engineering workflows. By highlighting underexplored tools and novel methodologies, such as advanced protein–ligand interaction predictors and neural network–based stability assessment models, this study establishes itself as a unique reference for researchers aiming to develop tailored proteins for therapeutic, industrial, and biomedical applications. Illustration of modern computational approaches in protein engineering, encompassing mutation analysis, protein dynamics, high‐throughput screening, and enzyme optimization to enhance de novo protein design and functional understanding
Author Amin, Md. Al
Mia, Md. Mojnu
Sultana, Habiba
Mahmud, Shahin
Hossain, Md. Sakhawat
Mohiuddin, A. K. M.
Imam, Hasan
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  surname: Mahmud
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  email: shahin018mbstu@gmail.com, shahinbge@mbstu.ac.bd
  organization: Mawlana Bhashani Science and Technology University
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Cites_doi 10.3390/PR7120869
10.1002/wcms.1220
10.1016/j.jconrel.2019.02.016
10.1186/1471‐2105‐8‐126
10.1093/bib/bbz169
10.1016/j.csbj.2018.01.002
10.1016/j.copbio.2011.11.008
10.1101/cshperspect.a033845
10.1371/journal.pone.0183318
10.1093/nar/gkad989
10.1016/j.gpb.2020.01.001
10.1186/s13321‐023‐00788‐8
10.7454/mss.v23i1.7609
10.1007/978-1-4939-9173-0_1
10.1038/s41467‐024‐46485‐4
10.1093/bib/bbaa150
10.2174/1389203724666230110163234
10.3109/10409238509086784
10.1038/s41586‐021‐03819‐2
10.1021/acs.jctc.9b00366
10.1146/annurev.bb.13.060184.001555
10.1038/s41592‐020‐0848‐2
10.1002/cctc.202000933
10.1093/molbev/msu300
10.1093/bioinformatics/btv291
10.1093/bioinformatics/btw192
10.1093/bib/bbab184
10.1038/nbt1208‐1339
10.1093/molbev/msy096
10.1146/annurev.genom.9.081307.164359
10.1186/1471‐2105‐12‐151
10.17760/D20409258
10.1038/msb4100182
10.1038/nprot.2015.123
10.1093/bioinformatics/bti263
10.1101/gr.1224503
10.1093/bioinformatics/btm098
10.1093/nar/gkh430
10.1021/ci800324m
10.1039/d3ra06476j
10.1016/j.jconrel.2018.12.032
10.1016/j.csbj.2023.04.027
10.1093/bioinformatics/10.2.189
10.1093/bioinformatics/btz854
10.1073/PNAS.78.9.5275
10.1093/bioinformatics/btp386
10.1007/978-1-4939-2343-4_10
10.1093/nar/gkad383
10.1093/nar/gkr366
10.1093/bioinformatics/btx662
10.1093/nar/gku411
10.1007/978-1-4939-7366-8_4
10.1016/s0021‐9258(18)45665‐7
10.1038/emboj.2013.79
10.1021/acs.bioconjchem.3c00374
10.1038/srep23257
10.1093/bioinformatics/btr088
10.1093/nar/gkl163
10.1002/humu.21242
10.2174/0929866530666230519122612
10.1371/journal.pone.0055844
10.1038/nmeth.3959
10.1093/nar/27.23.4636
10.1002/JCC.21787
10.1093/bioinformatics/btz773
10.3390/pharmaceutics14112533
10.1016/j.csbj.2022.12.008
10.1073/pnas.1821309116
10.1093/bioinformatics/btx417
10.1093/nar/gks539
10.1093/nar/gkg584
10.1007/978-1-4939-6798-8_14
10.1093/nar/gkl190
10.1186/s12915‐023‐01510‐8
10.1093/nar/gkr407
10.1038/nmeth.4197
10.1093/nar/gkt1055
10.1016/j.softx.2015.06.001
10.1093/molbev/msaa015
10.3390/ijms161024918
10.1201/9781003283119-15
10.1093/nar/gkt427
10.1002/0471142905.hg0720s76
10.1002/jcc.21287
10.1038/s41586‐023‐06415‐8
10.1186/s12859‐015‐0548‐6
10.1093/nar/gkx313
10.1093/sysbio/syq010
10.1093/nar/30.1.200
10.1093/nar/gkm1005
10.1021/acs.jcim.5b00276
10.1002/cbic.202200152
10.1093/nar/29.12.2607
10.1002/pro.4218
10.1093/database/baab012
10.1093/nar/gky1016
10.1093/nar/gki372
10.1093/bioinformatics/bti486
10.1093/bioinformatics/btl623
10.1186/1471‐2105‐7‐166
10.1016/j.jprot.2011.09.014
10.1093/bioinformatics/18.suppl_1.s71
10.1016/j.celrep.2013.10.041
10.1186/s13073‐021‐00835‐9
10.1038/srep01448
10.1093/bioinformatics/btu420
10.1093/nar/gki458
10.1101/2023.05.03.539278
10.1002/pmic.200300771
10.1093/nar/gkr367
10.1002/pro.3313
10.1016/j.molcel.2018.08.033
10.1016/j.commatsci.2019.109363
10.1093/molbev/msm088
10.1186/gb-2014-15-1-r17
10.1093/nar/gkx369
10.1093/nar/gkp410
10.1093/nar/gki404
10.1007/978‐1‐59745‐177‐2_13
10.1146/annurev.biochem.77.062906.171838
10.1002/jcc.20289
10.1073/pnas.2206111119
10.1093/nar/gku1151
10.1016/j.copbio.2017.12.020
10.1016/j.compbiomed.2022.105695
10.1093/nar/25.17.3389
10.1038/nbt.1621
10.1093/bioinformatics/btac115
10.1093/bioinformatics/bts139
10.1016/j.plipres.2018.07.001
10.1093/nar/gkl922
10.1186/1471‐2164‐14‐s3‐s6
10.1093/bioinformatics/btu033
10.1093/nar/gkw408
10.1093/nar/gkx412
10.1016/0263‐7855(96)00018‐5
10.1371/journal.pone.0011290
10.1093/bib/bbad090
10.1002/prot.26614
10.1038/s41592‐019‐0496‐6
10.1093/nar/gkl233
10.1093/bioinformatics/btu852
10.1093/bioinformatics/btw361
10.2174/1570180819666220510140605
10.2174/0929866526666191002111404
10.1371/journal.pone.0049108
10.1038/nbt.4247
10.7150/ijbs.31957
10.1038/s41467‐020‐19669‐x
10.1002/pro.3978
10.3390/molecules28135169
10.1016/j.jmb.2014.09.026
10.1093/nar/gkaa372
10.1146/annurev.physchem.58.032806.104614
10.1093/bioinformatics/bty348
10.1093/nar/gkaa1104
10.1093/nar/gkm659
10.1093/nar/gkv1194
10.1093/nar/gkm764
10.1038/nmeth0810‐575
10.1016/j.sbi.2020.01.008
10.1093/nar/gkj083
10.1093/bioinformatics/btx345
10.7150/ijbs.24121
10.1021/acs.jcim.8b00697
10.1093/bioinformatics/bty166
10.1002/0471142727.mb1911s96
10.1038/nmeth0410‐248
10.1109/TPAMI.2021.3095381
10.1093/nar/gkt1240
10.1002/jcc.20290
10.1186/1471‐2164‐14‐s3‐s7
10.1016/S0022-2836(03)00888-X
10.1016/j.gpb.2023.03.007
10.1038/s42256‐019‐0049‐9
10.1093/nar/gku1081
10.1371/journal.pone.0089575
10.1093/bib/bbaa134
10.1093/bioinformatics/btaa578
10.1093/nar/gki375
10.3390/biology12020166
10.1093/bib/bbad004
10.1093/bioinformatics/btw387
10.1016/j.bbrc.2004.11.001
10.1016/j.cpc.2021.108171
10.1093/bioinformatics/btv195
10.1093/bioinformatics/btp445
10.1093/bioinformatics/bts507
10.1093/bioinformatics/bty341
10.1002/prot.20810
10.1093/bib/bbs029
10.1002/jcc.20303
10.1016/j.gpb.2022.11.014
10.1093/bioinformatics/btv769
10.1038/nmeth0607-466
10.1038/nmeth.2890
10.1002/humu.22225
10.1016/B978‐0‐32‐390644‐9.00085‐8
10.1093/bioinformatics/bty862
10.1007/978‐1‐4939‐7366‐8_3
10.1093/bioinformatics/bti130
10.1038/s41598‐018‐22531‐2
10.1038/nchembio.1199
10.1155/2022/8929715
10.1093/bioinformatics/19.1.163
10.1093/nar/gkac1071
10.1093/nar/gkm772
10.1007/978-94-007-6178-0_100946-1
10.1093/nar/gki387
10.1093/bioinformatics/btw377
10.1021/acs.analchem.1C00895
10.1038/nature01511
10.1021/acs.jpcb.3c06662.OpenMM
10.1038/s41598‐018‐28948‐z
10.1016/BS.APCSB.2022.01.003
10.1093/nar/gku557
10.1021/acsptsci.3c00269
10.1093/bioinformatics/btac678
10.1093/bioinformatics/btg241
10.1016/j.csbj.2017.03.004
10.1242/dmm.049874
10.1126/science.6572017
10.1093/nar/gkv315
10.1101/2022.02.17.480964
10.1111/j.1742‐4658.2012.08603.x
10.1038/s42256‐021‐00348‐5
10.1002/0471250953.bi0614s51
10.1093/nar/gkj118
10.1021/cen‐10112‐cover
10.21474/ijar01/14120
10.7554/eLife.82593
10.1002/bmb.2005.494033032449
10.3390/ijms161025831
10.1186/1471‐2105‐5‐79
10.1021/acs.jpcb.0c11640
10.1002/pro.3923
10.1186/gb‐2007‐8‐11‐r250
10.1093/nar/gkab1017
10.1093/nar/gkq1159
10.1371/journal.pcbi.1002285
10.1371/journal.pone.0046688
10.1093/bioinformatics/btx536
10.1101/gr.235028.118.29
10.2147/dddt.s236788
10.1093/bioinformatics/17.9.847
10.1093/nar/gkq936
10.1016/j.str.2007.09.024
10.1093/nar/gki385
10.33545/27076636.2022.v3.i1a.33
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Notes The authors received no specific funding for this work.
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Md. Mojnu Mia and Habiba Sultana equally contributed as first author.
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References 2015; 1–2
2004; 325
April 2011; 27
2019; 11
2019; 15
2020; 17
2016; 32
2004; 4
2019; 16
2004; 5
2020; 12
2020; 11
October 2009; 25
2012; 14
2004; 32
2019; 23
2008; 26
2012; 28
2012; 23
July 2023; 51
February 2013; 8
2010; 7
September 2011; 39
2016; 44
March 2020; 36
2021; 49
2021; 48
October 2014; 30
2019; 32
April 2018; 34
1999; 27
2020; 37
2020; 36
2001; 29
2024; 15
2011; 7
2016; 13
2007; 15
2016; 11
2016; 6
January 2008; 36
2013; 76
May 2005; 21
May 2016; 32
2020; 27
November 2012; 7
2019; 295
1994; 10
2023; 30
2010; 59
2023; 36
November 2017; 33
2023; 34
July 2008
2021; 125
2020; 61
2019; 59
2008; 9
2011; 96
May 2019; 35
2008; 77
August 2022
May 2021; 22
2023; 20
2023; 21
2002; 2001
February2014; 9
2023; 24
2013; 14
2023; 28
August 2018; 34
2021; 596
2017; 33
1984; 13
2001; 17
2018; 72
2018; 71
2007; 23
January 2018; 8
2023; 13
2015; 5
2021; 3
2023; 12
2012
2002; 30
2023; 15
2023; 16
2019; 301
2008; 443
April 2022; 23
2021; 93
January 2007; 35
2007; 58
May 2015; 31
2022; 2022
2017; 15
2023
2022
2013; 34
2020
2017; 12
January 2024; 52
January 2017; 14
2019
2015
2003; 422
2009; 2
2018; 53
February 2022
January 2022; 10
2013; 3
September 1981; 78
2002; 18
2006; 34
1997; 44
January 2022
2023; 620
2015; 427
2013; 5
2019; 1962
2013; 9
2018; 8
1985; 18
January 2011; 39
May 2014; 30
April 2005; 21
2010; 28
2024; 7
May 2011; 39
October 2007; 23
2007; 8
2014; 15
April 2023; 101
2007; 4
2022; 31
2007; 3
July 2013; 41
2018; 34
2022; 38
2014; 11
2021; 2021
2018; 36
2018; 35
2019; 7
December 2022; 38
2023; 51
2010; 31
2019; 3
January 2006; 34
2015; 51
2024; 128
2019; 1
1997; 25
2015; 55
2011; 75
August 2007; 24
2022; 119
1996; 14
January 2014; 42
2003; 332
2003; 31
October 2012; 7
2018; 27
2014; 42
April 2007; 8
January 2003; 19
January 2019; 47
January 2022; 130
2022; 14
July 2005; 33
July 2016; 44
January 2022; 3
2018; 16
2022; 16
2018; 14
February 2020; 18
2021; 22
July 2005; 21
2015; 31
March 2023; 24
2011; 12
2005; 26
2021; 30
1990; 265
October 2016; 32
2006; 62
July 2012; 40
2015; 43
2019; 116
November 2019; 36
September 2003; 19
May 2013; 32
September 2003; 13
2005; 33
September 2009; 25
2015; 16
2022; 271
2022; 50
January 2015; 43
2017; 1561
2006; 7
April 2020; 173
2011; 32
2022; 44
2011; 39
1983; 219
July 2006; 34
2021; 13
2009; 30
July 2017; 45
2018; 1685
November 2022
June 2010; 5
January 2015; 32
August 2015; 31
January 2021; 22
2012; 279
2023; 93
2009; 37
2022; 147
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Yang Z. (e_1_2_7_157_1) 1997; 44
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Adamou C. (e_1_2_7_78_1) 2019; 1
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Rao R. (e_1_2_7_235_1) 2019; 32
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Gupta R. (e_1_2_7_96_1) 2002; 2001
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Blanc M. (e_1_2_7_114_1) 2019
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Patel S. (e_1_2_7_180_1) 2012
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Shroff R. (e_1_2_7_238_1) 2019
e_1_2_7_161_1
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Lisanza S. L. (e_1_2_7_246_1) 2023
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Tripathi T. (e_1_2_7_253_1) 2022
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Chow E. (e_1_2_7_223_1) 2008
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Datta N. (e_1_2_7_124_1) 2023; 15
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e_1_2_7_84_1
e_1_2_7_61_1
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Johnston K. E. (e_1_2_7_233_1) 2023
e_1_2_7_190_1
e_1_2_7_10_1
e_1_2_7_46_1
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Madani A. (e_1_2_7_244_1) 2020
e_1_2_7_138_1
e_1_2_7_251_1
References_xml – volume: 45
  start-page: W247
  issue: W1
  year: July 2017
  end-page: W252
  article-title: PhD‐SNPg: A Webserver and Lightweight Tool for Scoring Single Nucleotide Variants
  publication-title: Nucleic Acids Research
– volume: 33
  start-page: 3098
  issue: 19
  year: 2017
  end-page: 3100
  article-title: Protein‐Sol: A Web Tool for Predicting Protein Solubility From Sequence
  publication-title: Bioinformatics
– start-page: 1
  year: February 2022
  end-page: 14
  article-title: Assessing Protein Homology Models With Docking Reproducibility
  publication-title: bioRxiv
– volume: 38
  start-page: 5168
  issue: 23
  year: December 2022
  end-page: 5174
  article-title: E‐SNPs&GO: Embedding of Protein Sequence and Function Improves the Annotation of Human Pathogenic Variants
  publication-title: Bioinformatics
– volume: 44
  start-page: 7112
  issue: 10
  year: 2022
  end-page: 7127
  article-title: ProtTrans: Toward Understanding the Language of Life Through Self‐Supervised Learning
  publication-title: IEEE Transactions on Pattern Analysis and Machine Intelligence
– volume: 24
  start-page: 113
  issue: 2
  year: 2023
  end-page: 129
  article-title: Protein Engineering Strategies for Tailoring the Physical and Catalytic Properties of Enzymes for Defined Industrial Applications
  publication-title: Current Protein & Peptide Science
– volume: 30
  start-page: 2975
  issue: 20
  year: October 2014
  end-page: 2977
  article-title: Cc SOL Omics : A Webserver for Solubility Prediction of Endogenous and Heterologous Expression in
  publication-title: Bioinformatics
– volume: 10
  start-page: 189
  issue: 2
  year: 1994
  end-page: 191
  article-title: MEGA: Molecular Evolutionary Genetics Analysis Software for Microcomputers
  publication-title: Bioinformatics
– volume: 12
  start-page: 1
  year: 2023
  end-page: 19
  article-title: Rapid Protein Stability Prediction Using Deep Learning Representations
  publication-title: eLife
– volume: 12
  issue: 1
  year: 2011
  article-title: PoPMuSiC 2.1: A Web Server for the Estimation of Protein Stability Changes Upon Mutation and Sequence Optimality
  publication-title: BioMed Central Bioinformatics
– volume: 101
  start-page: 20
  issue: 12
  year: April 2023
  end-page: 25
  article-title: Powering Up Protein Design
  publication-title: C&EN Global Enterprise
– volume: 2022
  start-page: 1
  year: 2022
  end-page: 7
  article-title: Protein PEGylation: Navigating Recombinant Protein Stability, Aggregation, and Bioactivity
  publication-title: BioMed Research International
– volume: 36
  start-page: D240
  issue: Suppl. 1
  year: January 2008
  end-page: D244
  article-title: Phospho.ELM: A Database of Phosphorylation Sites—Update 2008
  publication-title: Nucleic Acids Research
– volume: 25
  start-page: 3389
  issue: 17
  year: 1997
  end-page: 3402
  article-title: Gapped BLAST and PSI‐BLAST: A New Generation of Protein Database Search Programs
  publication-title: Nucleic Acids Research
– volume: 13
  start-page: 2178
  issue: 9
  year: September 2003
  end-page: 2189
  article-title: OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
  publication-title: Genome Research
– volume: 41
  start-page: W8
  issue: W1
  year: July 2013
  end-page: W14
  article-title: MISTIC: Mutual Information Server to Infer Coevolution
  publication-title: Nucleic Acids Research
– volume: 23
  start-page: 9
  issue: 1
  year: 2019
  end-page: 14
  article-title: Bioinformatics Toxicity Assessment of RB Protein from Transgenic Potato Resistant to Bioinformatics Toxicity Assessment of RB Protein from Transgenic Potato Resistant to
  publication-title: Makara Journal of Science
– volume: 9
  start-page: 232
  issue: 4
  year: 2013
  end-page: 240
  article-title: Target Identification and Mechanism of Action in Chemical Biology and Drug Discovery
  publication-title: Nature Chemical Biology
– volume: 32
  start-page: 1478
  issue: 10
  year: May 2013
  end-page: 1488
  article-title: Precision Mapping of the Human O‐GalNAc Glycoproteome Through SimpleCell Technology
  publication-title: EMBO Journal
– volume: 31
  start-page: 675
  issue: 6
  year: 2010
  end-page: 684
  article-title: Performance of Protein Stability Predictors
  publication-title: Human Mutation
– volume: 36
  start-page: 4691
  issue: 18
  year: 2020
  end-page: 4698
  article-title: Solubility‐Weighted Index: Fast and Accurate Prediction of Protein Solubility
  publication-title: Bioinformatics
– volume: 51
  start-page: 942
  year: 2023
  end-page: 949
  article-title: GENCODE: Reference Annotation for the Human and Mouse Genomes in 2023
  publication-title: Nucleic Acids Research
– volume: 11
  start-page: 361
  issue: 4
  year: 2014
  end-page: 362
  article-title: MutationTaster2: Mutation Prediction for the Deep‐Sequencing Age
  publication-title: Nature Methods
– volume: 125
  start-page: 1806
  issue: 7
  year: 2021
  end-page: 1814
  article-title: Engineering an Allosteric Control of Protein Function
  publication-title: Journal of Physical Chemistry B
– start-page: 1
  year: January 2022
  end-page: 14
  article-title: Software Tools for Optimization of Biocatalysts
  publication-title: Reference Module in Chemistry, Molecular Sciences and Chemical Engineering
– volume: 12
  start-page: 5590
  issue: 22
  year: 2020
  end-page: 5598
  article-title: Predicting Protein Stability and Solubility Changes Upon Mutations: Data Perspective
  publication-title: ChemCatChem
– volume: 43
  start-page: D856
  issue: D1
  year: 2015
  end-page: D861
  article-title: MethHC: A Database of DNA Methylation and Gene Expression in Human Cancer
  publication-title: Nucleic Acids Research
– volume: 25
  start-page: 2200
  issue: 17
  year: September 2009
  end-page: 2207
  article-title: SOLpro: Accurate Sequence‐Based Prediction of Protein Solubility
  publication-title: Bioinformatics
– volume: 271
  year: 2022
  article-title: LAMMPS – a Flexible Simulation Tool for Particle‐Based Materials Modeling at the Atomic, Meso, and Continuum Scales
  publication-title: Computer Physics Communications
– volume: 14
  start-page: 1
  issue: Suppl. 3
  year: 2013
  end-page: 13
  article-title: Assessment of Computational Methods for Predicting the Effects of Missense Mutations in Human Cancers
  publication-title: BioMed Central Genomics
– volume: 8
  start-page: R250
  issue: 11
  year: 2007
  article-title: PHOSIDA (Phosphorylation Site Database): Management, Structural and Evolutionary Investigation, and Prediction of Phosphosites
  publication-title: Genome Biology
– volume: 7
  start-page: 248
  issue: 4
  year: 2010
  end-page: 249
  article-title: A Method and Server for Predicting Damaging Missense Mutations
  publication-title: Nature Methods
– volume: 119
  issue: 43
  year: 2022
  article-title: A Generic Framework for Hierarchical De Novo Protein Design
  publication-title: Proceedings of the National Academy of Sciences of the United States of America
– volume: 33
  start-page: W480
  issue: Suppl. 2
  year: 2005
  end-page: W482
  article-title: nsSNPAnalyzer: Identifying Disease‐Associated Nonsynonymous Single Nucleotide Polymorphisms
  publication-title: Nucleic Acids Research
– volume: 30
  start-page: 1545
  issue: 10
  year: 2009
  end-page: 1614
  article-title: CHARMM: The Biomolecular Simulation Program
  publication-title: Journal of Computational Chemistry
– volume: 2021
  start-page: 1
  issue: 7
  year: 2021
  end-page: 20
  article-title: Post‐Translational Modifications in Proteins: Resources, Tools and Prediction Methods
  publication-title: Database
– volume: 13
  start-page: 31
  issue: 1
  year: 2021
  article-title: CADD‐Splice—Improving Genome‐Wide Variant Effect Prediction Using Deep Learning‐Derived Splice Scores
  publication-title: Genome Medicine
– volume: 21
  start-page: 2104
  issue: 9
  year: May 2005
  end-page: 2105
  article-title: ProtTest: Selection of Best‐Fit Models of Protein Evolution
  publication-title: Bioinformatics
– volume: 14
  start-page: 33
  issue: 1
  year: 1996
  end-page: 38
  article-title: VMD: Visual molecular dynamics
  publication-title: Journal of Molecular Graphics
– volume: 53
  start-page: 158
  year: 2018
  end-page: 163
  article-title: Continuous Directed Evolution for Strain and Protein Engineering
  publication-title: Current Opinion in Biotechnology
– volume: 9
  start-page: 387
  year: 2008
  end-page: 402
  article-title: Next‐Generation DNA Sequencing Methods
  publication-title: Annual Review of Genomics and Human Genetics
– volume: 116
  start-page: 16856
  issue: 34
  year: 2019
  end-page: 16865
  article-title: Distance‐Based Protein Folding Powered by Deep Learning
  publication-title: Proceedings of the National Academy of Sciences of the United States of America
– volume: 35
  start-page: D229
  issue: Suppl. 1
  year: January 2007
  end-page: D231
  article-title: Phospho3D: A Database of Three‐Dimensional Structures of Protein Phosphorylation Sites
  publication-title: Nucleic Acids Research
– start-page: 922
  year: 2012
  end-page: 926
– volume: 8
  issue: 2
  year: February 2013
  article-title: iSNO‐PseAAC: Predict Cysteine S‐Nitrosylation Sites in Proteins by Incorporating Position Specific Amino Acid Propensity Into Pseudo Amino Acid Composition
  publication-title: PLoS One
– volume: 11
  start-page: 1
  issue: 1
  year: 2016
  end-page: 9
  article-title: SIFT Missense Predictions for Genomes
  publication-title: Nature Protocols
– volume: 7
  start-page: 575
  issue: 8
  year: 2010
  end-page: 576
  article-title: MutationTaster Evaluates Disease‐Causing Potential of Sequence Alterations
  publication-title: Nature Methods
– volume: 31
  start-page: 1411
  issue: 9
  year: May 2015
  end-page: 1419
  article-title: GlycoMine: A Machine Learning‐Based Approach for Predicting N‐, C‐ and O‐Linked Glycosylation in the Human Proteome
  publication-title: Bioinformatics
– volume: 34
  start-page: 2605
  issue: 15
  year: August 2018
  end-page: 2613
  article-title: DeepSol: A Deep Learning Framework for Sequence‐Based Protein Solubility Prediction
  publication-title: Bioinformatics
– volume: 1685
  start-page: 43
  year: 2018
  end-page: 67
  article-title: YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations
  publication-title: Methods in Molecular Biology
– volume: 27
  start-page: 1164
  issue: 8
  year: April 2011
  end-page: 1165
  article-title: ProtTest 3: Fast Selection of Best‐Fit Models of Protein Evolution
  publication-title: Bioinformatics
– volume: 29
  start-page: 2607
  issue: 12
  year: 2001
  end-page: 2618
  article-title: GeneMarkS: A Self‐Training Method for Prediction of Gene Starts in Microbial Genomes. Implications for Finding Sequence Motifs in Regulatory Regions
  publication-title: Nucleic Acids Research
– volume: 3
  start-page: 485
  year: 2019
  end-page: 493
  article-title: PepQuery Enables Fast, Accurate, and Convenient Proteomic Validation of Novel Genomic Alterations
  publication-title: Genome Research
– volume: 24
  start-page: 1586
  issue: 8
  year: August 2007
  end-page: 1591
  article-title: PAML 4: Phylogenetic Analysis by Maximum Likelihood
  publication-title: Molecular Biology and Evolution
– volume: 61
  start-page: 173
  year: 2020
  end-page: 181
  article-title: Integrating Cryo‐EM and NMR Data
  publication-title: Current Opinion in Structural Biology
– volume: 36
  start-page: 819
  issue: 9
  year: 2018
  article-title: EvolvR‐Ing to Targeted Mutagenesis
  publication-title: Nature Biotechnology
– volume: 22
  issue: 3
  year: May 2021
  article-title: Bioinformatics Toolbox for Exploring Protein Phosphorylation Network
  publication-title: Briefings in Bioinformatics
– volume: 427
  start-page: 478
  issue: 2
  year: 2015
  end-page: 490
  article-title: The CamSol Method of Rational Design of Protein Mutants With Enhanced Solubility
  publication-title: Journal of Molecular Biology
– year: 2023
  article-title: Joint Generation of Protein Sequence and Structure With RoseTTAFold Sequence Space Diffusion
  publication-title: bioRxiv
– start-page: 139
  year: 2015
  end-page: 147
  article-title: Analyzing Glycan Structure Synthesis With the Glycan Pathway Predictor (GPP) Tool
  publication-title: Glycoinformatics
– start-page: 1
  year: July 2008
  end-page: 14
  article-title: Desmond Performance on a Cluster of Multicore Processors
  publication-title: Simulation
– volume: 45
  start-page: W236
  issue: W1
  year: July 2017
  end-page: W240
  article-title: SODA: Prediction of Protein Solubility From Disorder and Aggregation Propensity
  publication-title: Nucleic Acids Research
– start-page: 261
  year: 2019
  end-page: 24
  article-title: SwissPalm: Protein Palmitoylation Database [Version 1; Peer Review: 3 Approved]
  publication-title: F1000Research
– volume: 5
  start-page: 1469
  issue: 5
  year: 2013
  end-page: 1478
  article-title: Quantitative and Qualitative Proteome Characteristics Extracted From In‐Depth Integrated Genomics and Proteomics Analysis
  publication-title: Cell Reports
– volume: 219
  start-page: 666
  issue: 4585
  year: 1983
  end-page: 671
  article-title: Protein Engineering
  publication-title: Science
– volume: 31
  start-page: 8
  issue: 1
  year: 2022
  end-page: 22
  article-title: PANTHER: Making Genome‐Scale Phylogenetics Accessible to all
  publication-title: Protein Science
– volume: 3
  start-page: 601
  issue: 7
  year: 2021
  end-page: 609
  article-title: Improved Protein Structure Prediction by Deep Learning Irrespective of Co‐Evolution Information
  publication-title: Nature Machine Intelligence
– volume: 7
  issue: 10
  year: October 2012
  article-title: Predicting the Functional Effect of Amino Acid Substitutions and Indels
  publication-title: PLoS One
– volume: 32
  start-page: 2319
  issue: 10
  year: 2011
  end-page: 2327
  article-title: MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations
  publication-title: Journal of Computational Chemistry
– volume: 9
  issue: 2
  year: February2014
  article-title: LAceP: Lysine Acetylation Site Prediction Using Logistic Regression Classifiers
  publication-title: PLoS One
– volume: 39
  start-page: D268
  issue: Suppl. 1
  year: January 2011
  end-page: D271
  article-title: Phospho3D 2.0: An Enhanced Database of Three‐Dimensional Structures of Phosphorylation Sites
  publication-title: Nucleic Acids Research
– volume: 128
  start-page: 109
  issue: 1
  year: 2024
  end-page: 116
  article-title: OpenMM 8: Molecular Dynamics Simulation With Machine Learning Potentials
  publication-title: Journal of Physical Chemistry B
– volume: 7
  start-page: 1
  issue: 12
  year: 2011
  end-page: 7
  article-title: Integrating Bioinformatics Tools to Handle Glycosylation
  publication-title: PLoS Computational Biology
– volume: 422
  start-page: 198
  issue: 6928
  year: 2003
  end-page: 207
  article-title: Mass Spectrometry‐Based Proteomics
  publication-title: Nature
– volume: 16
  start-page: 116
  issue: 1
  year: 2015
  article-title: MAESTRO – Multi Agent Stability Prediction Upon Point Mutations
  publication-title: BioMed Central Bioinformatics
– volume: 34
  start-page: 1092
  issue: 7
  year: April 2018
  end-page: 1098
  article-title: PaRSnIP: Sequence‐Based Protein Solubility Prediction Using Gradient Boosting Machine
  publication-title: Bioinformatics
– volume: 30
  start-page: 200
  issue: 1
  year: 2002
  end-page: 202
  article-title: ASPD (Artificially Selected Proteins/Peptides Database): A Database of Proteins and Peptides Evolved In Vitro
  publication-title: Nucleic Acids Research
– volume: 596
  start-page: 583
  issue: 7873
  year: 2021
  end-page: 589
  article-title: Highly Accurate Protein Structure Prediction With AlphaFold
  publication-title: Nature
– year: 2019
  article-title: A Structure‐Based Deep Learning Framework for Protein Engineering
  publication-title: bioRxiv
– start-page: 273
  year: November 2022
  end-page: 284
– volume: 15
  start-page: 614
  issue: 2
  year: 2023
  article-title: Unleashing the Power of MutationTaster2 and MutationTaster2021: The Machine Learning Approach to Genetic Variant Analysis
  publication-title: Revista Cubana de Informática Médica
– volume: 1685
  start-page: 25
  issue: 2
  year: 2018
  end-page: 42
  article-title: Computational Analysis of Protein Tunnels and Channels
  publication-title: Methods in Molecular Biology
– volume: 14
  start-page: 417
  year: January 2017
  end-page: 419
  article-title: Salmon Provides Fast and Bias‐Aware Quantification of Transcript Expression
  publication-title: Nature Methods
– volume: 36
  start-page: D800
  issue: Suppl. 1
  year: January 2008
  end-page: D808
  article-title: Human PAML Browser: A Database of Positive Selection on Human Genes Using Phylogenetic Methods
  publication-title: Nucleic Acids Research
– volume: 72
  start-page: 178
  issue: 1
  year: 2018
  end-page: 186.e5
  article-title: Automated Design of Efficient and Functionally Diverse Enzyme Repertoires
  publication-title: Molecular Cell
– volume: 43
  start-page: D494
  issue: D1
  year: January 2015
  end-page: D502
  article-title: PTMcode v2: A Resource for Functional Associations of Post‐Translational Modifications Within and Between Proteins
  publication-title: Nucleic Acids Research
– volume: 32
  start-page: 3133
  issue: 20
  year: October 2016
  end-page: 3141
  article-title: pSumo‐CD: Predicting Sumoylation Sites in Proteins With Covariance Discriminant Algorithm by Incorporating Sequence‐Coupled Effects Into General PseAAC
  publication-title: Bioinformatics
– volume: 8
  start-page: 4480
  issue: 1
  year: 2018
  article-title: Prediction and Interpretation of Deleterious Coding Variants in Terms of Protein Structural Stability
  publication-title: Scientific Reports
– volume: 37
  start-page: 1530
  issue: 5
  year: 2020
  end-page: 1534
  article-title: IQ‐TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
  publication-title: Molecular Biology and Evolution
– year: 2015
– volume: 13
  start-page: 35947
  issue: 51
  year: 2023
  end-page: 35963
  article-title: Stabilization Challenges and Aggregation in Protein‐Based Therapeutics in the Pharmaceutical Industry
  publication-title: Royal Society of Chemistry Advances
– volume: 34
  start-page: 57
  issue: 1
  year: 2013
  end-page: 65
  article-title: Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions Using Hidden Markov Models
  publication-title: Human Mutation
– volume: 30
  start-page: 1312
  issue: 9
  year: May 2014
  end-page: 1313
  article-title: RAxML Version 8: A Tool for Phylogenetic Analysis and Post‐Analysis of Large Phylogenies
  publication-title: Bioinformatics
– volume: 19
  start-page: 163
  issue: 1
  year: January 2003
  end-page: 164
  article-title: ConSurf: Identification of Functional Regions in Proteins by Surface‐Mapping of Phylogenetic Information
  publication-title: Bioinformatics
– volume: 14
  start-page: 946
  issue: 8
  year: 2018
  end-page: 956
  article-title: PTM‐ssMP: A Web Server for Predicting Different Types of Post‐Translational Modification Sites Using Novel Site‐Specific Modification Profile
  publication-title: International Journal of Biological Sciences
– volume: 20
  start-page: 536
  issue: 5
  year: 2023
  end-page: 544
  article-title: Insights Into Evolutionary and Conservancy Analytics on Human Insulin Receptor Proteins
  publication-title: Letters in Drug Design & Discovery
– volume: 295
  start-page: 1
  year: 2019
  end-page: 12
  article-title: A Review of Lipidation in the Development of Advanced Protein and Peptide Therapeutics
  publication-title: Journal of Controlled Release
– volume: 12
  start-page: 2909
  issue: 2
  year: 2023
  end-page: 2926
  article-title: What Can De Novo Protein Design Bring to the Treatment of Hematological Disorders?
  publication-title: Biology
– volume: 36
  start-page: D735
  issue: Suppl. 1
  year: January 2008
  end-page: D740
  article-title: TreeFam: 2008 Update
  publication-title: Nucleic Acids Research
– volume: 325
  start-page: 1443
  issue: 4
  year: 2004
  end-page: 1448
  article-title: GPS: A Novel Group‐Based Phosphorylation Predicting and Scoring Method
  publication-title: Biochemical and Biophysical Research Communications
– volume: 7
  start-page: 869
  issue: 12
  year: 2019
  end-page: 886
  article-title: In Silico Tools and Phosphoproteomic Software Exclusives
  publication-title: Processes
– volume: 38
  start-page: 2612
  year: 2022
  end-page: 2614
  article-title: Genome Analysis m ProteInS—A Proteogenomics Pipeline for Finding Novel Bacterial Microproteins Encoded by Small ORFs
  publication-title: Bioinformatics
– volume: 34
  start-page: W249
  issue: Suppl. 2
  year: July 2006
  end-page: W253
  article-title: MeMo: A Web Tool for Prediction of Protein Methylation Modifications
  publication-title: Nucleic Acids Research
– volume: 36
  start-page: 1955
  year: November 2019
  end-page: 1956
  article-title: Gene Expression RaNA‐Seq: Interactive RNA‐Seq Analysis From FASTQ Files to Functional Analysis
  publication-title: Bioinformatics
– volume: 36
  start-page: 1445
  issue: 5
  year: March 2020
  end-page: 1452
  article-title: SOLart: A Structure‐Based Method to Predict Protein Solubility and Aggregation
  publication-title: Bioinformatics
– volume: 27
  start-page: 259
  issue: 1
  year: 2018
  end-page: 268
  article-title: Web‐Accessible Molecular Modeling With Rosetta: The Rosetta Online Server That Includes Everyone (ROSIE)
  publication-title: Protein Science
– volume: 28
  start-page: 516
  issue: 5
  year: 2010
  end-page: 520
  article-title: Transcript Assembly and Quantification by RNA‐Seq Reveals Unannotated Transcripts and Isoform Switching During Cell Differentiation
  publication-title: Nature Biotechnology
– volume: 620
  start-page: 1089
  issue: 7976
  year: 2023
  end-page: 1100
  article-title: De Novo Design of Protein Structure and Function With RFdiffusion
  publication-title: Nature
– volume: 34
  start-page: 235
  year: 2006
  end-page: 238
  article-title: RosettaDesign server for protein design
  publication-title: Nucleic Acids Research
– volume: 18
  start-page: 281
  issue: 4
  year: 1985
  end-page: 325
  article-title: The Mechanism of N‐Terminal Acetylation of Protein
  publication-title: Critical Reviews in Biochemistry
– volume: 32
  start-page: 1414
  issue: 9
  year: May 2016
  end-page: 1416
  article-title: MAESTROweb: A Web Server for Structure‐Based Protein Stability Prediction
  publication-title: Bioinformatics
– volume: 26
  start-page: 1668
  issue: 16
  year: 2005
  end-page: 1688
  article-title: The Amber Biomolecular Simulation Programs
  publication-title: Journal of Computational Chemistry
– volume: 33
  start-page: 3415
  issue: 21
  year: November 2017
  end-page: 3422
  article-title: SCooP: An Accurate and Fast Predictor of Protein Stability Curves as a Function of Temperature
  publication-title: Bioinformatics
– volume: 34
  start-page: 511
  issue: 3
  year: 2018
  end-page: 513
  article-title: FATHMM‐XF: Accurate Prediction of Pathogenic Point Mutations via Extended Features
  publication-title: Bioinformatics
– year: 2020
– volume: 3
  start-page: 1
  issue: 1
  year: January 2022
  end-page: 4
  article-title: Protein Structural Databases in Computational Biology
  publication-title: International Journal of Computing, Programming and Database Management
– volume: 19
  start-page: 1858
  issue: 14
  year: September 2003
  end-page: 1860
  article-title: MutDB: Annotating Human Variation With Functionally Relevant Data
  publication-title: Bioinformatics
– volume: 33
  start-page: W214
  issue: Suppl. 2
  year: July 2005
  end-page: W219
  article-title: GlyProt: In Silico Glycosylation of Proteins
  publication-title: Nucleic Acids Research
– volume: 39
  start-page: W270
  year: May 2011
  end-page: W277
  article-title: SwissDock, a Protein–Small Molecule Docking Web Service Based on EADock DSS
  publication-title: Nucleic Acids Research
– volume: 51
  start-page: W243
  issue: W1
  year: July 2023
  end-page: W250
  article-title: GPS 6.0: An Updated Server for Prediction of Kinase‐Specific Phosphorylation Sites in Proteins
  publication-title: Nucleic Acids Research
– volume: 1962
  start-page: 1
  year: 2019
  end-page: 14
  article-title: tRNAscan‐SE: Searching for tRNA Genes in Genomic Sequences
  publication-title: Methods in Molecular Biology
– volume: 25
  start-page: 2537
  issue: 19
  year: October 2009
  end-page: 2543
  article-title: Fast and Accurate Predictions of Protein Stability Changes Upon Mutations Using Statistical Potentials and Neural Networks: PoPMuSiC‐2.0
  publication-title: Bioinformatics
– volume: 34
  start-page: 3308
  issue: 19
  year: 2018
  end-page: 3315
  article-title: High Precision in Protein Contact Prediction Using Fully Convolutional Neural Networks and Minimal Sequence Features
  publication-title: Bioinformatics
– volume: 4
  start-page: 466
  issue: 6
  year: 2007
  end-page: 467
  article-title: Eris: An Automated Estimator of Protein Stability
  publication-title: Nature Methods
– volume: 31
  start-page: 3635
  issue: 13
  year: 2003
  end-page: 3641
  article-title: Scansite 2.0: Proteome‐Wide Prediction of Cell Signalling Interactions Using Short Sequence Motifs
  publication-title: Nucleic Acids Research
– volume: 173
  year: April 2020
  article-title: HOOMD‐Blue: A Python Package for High‐Performance Molecular Dynamics and Hard Particle Monte Carlo Simulations
  publication-title: Computational Materials Science
– volume: 26
  start-page: 1719
  issue: 16
  year: 2005
  end-page: 1751
  article-title: The GROMOS Software for Biomolecular Simulation: GROMOS05
  publication-title: Journal of Computational Chemistry
– year: 2023
  article-title: In Silico Evolution of Protein Binders With Deep Learning Models for Structure Prediction and Sequence Design
  publication-title: bioRxiv
– volume: 28
  start-page: 5169
  issue: 13
  year: 2023
  end-page: 5204
  article-title: Recent Advances in Deep Learning for Protein–Protein Interaction Analysis: A Comprehensive Review
  publication-title: Molecules
– volume: 71
  start-page: 101
  year: 2018
  end-page: 123
  article-title: Innovations in Improving Lipid Production: Algal Chemical Genetics
  publication-title: Progress in Lipid Research
– volume: 33
  start-page: W311
  year: July 2005
  end-page: W314
  article-title: MutDB Services: Interactive Structural Analysis of Mutation Data
  publication-title: Nucleic Acids Research
– volume: 59
  start-page: 1508
  issue: 4
  year: 2019
  end-page: 1514
  article-title: DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks
  publication-title: Journal of Chemical Information and Modeling
– volume: 11
  start-page: 1
  issue: 12
  year: 2019
  end-page: 12
  article-title: Protein Solubility Predictions Using the Camsol Method in the Study of Protein Homeostasis
  publication-title: Cold Spring Harbor Perspectives in Biology
– volume: 1
  start-page: 12
  issue: 1
  year: 2019
  end-page: 22
  publication-title: Aristotle Biomed Journal
– volume: 13
  start-page: 741
  issue: 9
  year: 2016
  end-page: 748
  article-title: OpenMS : A Flexible Open‐Source Software Platform for Mass Spectrometry Data Analysis
  publication-title: Nature Methods
– volume: 33
  start-page: W465
  issue: Suppl. 2
  year: 2005
  end-page: W467
  article-title: AUGUSTUS: A Web Server for Gene Prediction in Eukaryotes That Allows User‐Defined Constraints
  publication-title: Nucleic Acids Research
– volume: 12
  start-page: 1
  issue: 8
  year: 2017
  end-page: 12
  article-title: PRmePRed: A Protein Arginine Methylation Prediction Tool
  publication-title: PLoS One
– volume: 42
  start-page: D922
  issue: D1
  year: January 2014
  end-page: D925
  article-title: TreeFam v9: A New Website, More Species and Orthology‐On‐The‐Fly
  publication-title: Nucleic Acids Research
– volume: 15
  start-page: 1
  year: 2014
  end-page: 18
  article-title: GraphProt: Modeling Binding Preferences of RNA‐Binding Proteins or How to Make Sense out of CLIP‐Seq Data
  publication-title: Genome Biology
– volume: 3
  start-page: 1448
  year: 2013
  end-page: 1455
  article-title: Protein Structure Alignment Beyond Spatial Proximity
  publication-title: Scientific Reports
– volume: 34
  start-page: D622
  issue: Suppl. 1
  year: 2006
  end-page: D627
  article-title: dbPTM: An Information Repository of Protein Post‐Translational Modification
  publication-title: Nucleic Acids Research
– volume: 1561
  start-page: 235
  year: 2017
  end-page: 254
  article-title: Investigating Protein–Peptide Interactions Using the schrödinger Computational Suite
  publication-title: Methods in Molecular Biology
– volume: 76
  start-page: 7
  issue: 1
  year: 2013
  end-page: 20
  article-title: Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2
  publication-title: Current Protocols in Human Genetics
– volume: 52
  start-page: D1143
  issue: D1
  year: January 2024
  end-page: D1154
  article-title: CADD v1.7: Using Protein Language Models, Regulatory CNNs and Other Nucleotide‐Level Scores to Improve Genome‐Wide Variant Predictions
  publication-title: Nucleic Acids Research
– volume: 14
  start-page: 131
  issue: 2
  year: 2012
  end-page: 143
  article-title: A Brief Introduction to Web‐Based Genome Browsers
  publication-title: Briefings in Bioinformatics
– volume: 7
  issue: 1
  year: 2006
  article-title: SNPs3D: Candidate Gene and SNP Selection for Association Studies
  publication-title: BioMed Central Bioinformatics
– volume: 443
  start-page: 229
  year: 2008
  end-page: 255
  article-title: Nuclear Magnetic Resonance‐Based Modeling and Refinement of Protein Three‐Dimensional Structures and Their Complexes
  publication-title: Methods in Molecular Biology
– volume: 130
  start-page: 1
  year: January 2022
  end-page: 38
  article-title: Algorithms for Protein Design
  publication-title: Advances in Protein Chemistry and Structural Biology
– volume: 15
  start-page: 307
  year: 2017
  end-page: 319
  article-title: Protein Post‐Translational Modifications: In Silico Prediction Tools and Molecular Modeling
  publication-title: Computational and Structural Biotechnology Journal
– volume: 5
  start-page: 310
  issue: 4
  year: 2015
  end-page: 323
  article-title: GENESIS: A Hybrid‐Parallel and Multi‐Scale Molecular Dynamics Simulator With Enhanced Sampling Algorithms for Biomolecular and Cellular Simulations
  publication-title: Wiley Interdisciplinary Reviews: Computational Molecular Science
– volume: 75
  start-page: 127
  issue: 1
  year: 2011
  end-page: 144
  article-title: Proteomic Databases and Tools to Decipher Post‐Translational Modifications
  publication-title: Journal of Proteomics
– volume: 1–2
  start-page: 19
  year: 2015
  end-page: 25
  article-title: Gromacs: High Performance Molecular Simulations Through Multi‐Level Parallelism From Laptops to Supercomputers
  publication-title: SoftwareX
– volume: 44
  start-page: D336
  issue: D1
  year: 2016
  end-page: D342
  article-title: PANTHER Version 10: Expanded Protein Families and Functions, and Analysis Tools
  publication-title: Nucleic Acids Research
– volume: 24
  issue: 2
  year: March 2023
  article-title: Sequence‐Based Prediction of pH‐Dependent Protein Solubility Using CamSol
  publication-title: Briefings in Bioinformatics
– volume: 49
  start-page: D1268
  issue: D1
  year: 2021
  end-page: D1275
  article-title: MethHC 2.0: Information Repository of DNA Methylation and Gene Expression in Human Cancer
  publication-title: Nucleic Acids Research
– volume: 32
  start-page: 3107
  issue: 20
  year: 2016
  end-page: 3115
  article-title: Accurate In Silico Prediction of Species‐Specific Methylation Sites Based on Information Gain Feature Optimization
  publication-title: Bioinformatics
– volume: 33
  start-page: 382
  issue: Suppl. 2
  year: 2005
  end-page: 388
  article-title: The FoldX Web Server: An Online Force Field
  publication-title: Nucleic Acids Research
– volume: 23
  start-page: 585
  issue: 4
  year: 2012
  end-page: 590
  article-title: Protein Phosphorylation From the Perspective of Systems Biology
  publication-title: Current Opinion in Biotechnology
– volume: 30
  start-page: 541
  issue: 7
  year: 2023
  end-page: 551
  article-title: Protein Engineering, a Robust Tool to Engineer Novel Functions in Protein
  publication-title: Protein and Peptide Letters
– volume: 44
  start-page: 1
  year: 1997
  end-page: 41
  article-title: Phylogenetic Analysis by Maximum Likelihood (PAML)
  publication-title: Distribution Over Internet
– volume: 59
  start-page: 307
  issue: 3
  year: 2010
  end-page: 321
  article-title: New Algorithms and Methods to Estimate Maximim‐Likelihood Phylogenies Assessing the Performance of PhyML 3.0
  publication-title: Systematic Biology
– volume: 40
  start-page: W452
  issue: W1
  year: July 2012
  end-page: W457
  article-title: SIFT Web Server: Predicting Effects of Amino Acid Substitutions on Proteins
  publication-title: Nucleic Acids Research
– volume: 28
  start-page: 1278
  issue: 9
  year: 2012
  end-page: 1279
  article-title: MDWeb and MDMoby: An Integrated Web‐Based Platform for Molecular Dynamics Simulations
  publication-title: Bioinformatics
– volume: 4
  start-page: 1633
  issue: 6
  year: 2004
  end-page: 1649
  article-title: Prediction of Post‐Translational Glycosylation and Phosphorylation of Proteins From the Amino Acid Sequence
  publication-title: Proteomics
– volume: 16
  start-page: 687
  issue: 8
  year: 2019
  end-page: 694
  article-title: Machine‐Learning‐Guided Directed Evolution for Protein Engineering
  publication-title: Nature Methods
– volume: 15
  start-page: 1567
  issue: 12
  year: 2007
  end-page: 1576
  article-title: Modeling Backbone Flexibility Improves Protein Stability Estimation
  publication-title: Structure
– volume: 34
  start-page: 239
  year: 2006
  end-page: 242
  article-title: CUPSAT: Prediction of Protein Stability Upon Point Mutations
  publication-title: Nucleic Acids Research
– volume: 14
  start-page: 2533
  issue: 11
  year: 2022
  end-page: 2571
  article-title: Instability Challenges and Stabilization Strategies of Pharmaceutical Proteins
  publication-title: Pharmaceutics
– volume: 5
  issue: 6
  year: June 2010
  article-title: GPS‐SNO: Computational Prediction of Protein S‐Nitrosylation Sites With a Modified GPS Algorithm
  publication-title: PLoS One
– volume: 77
  start-page: 363
  year: 2008
  end-page: 382
  article-title: Macromolecular Modeling With Rosetta
  publication-title: Annual Review of Biochemistry
– volume: 21
  start-page: 2909
  year: 2023
  end-page: 2926
  article-title: Accelerating Therapeutic Protein Design With Computational Approaches Toward the Clinical Stage
  publication-title: Computational and Structural Biotechnology Journal
– volume: 332
  start-page: 449
  issue: 2
  year: 2003
  end-page: 460
  article-title: A Large Scale Test of Computational Protein Design: Folding and Stability of Nine Completely Redesigned Globular Proteins
  publication-title: Journal of Molecular Biology
– volume: 32
  start-page: 2542
  issue: 16
  year: 2016
  end-page: 2544
  article-title: INPS‐MD: A Web Server to Predict Stability of Protein Variants From Sequence and Structure
  publication-title: Bioinformatics
– volume: 34
  start-page: D572
  issue: Suppl. 1
  year: January 2006
  end-page: D580
  article-title: TreeFam: A Curated Database of Phylogenetic Trees of Animal Gene Families
  publication-title: Nucleic Acids Research
– volume: 7
  start-page: 309
  issue: 2
  year: 2024
  end-page: 334
  article-title: Peptide‐Drug Conjugates: Design, Chemistry, and Drug Delivery System as a Novel Cancer Theranostic
  publication-title: Americal Chemical Society Pharmacology and Translational Science
– volume: 39
  start-page: W29
  issue: Suppl. 2
  year: 2011
  end-page: W37
  article-title: HMMER Web Server: Interactive Sequence Similarity Searching
  publication-title: Nucleic Acids Research
– volume: 31
  start-page: 2816
  issue: 17
  year: 2015
  end-page: 2821
  article-title: INPS: Predicting the Impact of Non‐synonymous Variations on Protein Stability From Sequence
  publication-title: Bioinformatics
– volume: 39
  issue: 17
  year: September 2011
  article-title: Predicting the Functional Impact of Protein Mutations: Application to Cancer Genomics
  publication-title: Nucleic Acids Research
– volume: 17
  start-page: 847
  issue: 9
  year: 2001
  end-page: 848
  article-title: InterProScan – An Integration Platform for the Signature‐Recognition Methods in InterPro
  publication-title: Bioinformatics
– volume: 26
  start-page: 1339
  issue: 12
  year: 2008
  end-page: 1340
  article-title: PhosphoPep—A Database of Protein Phosphorylation Sites in Model Organisms
  publication-title: Nature Biotechnology
– volume: 36
  start-page: 277
  year: 2023
  end-page: 311
– volume: 42
  start-page: D304
  issue: D1
  year: 2014
  end-page: D309
  article-title: SCOPe: Structural Classification of Proteins – Extended, Integrating SCOP and ASTRAL Data and Classification of New Structures
  publication-title: Nucleic Acids Research
– volume: 24
  issue: 2
  year: March 2023
  article-title: Protein Phosphorylation Database and Prediction Tools
  publication-title: Briefings in Bioinformatics
– volume: 21
  start-page: 12
  issue: 1
  year: 2023
  article-title: Prediction of Protein Solubility Based on Sequence Physicochemical Patterns and Distributed Representation Information With DeepSoluE
  publication-title: BioMed Central Biology
– volume: 55
  start-page: 2015
  issue: 9
  year: 2015
  end-page: 2025
  article-title: In Silico Identification of Protein S‐Palmitoylation Sites and Their Involvement in Human Inherited Disease
  publication-title: Journal of Chemical Information and Modeling
– volume: 32
  start-page: 582
  year: 2004
  end-page: 585
  article-title: FATCAT: A Web Server for Flexible Structure Comparison and Structure Similarity Searching
  publication-title: Nucleic Acids Research
– volume: 93
  start-page: 14946
  issue: 45
  year: 2021
  end-page: 14954
  article-title: Proteomic Database Search Engine for Two‐Dimensional Partial Covariance Mass Spectrometry
  publication-title: Analytical Chemistry
– volume: 16
  start-page: 25
  year: 2018
  end-page: 33
  article-title: FoldX as Protein Engineering Tool: Better Than Random Based Approaches?
  publication-title: Computational and Structural Biotechnology Journal
– volume: 58
  start-page: 57
  year: 2007
  end-page: 83
  article-title: Protein‐Folding Dynamics: Overview of Molecular Simulation Techniques
  publication-title: Annual Review of Physical Chemistry
– volume: 16
  start-page: 25831
  issue: 10
  year: 2015
  end-page: 25864
  article-title: Site‐Specific Pegylation of Therapeutic Proteins
  publication-title: International Journal of Molecular Sciences
– volume: 22
  start-page: 1
  issue: 6
  year: 2021
  end-page: 23
  article-title: Assessing the Performance of Computational Predictors for Estimating Protein Stability Changes Upon Missense Mutations
  publication-title: Briefings in Bioinformatics
– volume: 5
  issue: 1
  year: 2004
  article-title: Phospho.ELM: A Database of Experimentally Verified Phosphorylation Sites in Eukaryotic Proteins
  publication-title: BioMed Central Bioinformatics
– volume: 2
  start-page: 377
  year: 2009
  end-page: 389
  article-title: Identifying and Characterizing Binding Sites and Assessing Druggability
  publication-title: Journal of Chemical Information and Modeling
– volume: 2001
  start-page: 310
  year: 2002
  end-page: 322
  article-title: Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function
  publication-title: Biocomputing
– volume: 301
  start-page: 176
  year: 2019
  end-page: 189
  article-title: Current Strategies in Extending Half‐Lives of Therapeutic Proteins
  publication-title: Journal of Controlled Release
– volume: 6
  issue: 1
  year: 2016
  article-title: Predicting Protein Thermal Stability Changes Upon Point Mutations Using Statistical Potentials: Introducing HoTMuSiC
  publication-title: Scientific Reports
– start-page: 01 685
  year: 2022
– volume: 23
  start-page: 1
  issue: 12
  year: April 2022
  end-page: 23
  article-title: Proteomic Tools for the Quantitative Analysis of Artificial Peptide Libraries: Detection and Characterization of Target‐Amplified PD‐1 Inhibitors
  publication-title: ChemBioChem
– volume: 14
  start-page: 1
  issue: Suppl. 3
  year: 2013
  end-page: 7
  article-title: WS‐SNPs&GO: A Web Server for Predicting the Deleterious Effect of Human Protein Variants Using Functional Annotation
  publication-title: BioMed Central Genomics
– volume: 21
  start-page: 354
  year: 2023
  end-page: 364
  article-title: Prediction of Protein Stability Changes Upon Single‐Point Variant Using 3D Structure Profile
  publication-title: Computational and Structural Biotechnology Journal
– volume: 26
  start-page: 1781
  issue: 16
  year: 2005
  end-page: 1802
  article-title: Scalable Molecular Dynamics With NAMD
  publication-title: Journal of Computational Chemistry
– volume: 48
  start-page: W104
  issue: W1
  year: 2021
  end-page: W109
  article-title: EnzymeMiner: Automated Mining of Soluble Enzymes With Diverse Structures, Catalytic Properties and Stabilities
  publication-title: Nucleic Acids Research
– volume: 78
  start-page: 5275
  issue: 9
  year: September 1981
  end-page: 5278
  article-title: Molecular Engineering: An Approach to the Development of General Capabilities for Molecular Manipulation
  publication-title: Proceedings of the National Academy of Sciences of the United States of America
– volume: 42
  start-page: W314
  issue: W1
  year: 2014
  end-page: W319
  article-title: DUET: A Server for Predicting Effects of Mutations on Protein Stability Using an Integrated Computational Approach
  publication-title: Nucleic Acids Research
– volume: 147
  start-page: 105695
  year: 2022
  end-page: 105722
  article-title: Protein Structural Bioinformatics: An Overview
  publication-title: Computers in Biology and Medicine
– volume: 15
  start-page: 5116
  issue: 9
  year: 2019
  end-page: 5134
  article-title: EnzyDock: Protein–Ligand Docking of Multiple Reactive States Along a Reaction Coordinate in Enzymes
  publication-title: Journal of Chemical Theory and Computation
– volume: 23
  start-page: 2536
  issue: 19
  year: October 2007
  end-page: 2542
  article-title: Protein Solubility: Sequence Based Prediction and Experimental Verification
  publication-title: Bioinformatics
– volume: 31
  start-page: 2745
  issue: 16
  year: August 2015
  end-page: 2747
  article-title: PROVEAN Web Server: A Tool to Predict the Functional Effect of Amino Acid Substitutions and Indels
  publication-title: Bioinformatics
– volume: 44
  start-page: W344
  issue: W1
  year: July 2016
  end-page: W350
  article-title: ConSurf 2016: An Improved Methodology to Estimate and Visualize Evolutionary Conservation in Macromolecules
  publication-title: Nucleic Acids Research
– volume: 30
  start-page: 20
  year: 2021
  end-page: 30
  article-title: The Bio3D Packages for Structural Bioinformatics
  publication-title: Protein Science
– volume: 21
  start-page: 1269
  issue: 7
  year: April 2005
  end-page: 1270
  article-title: NetAcet: Prediction of N‐Terminal Acetylation Sites
  publication-title: Bioinformatics
– volume: 36
  start-page: D815
  year: January 2008
  article-title: MutDB: Update on Development of Tools for the Biochemical Analysis of Genetic Variation
  publication-title: Nucleic Acids Research
– volume: 32
  start-page: 268
  issue: 1
  year: January 2015
  end-page: 274
  article-title: IQ‐TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum‐Likelihood Phylogenies
  publication-title: Molecular Biology and Evolution
– volume: 21
  start-page: 1266
  issue: 6
  year: 2023
  end-page: 1285
  article-title: A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction
  publication-title: Genomics, Proteomics & Bioinformatics
– volume: 27
  start-page: 178
  issue: 3
  year: 2020
  end-page: 186
  article-title: Nglyc: A Random Forest Method for Prediction of N‐Glycosylation Sites in Eukaryotic Protein Sequence
  publication-title: Protein & Peptide Letters
– volume: 28
  start-page: 2685
  issue: 20
  year: 2012
  end-page: 2686
  article-title: MEGA‐CC: Computing Core of Molecular Evolutionary Genetics Analysis Program for Automated and Iterative Data Analysis
  publication-title: Bioinformatics
– volume: 45
  start-page: W222
  issue: W1
  year: July 2017
  end-page: W228
  article-title: PMut: A Web‐Based Tool for the Annotation of Pathological Variants on Proteins, 2017 Update
  publication-title: Nucleic Acids Research
– year: August 2022
– volume: 35
  start-page: 1547
  issue: 6
  year: 2018
  end-page: 1549
  article-title: MEGA X: Molecular Evolutionary Genetics Analysis Across Computing Platforms
  publication-title: Molecular Biology and Evolution
– volume: 34
  start-page: 3659
  issue: 21
  year: 2018
  end-page: 3665
  article-title: Quantification of Biases in Predictions of Protein Stability Changes Upon Mutations
  publication-title: Bioinformatics
– volume: 11
  start-page: 5905
  issue: 1
  year: 2020
  end-page: 5918
  article-title: Inferring the Molecular and Phenotypic Impact of Amino Acid Variants With MutPred2
  publication-title: Nature Communications
– volume: 279
  start-page: 2192
  issue: 12
  year: 2012
  end-page: 2200
  article-title: PROSO II – A New Method for Protein Solubility Prediction
  publication-title: FEBS Journal
– volume: 18
  start-page: 72
  issue: 1
  year: February 2020
  end-page: 80
  article-title: GPS 5.0: An Update on the Prediction of Kinase‐Specific Phosphorylation Sites in Proteins
  publication-title: Genomics, Proteomics & Bioinformatics
– volume: 16
  start-page: 3109
  year: 2022
  end-page: 3116
  article-title: Albumin‐Fusion Recombinant FIX in the Management of People With Hemophilia B: An Evidence‐Based Review
  publication-title: Drug Design, Development and Therapy
– volume: 39
  start-page: D253
  issue: Suppl. 1
  year: January 2011
  end-page: D260
  article-title: PHOSIDA 2011: The Posttranslational Modification Database
  publication-title: Nucleic Acids Research
– volume: 27
  start-page: 4636
  issue: 23
  year: 1999
  end-page: 4641
  article-title: Improved Microbial Gene Identification With GLIMMER
  publication-title: Nucleic Acids Research
– volume: 21
  start-page: 913
  issue: 5
  year: 2023
  end-page: 925
  article-title: Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms
  publication-title: Genomics, Proteomics & Bioinformatics
– volume: 35
  start-page: 1582
  issue: 9
  year: May 2019
  end-page: 1584
  article-title: The EVcouplings Python Framework for Coevolutionary Sequence Analysis
  publication-title: Bioinformatics
– volume: 51
  start-page: 6
  issue: 1
  year: 2015
  end-page: 14
  article-title: Using RAxML to Infer Phylogenies
  publication-title: Current Protocols in Bioinformatics
– volume: 16
  start-page: 24918
  issue: 10
  year: 2015
  end-page: 24945
  article-title: High‐Throughput Screening in Protein Engineering: Recent Advances and Future Perspectives
  publication-title: International Journal of Molecular Sciences
– volume: 16
  start-page: 1
  issue: 2
  year: 2023
  end-page: 15
  article-title: New Advances in CRISPR/Cas‐Mediated Precise Gene‐Editing Techniques
  publication-title: Disease Models and Mechanisms
– volume: 62
  start-page: 1125
  issue: 4
  year: 2006
  end-page: 1132
  article-title: Prediction of Protein Stability Changes for Single‐Site Mutations Using Support Vector Machines
  publication-title: Proteins: Structure, Function, and Genetics
– volume: 13
  start-page: 331
  year: 1984
  end-page: 371
  article-title: Fluctuations in Protein Structure From X‐Ray Diffraction
  publication-title: Annual Review of Biophysics and Bioengineering
– volume: 37
  start-page: 376
  issue: Suppl. 2
  year: 2009
  end-page: 383
  article-title: HotSpot Wizard: A Web Server for Identification of Hot Spots in Protein Engineering
  publication-title: Nucleic Acids Research
– volume: 33
  start-page: 194
  issue: 3
  year: 2005
  end-page: 201
  article-title: Molecular Modeling of Heme Proteins Using MOE: Bio‐inorganic and Structure‐Function Activity for Undergraduates*S
  publication-title: Biochemistry and Molecular Biology Education
– volume: 33
  start-page: W306
  year: July 2005
  end-page: W310
  article-title: I‐Mutant2.0: Predicting Stability Changes Upon Mutation From the Protein Sequence or Structure
  publication-title: Nucleic Acids Research
– volume: 1
  start-page: 225
  issue: 5
  year: 2019
  end-page: 235
  article-title: Leveraging Implicit Knowledge in Neural Networks for Functional Dissection and Engineering of Proteins
  publication-title: Nature Machine Intelligence
– volume: 3
  start-page: 1
  issue: 139
  year: 2007
  end-page: 11
  article-title: PhosphoPep – A Phosphoproteome Resource for Systems Biology Research in Kc167 Cells
  publication-title: Molecular Systems Biology
– volume: 10
  start-page: 879
  issue: 1
  year: January 2022
  end-page: 895
  article-title: Protein Sequencing and Drug Discovery by Using a High Throughput Screening Assay
  publication-title: International Journal of Advanced Research
– volume: 50
  start-page: D471
  issue: D1
  year: 2022
  end-page: D479
  article-title: dbPTM in 2022: An Updated Database for Exploring Regulatory Networks and Functional Associations of Protein Post‐Translational Modifications
  publication-title: Nucleic Acids Research
– volume: 42
  start-page: 1
  issue: 15
  year: 2014
  end-page: 8
  article-title: Integration of Mapped RNA‐Seq Reads Into Automatic Training of Eukaryotic Gene Finding Algorithm
  publication-title: Nucleic Acids Research
– volume: 96
  start-page: 11
  issue: 1
  year: 2011
  end-page: 19
  article-title: Phylogenetic Analysis of Protein Sequence Data Using the Randomized Axelerated Maximum Likelihood (RAXML) Program
  publication-title: Current Protocols in Molecular Biology
– volume: 265
  start-page: 22059
  issue: 36
  year: 1990
  end-page: 22062
  article-title: Protein Structure Determination in Solution by NMR Spectroscopy
  publication-title: Journal of Biological Chemistry
– volume: 8
  start-page: 1
  year: January 2018
  end-page: 17
  article-title: GOATOOLS: A Python Library for Gene Ontology Analyses
  publication-title: Scientific Reports
– volume: 34
  start-page: 1951
  issue: 11
  year: 2023
  end-page: 2000
  article-title: The Evolving Landscape of Antibody‐Drug Conjugates: In Depth Analysis of Recent Research Progress
  publication-title: Bioconjugate Chemistry
– volume: 32
  start-page: 1
  year: 2019
  end-page: 13
  article-title: Evaluating Protein Transfer Learning With TAPE
  publication-title: Advances in Neural Information Processing Systems
– volume: 8
  year: April 2007
  article-title: UbiProt: A Database of Ubiquitylated Proteins
  publication-title: BioMed Central Bioinformatics
– volume: 22
  start-page: 1
  issue: 3
  year: May 2021
  end-page: 15
  article-title: Recent Advances in User‐Friendly Computational Tools to Engineer Protein Function
  publication-title: Briefings in Bioinformatics
– volume: 47
  start-page: D886
  issue: D1
  year: January 2019
  end-page: D894
  article-title: CADD: Predicting the Deleteriousness of Variants Throughout the Human Genome
  publication-title: Nucleic Acids Research
– volume: 18
  start-page: S71
  issue: Suppl. 1
  year: 2002
  end-page: S77
  article-title: Rate4Site: An Algorithmic Tool for the Identification of Functional Regions in Proteins by Surface Mapping of Evolutionary Determinants Within Their Homologues
  publication-title: Bioinformatics
– volume: 15
  start-page: 1452
  issue: 7
  year: 2019
  end-page: 1459
  article-title: Sarotup: A Suite of Tools for Finding Potential Target‐Unrelated Peptides From Phage Display Data
  publication-title: International Journal of Biological Sciences
– volume: 7
  issue: 11
  year: November 2012
  article-title: Position‐Specific Analysis and Prediction for Protein Lysine Acetylation Based on Multiple Features
  publication-title: PLoS One
– volume: 22
  start-page: 298
  issue: 1
  year: January 2021
  end-page: 307
  article-title: EPSD: A Well‐Annotated Data Resource of Protein Phosphorylation Sites in Eukaryotes
  publication-title: Briefings in Bioinformatics
– volume: 30
  start-page: 187
  issue: 1
  year: 2021
  end-page: 200
  article-title: The BioGRID Database: A Comprehensive Biomedical Resource of Curated Protein, Genetic, and Chemical Interactions
  publication-title: Protein Science
– volume: 15
  start-page: 1
  issue: 1
  year: 2024
  end-page: 16
  article-title: AlphaPept: A Modern and Open Framework for MS‐Based Proteomics
  publication-title: Nature Communications
– volume: 93
  start-page: 400
  year: 2023
  end-page: 410
  article-title: Challenges in Bridging the Gap Between Protein Structure Prediction and Functional Interpretation
  publication-title: Proteins: Structure, Function, and Bioinformatics
– volume: 17
  start-page: 665
  issue: 7
  year: 2020
  end-page: 680
  article-title: Macromolecular Modeling and Design in Rosetta: Recent Methods and Frameworks
  publication-title: Nature Methods
– volume: 23
  start-page: 1282
  issue: 10
  year: 2007
  end-page: 1288
  article-title: UniRef: Comprehensive and Non‐redundant UniProt Reference Clusters
  publication-title: Bioinformatics
– volume: 43
  start-page: W443
  issue: W1
  year: 2015
  end-page: W447
  article-title: PLIP: Fully Automated Protein–Ligand Interaction Profiler
  publication-title: Nucleic Acids Research
– volume: 32
  start-page: 2936
  issue: 19
  year: October 2016
  end-page: 2946
  article-title: STRUM: Structure‐Based Prediction of Protein Stability Changes Upon Single‐Point Mutation
  publication-title: Bioinformatics
– volume: 15
  start-page: 118
  issue: 1
  year: 2023
  article-title: HybridGCN for Protein Solubility Prediction With Adaptive Weighting of Multiple Features
  publication-title: Journal of Cheminformatics
– volume: 21
  start-page: 3176
  issue: 14
  year: July 2005
  end-page: 3178
  article-title: PMUT: A Web‐Based Tool for the Annotation of Pathological Mutations on Proteins
  publication-title: Bioinformatics
– ident: e_1_2_7_80_1
  doi: 10.3390/PR7120869
– ident: e_1_2_7_229_1
  doi: 10.1002/wcms.1220
– ident: e_1_2_7_262_1
  doi: 10.1016/j.jconrel.2019.02.016
– ident: e_1_2_7_112_1
  doi: 10.1186/1471‐2105‐8‐126
– ident: e_1_2_7_84_1
  doi: 10.1093/bib/bbz169
– ident: e_1_2_7_30_1
  doi: 10.1016/j.csbj.2018.01.002
– ident: e_1_2_7_77_1
  doi: 10.1016/j.copbio.2011.11.008
– ident: e_1_2_7_61_1
  doi: 10.1101/cshperspect.a033845
– ident: e_1_2_7_103_1
  doi: 10.1371/journal.pone.0183318
– ident: e_1_2_7_131_1
  doi: 10.1093/nar/gkad989
– ident: e_1_2_7_91_1
  doi: 10.1016/j.gpb.2020.01.001
– ident: e_1_2_7_54_1
  doi: 10.1186/s13321‐023‐00788‐8
– ident: e_1_2_7_182_1
  doi: 10.7454/mss.v23i1.7609
– ident: e_1_2_7_189_1
  doi: 10.1007/978-1-4939-9173-0_1
– ident: e_1_2_7_241_1
  doi: 10.1038/s41467‐024‐46485‐4
– ident: e_1_2_7_10_1
  doi: 10.1093/bib/bbaa150
– ident: e_1_2_7_4_1
  doi: 10.2174/1389203724666230110163234
– ident: e_1_2_7_108_1
  doi: 10.3109/10409238509086784
– ident: e_1_2_7_217_1
  doi: 10.1038/s41586‐021‐03819‐2
– ident: e_1_2_7_200_1
  doi: 10.1021/acs.jctc.9b00366
– ident: e_1_2_7_8_1
  doi: 10.1146/annurev.bb.13.060184.001555
– ident: e_1_2_7_23_1
  doi: 10.1038/s41592‐020‐0848‐2
– ident: e_1_2_7_28_1
  doi: 10.1002/cctc.202000933
– ident: e_1_2_7_169_1
  doi: 10.1093/molbev/msu300
– volume: 32
  start-page: 1
  year: 2019
  ident: e_1_2_7_235_1
  article-title: Evaluating Protein Transfer Learning With TAPE
  publication-title: Advances in Neural Information Processing Systems
– ident: e_1_2_7_39_1
  doi: 10.1093/bioinformatics/btv291
– ident: e_1_2_7_40_1
  doi: 10.1093/bioinformatics/btw192
– ident: e_1_2_7_48_1
  doi: 10.1093/bib/bbab184
– ident: e_1_2_7_88_1
  doi: 10.1038/nbt1208‐1339
– volume: 2001
  start-page: 310
  year: 2002
  ident: e_1_2_7_96_1
  article-title: Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function
  publication-title: Biocomputing
– ident: e_1_2_7_154_1
  doi: 10.1093/molbev/msy096
– ident: e_1_2_7_172_1
  doi: 10.1146/annurev.genom.9.081307.164359
– ident: e_1_2_7_43_1
  doi: 10.1186/1471‐2105‐12‐151
– ident: e_1_2_7_3_1
  doi: 10.17760/D20409258
– ident: e_1_2_7_89_1
  doi: 10.1038/msb4100182
– ident: e_1_2_7_120_1
  doi: 10.1038/nprot.2015.123
– ident: e_1_2_7_162_1
  doi: 10.1093/bioinformatics/bti263
– ident: e_1_2_7_161_1
  doi: 10.1101/gr.1224503
– ident: e_1_2_7_193_1
  doi: 10.1093/bioinformatics/btm098
– volume-title: ProGen: Language Modeling for Protein Generation
  year: 2020
  ident: e_1_2_7_244_1
– ident: e_1_2_7_203_1
  doi: 10.1093/nar/gkh430
– ident: e_1_2_7_204_1
  doi: 10.1021/ci800324m
– ident: e_1_2_7_257_1
  doi: 10.1039/d3ra06476j
– ident: e_1_2_7_264_1
  doi: 10.1016/j.jconrel.2018.12.032
– ident: e_1_2_7_26_1
  doi: 10.1016/j.csbj.2023.04.027
– ident: e_1_2_7_152_1
  doi: 10.1093/bioinformatics/10.2.189
– ident: e_1_2_7_177_1
  doi: 10.1093/bioinformatics/btz854
– start-page: 922
  volume-title: DNA Sequence Analysis by ORF FINDER & GENOMATIX Tool: Bioinformatics Analysis of Some Tree Species of Leguminosae Family
  year: 2012
  ident: e_1_2_7_180_1
– ident: e_1_2_7_6_1
  doi: 10.1073/PNAS.78.9.5275
– ident: e_1_2_7_59_1
  doi: 10.1093/bioinformatics/btp386
– ident: e_1_2_7_100_1
  doi: 10.1007/978-1-4939-2343-4_10
– ident: e_1_2_7_92_1
  doi: 10.1093/nar/gkad383
– start-page: 261
  year: 2019
  ident: e_1_2_7_114_1
  article-title: SwissPalm: Protein Palmitoylation Database [Version 1; Peer Review: 3 Approved]
  publication-title: F1000Research
– ident: e_1_2_7_201_1
  doi: 10.1093/nar/gkr366
– ident: e_1_2_7_64_1
  doi: 10.1093/bioinformatics/btx662
– ident: e_1_2_7_49_1
  doi: 10.1093/nar/gku411
– ident: e_1_2_7_228_1
  doi: 10.1007/978-1-4939-7366-8_4
– ident: e_1_2_7_7_1
  doi: 10.1016/s0021‐9258(18)45665‐7
– ident: e_1_2_7_97_1
  doi: 10.1038/emboj.2013.79
– ident: e_1_2_7_260_1
  doi: 10.1021/acs.bioconjchem.3c00374
– ident: e_1_2_7_45_1
  doi: 10.1038/srep23257
– ident: e_1_2_7_163_1
  doi: 10.1093/bioinformatics/btr088
– ident: e_1_2_7_67_1
  doi: 10.1093/nar/gkl163
– ident: e_1_2_7_38_1
  doi: 10.1002/humu.21242
– ident: e_1_2_7_2_1
  doi: 10.2174/0929866530666230519122612
– ident: e_1_2_7_107_1
  doi: 10.1371/journal.pone.0055844
– ident: e_1_2_7_185_1
  doi: 10.1038/nmeth.3959
– ident: e_1_2_7_190_1
  doi: 10.1093/nar/27.23.4636
– ident: e_1_2_7_224_1
  doi: 10.1002/JCC.21787
– ident: e_1_2_7_55_1
  doi: 10.1093/bioinformatics/btz773
– ident: e_1_2_7_188_1
– ident: e_1_2_7_256_1
  doi: 10.3390/pharmaceutics14112533
– ident: e_1_2_7_41_1
  doi: 10.1016/j.csbj.2022.12.008
– ident: e_1_2_7_234_1
  doi: 10.1073/pnas.1821309116
– ident: e_1_2_7_51_1
  doi: 10.1093/bioinformatics/btx417
– ident: e_1_2_7_119_1
  doi: 10.1093/nar/gks539
– ident: e_1_2_7_83_1
  doi: 10.1093/nar/gkg584
– ident: e_1_2_7_206_1
  doi: 10.1007/978-1-4939-6798-8_14
– ident: e_1_2_7_50_1
  doi: 10.1093/nar/gkl190
– ident: e_1_2_7_52_1
  doi: 10.1186/s12915‐023‐01510‐8
– ident: e_1_2_7_117_1
  doi: 10.1093/nar/gkr407
– ident: e_1_2_7_179_1
  doi: 10.1038/nmeth.4197
– volume: 15
  start-page: 614
  issue: 2
  year: 2023
  ident: e_1_2_7_124_1
  article-title: Unleashing the Power of MutationTaster2 and MutationTaster2021: The Machine Learning Approach to Genetic Variant Analysis
  publication-title: Revista Cubana de Informática Médica
– ident: e_1_2_7_159_1
  doi: 10.1093/nar/gkt1055
– ident: e_1_2_7_220_1
  doi: 10.1016/j.softx.2015.06.001
– ident: e_1_2_7_170_1
  doi: 10.1093/molbev/msaa015
– ident: e_1_2_7_22_1
  doi: 10.3390/ijms161024918
– ident: e_1_2_7_18_1
  doi: 10.1201/9781003283119-15
– ident: e_1_2_7_167_1
  doi: 10.1093/nar/gkt427
– ident: e_1_2_7_121_1
  doi: 10.1002/0471142905.hg0720s76
– ident: e_1_2_7_222_1
  doi: 10.1002/jcc.21287
– start-page: 01
  volume-title: Advances in Protein Molecular and Structural Biology Methods
  year: 2022
  ident: e_1_2_7_253_1
– ident: e_1_2_7_247_1
  doi: 10.1038/s41586‐023‐06415‐8
– ident: e_1_2_7_34_1
  doi: 10.1186/s12859‐015‐0548‐6
– ident: e_1_2_7_141_1
  doi: 10.1093/nar/gkx313
– ident: e_1_2_7_151_1
  doi: 10.1093/sysbio/syq010
– ident: e_1_2_7_215_1
  doi: 10.1093/nar/30.1.200
– ident: e_1_2_7_160_1
  doi: 10.1093/nar/gkm1005
– ident: e_1_2_7_115_1
  doi: 10.1021/acs.jcim.5b00276
– ident: e_1_2_7_14_1
  doi: 10.1002/cbic.202200152
– ident: e_1_2_7_181_1
  doi: 10.1093/nar/29.12.2607
– ident: e_1_2_7_136_1
  doi: 10.1002/pro.4218
– ident: e_1_2_7_70_1
  doi: 10.1093/database/baab012
– ident: e_1_2_7_129_1
  doi: 10.1093/nar/gky1016
– ident: e_1_2_7_139_1
  doi: 10.1093/nar/gki372
– ident: e_1_2_7_142_1
  doi: 10.1093/bioinformatics/bti486
– ident: e_1_2_7_57_1
  doi: 10.1093/bioinformatics/btl623
– ident: e_1_2_7_143_1
  doi: 10.1186/1471‐2105‐7‐166
– ident: e_1_2_7_68_1
  doi: 10.1016/j.jprot.2011.09.014
– volume: 1
  start-page: 12
  issue: 1
  year: 2019
  ident: e_1_2_7_78_1
  publication-title: Aristotle Biomed Journal
– ident: e_1_2_7_150_1
  doi: 10.1093/bioinformatics/18.suppl_1.s71
– ident: e_1_2_7_171_1
  doi: 10.1016/j.celrep.2013.10.041
– ident: e_1_2_7_130_1
  doi: 10.1186/s13073‐021‐00835‐9
– ident: e_1_2_7_242_1
  doi: 10.1038/srep01448
– ident: e_1_2_7_53_1
  doi: 10.1093/bioinformatics/btu420
– ident: e_1_2_7_191_1
  doi: 10.1093/nar/gki458
– ident: e_1_2_7_237_1
  doi: 10.1101/2023.05.03.539278
– ident: e_1_2_7_71_1
  doi: 10.1002/pmic.200300771
– ident: e_1_2_7_218_1
  doi: 10.1093/nar/gkr367
– ident: e_1_2_7_199_1
  doi: 10.1002/pro.3313
– year: 2023
  ident: e_1_2_7_246_1
  article-title: Joint Generation of Protein Sequence and Structure With RoseTTAFold Sequence Space Diffusion
  publication-title: bioRxiv
– ident: e_1_2_7_197_1
  doi: 10.1016/j.molcel.2018.08.033
– ident: e_1_2_7_230_1
  doi: 10.1016/j.commatsci.2019.109363
– ident: e_1_2_7_156_1
  doi: 10.1093/molbev/msm088
– ident: e_1_2_7_243_1
  doi: 10.1186/gb-2014-15-1-r17
– ident: e_1_2_7_138_1
  doi: 10.1093/nar/gkx369
– ident: e_1_2_7_196_1
  doi: 10.1093/nar/gkp410
– ident: e_1_2_7_144_1
  doi: 10.1093/nar/gki404
– ident: e_1_2_7_9_1
  doi: 10.1007/978‐1‐59745‐177‐2_13
– ident: e_1_2_7_24_1
  doi: 10.1146/annurev.biochem.77.062906.171838
– ident: e_1_2_7_232_1
  doi: 10.1002/jcc.20289
– ident: e_1_2_7_20_1
  doi: 10.1073/pnas.2206111119
– ident: e_1_2_7_105_1
  doi: 10.1093/nar/gku1151
– start-page: 1
  year: 2008
  ident: e_1_2_7_223_1
  article-title: Desmond Performance on a Cluster of Multicore Processors
  publication-title: Simulation
– ident: e_1_2_7_250_1
  doi: 10.1016/j.copbio.2017.12.020
– ident: e_1_2_7_254_1
  doi: 10.1016/j.compbiomed.2022.105695
– ident: e_1_2_7_174_1
  doi: 10.1093/nar/25.17.3389
– ident: e_1_2_7_178_1
  doi: 10.1038/nbt.1621
– ident: e_1_2_7_183_1
  doi: 10.1093/bioinformatics/btac115
– ident: e_1_2_7_209_1
  doi: 10.1093/bioinformatics/bts139
– ident: e_1_2_7_211_1
  doi: 10.1016/j.plipres.2018.07.001
– ident: e_1_2_7_93_1
  doi: 10.1093/nar/gkl922
– ident: e_1_2_7_134_1
  doi: 10.1186/1471‐2164‐14‐s3‐s6
– ident: e_1_2_7_165_1
  doi: 10.1093/bioinformatics/btu033
– ident: e_1_2_7_148_1
  doi: 10.1093/nar/gkw408
– ident: e_1_2_7_65_1
  doi: 10.1093/nar/gkx412
– ident: e_1_2_7_225_1
  doi: 10.1016/0263‐7855(96)00018‐5
– ident: e_1_2_7_113_1
  doi: 10.1371/journal.pone.0011290
– ident: e_1_2_7_76_1
  doi: 10.1093/bib/bbad090
– ident: e_1_2_7_251_1
  doi: 10.1002/prot.26614
– ident: e_1_2_7_249_1
  doi: 10.1038/s41592‐019‐0496‐6
– ident: e_1_2_7_102_1
  doi: 10.1093/nar/gkl233
– ident: e_1_2_7_101_1
  doi: 10.1093/bioinformatics/btu852
– ident: e_1_2_7_32_1
  doi: 10.1093/bioinformatics/btw361
– ident: e_1_2_7_147_1
  doi: 10.2174/1570180819666220510140605
– start-page: 277
  volume-title: Challenges and Advances in Computational Chemistry and Physics
  year: 2023
  ident: e_1_2_7_233_1
– ident: e_1_2_7_98_1
  doi: 10.2174/0929866526666191002111404
– ident: e_1_2_7_111_1
  doi: 10.1371/journal.pone.0049108
– ident: e_1_2_7_202_1
  doi: 10.1038/nbt.4247
– ident: e_1_2_7_216_1
  doi: 10.7150/ijbs.31957
– ident: e_1_2_7_128_1
  doi: 10.1038/s41467‐020‐19669‐x
– ident: e_1_2_7_214_1
  doi: 10.1002/pro.3978
– ident: e_1_2_7_25_1
  doi: 10.3390/molecules28135169
– ident: e_1_2_7_63_1
  doi: 10.1016/j.jmb.2014.09.026
– ident: e_1_2_7_195_1
  doi: 10.1093/nar/gkaa372
– ident: e_1_2_7_219_1
  doi: 10.1146/annurev.physchem.58.032806.104614
– ident: e_1_2_7_42_1
  doi: 10.1093/bioinformatics/bty348
– ident: e_1_2_7_104_1
  doi: 10.1093/nar/gkaa1104
– ident: e_1_2_7_145_1
  doi: 10.1093/nar/gkm659
– ident: e_1_2_7_137_1
  doi: 10.1093/nar/gkv1194
– ident: e_1_2_7_155_1
  doi: 10.1093/nar/gkm764
– ident: e_1_2_7_123_1
  doi: 10.1038/nmeth0810‐575
– ident: e_1_2_7_255_1
  doi: 10.1016/j.sbi.2020.01.008
– ident: e_1_2_7_74_1
  doi: 10.1093/nar/gkj083
– ident: e_1_2_7_58_1
  doi: 10.1093/bioinformatics/btx345
– ident: e_1_2_7_72_1
  doi: 10.7150/ijbs.24121
– ident: e_1_2_7_47_1
  doi: 10.1021/acs.jcim.8b00697
– ident: e_1_2_7_60_1
  doi: 10.1093/bioinformatics/bty166
– ident: e_1_2_7_164_1
  doi: 10.1002/0471142727.mb1911s96
– ident: e_1_2_7_122_1
  doi: 10.1038/nmeth0410‐248
– ident: e_1_2_7_236_1
  doi: 10.1109/TPAMI.2021.3095381
– ident: e_1_2_7_213_1
  doi: 10.1093/nar/gkt1240
– ident: e_1_2_7_221_1
  doi: 10.1002/jcc.20290
– ident: e_1_2_7_140_1
  doi: 10.1186/1471‐2164‐14‐s3‐s7
– ident: e_1_2_7_31_1
  doi: 10.1016/S0022-2836(03)00888-X
– ident: e_1_2_7_85_1
  doi: 10.1016/j.gpb.2023.03.007
– ident: e_1_2_7_239_1
  doi: 10.1038/s42256‐019‐0049‐9
– ident: e_1_2_7_75_1
  doi: 10.1093/nar/gku1081
– ident: e_1_2_7_110_1
  doi: 10.1371/journal.pone.0089575
– ident: e_1_2_7_79_1
  doi: 10.1093/bib/bbaa134
– ident: e_1_2_7_66_1
  doi: 10.1093/bioinformatics/btaa578
– ident: e_1_2_7_118_1
  doi: 10.1093/nar/gki375
– ident: e_1_2_7_27_1
  doi: 10.3390/biology12020166
– ident: e_1_2_7_62_1
  doi: 10.1093/bib/bbad004
– ident: e_1_2_7_116_1
  doi: 10.1093/bioinformatics/btw387
– ident: e_1_2_7_90_1
  doi: 10.1016/j.bbrc.2004.11.001
– ident: e_1_2_7_231_1
  doi: 10.1016/j.cpc.2021.108171
– ident: e_1_2_7_126_1
  doi: 10.1093/bioinformatics/btv195
– ident: e_1_2_7_44_1
  doi: 10.1093/bioinformatics/btp445
– ident: e_1_2_7_153_1
  doi: 10.1093/bioinformatics/bts507
– ident: e_1_2_7_240_1
  doi: 10.1093/bioinformatics/bty341
– ident: e_1_2_7_37_1
  doi: 10.1002/prot.20810
– ident: e_1_2_7_175_1
  doi: 10.1093/bib/bbs029
– ident: e_1_2_7_207_1
  doi: 10.1002/jcc.20303
– ident: e_1_2_7_252_1
  doi: 10.1016/j.gpb.2022.11.014
– ident: e_1_2_7_33_1
  doi: 10.1093/bioinformatics/btv769
– ident: e_1_2_7_35_1
  doi: 10.1038/nmeth0607-466
– ident: e_1_2_7_125_1
  doi: 10.1038/nmeth.2890
– ident: e_1_2_7_133_1
  doi: 10.1002/humu.22225
– ident: e_1_2_7_21_1
  doi: 10.1016/B978‐0‐32‐390644‐9.00085‐8
– volume: 44
  start-page: 1
  year: 1997
  ident: e_1_2_7_157_1
  article-title: Phylogenetic Analysis by Maximum Likelihood (PAML)
  publication-title: Distribution Over Internet
– ident: e_1_2_7_168_1
  doi: 10.1093/bioinformatics/bty862
– ident: e_1_2_7_198_1
  doi: 10.1007/978‐1‐4939‐7366‐8_3
– ident: e_1_2_7_109_1
  doi: 10.1093/bioinformatics/bti130
– ident: e_1_2_7_46_1
  doi: 10.1038/s41598‐018‐22531‐2
– ident: e_1_2_7_212_1
  doi: 10.1038/nchembio.1199
– ident: e_1_2_7_259_1
  doi: 10.1155/2022/8929715
– ident: e_1_2_7_149_1
  doi: 10.1093/bioinformatics/19.1.163
– ident: e_1_2_7_176_1
  doi: 10.1093/nar/gkac1071
– ident: e_1_2_7_81_1
  doi: 10.1093/nar/gkm772
– ident: e_1_2_7_208_1
  doi: 10.1007/978-94-007-6178-0_100946-1
– ident: e_1_2_7_29_1
  doi: 10.1093/nar/gki387
– ident: e_1_2_7_106_1
  doi: 10.1093/bioinformatics/btw377
– ident: e_1_2_7_16_1
  doi: 10.1021/acs.analchem.1C00895
– ident: e_1_2_7_173_1
  doi: 10.1038/nature01511
– ident: e_1_2_7_227_1
  doi: 10.1021/acs.jpcb.3c06662.OpenMM
– ident: e_1_2_7_186_1
  doi: 10.1038/s41598‐018‐28948‐z
– ident: e_1_2_7_11_1
  doi: 10.1016/BS.APCSB.2022.01.003
– ident: e_1_2_7_192_1
  doi: 10.1093/nar/gku557
– ident: e_1_2_7_261_1
  doi: 10.1021/acsptsci.3c00269
– ident: e_1_2_7_135_1
  doi: 10.1093/bioinformatics/btac678
– ident: e_1_2_7_146_1
  doi: 10.1093/bioinformatics/btg241
– ident: e_1_2_7_69_1
  doi: 10.1016/j.csbj.2017.03.004
– ident: e_1_2_7_248_1
  doi: 10.1242/dmm.049874
– ident: e_1_2_7_5_1
  doi: 10.1126/science.6572017
– ident: e_1_2_7_210_1
  doi: 10.1093/nar/gkv315
– ident: e_1_2_7_19_1
  doi: 10.1101/2022.02.17.480964
– ident: e_1_2_7_56_1
  doi: 10.1111/j.1742‐4658.2012.08603.x
– ident: e_1_2_7_245_1
  doi: 10.1038/s42256‐021‐00348‐5
– ident: e_1_2_7_166_1
  doi: 10.1002/0471250953.bi0614s51
– ident: e_1_2_7_158_1
  doi: 10.1093/nar/gkj118
– ident: e_1_2_7_12_1
  doi: 10.1021/cen‐10112‐cover
– ident: e_1_2_7_15_1
  doi: 10.21474/ijar01/14120
– ident: e_1_2_7_13_1
  doi: 10.7554/eLife.82593
– ident: e_1_2_7_205_1
  doi: 10.1002/bmb.2005.494033032449
– ident: e_1_2_7_258_1
  doi: 10.3390/ijms161025831
– ident: e_1_2_7_82_1
  doi: 10.1186/1471‐2105‐5‐79
– ident: e_1_2_7_194_1
  doi: 10.1021/acs.jpcb.0c11640
– ident: e_1_2_7_226_1
  doi: 10.1002/pro.3923
– ident: e_1_2_7_86_1
  doi: 10.1186/gb‐2007‐8‐11‐r250
– ident: e_1_2_7_73_1
  doi: 10.1093/nar/gkab1017
– ident: e_1_2_7_87_1
  doi: 10.1093/nar/gkq1159
– ident: e_1_2_7_95_1
  doi: 10.1371/journal.pcbi.1002285
– year: 2019
  ident: e_1_2_7_238_1
  article-title: A Structure‐Based Deep Learning Framework for Protein Engineering
  publication-title: bioRxiv
– ident: e_1_2_7_127_1
  doi: 10.1371/journal.pone.0046688
– ident: e_1_2_7_132_1
  doi: 10.1093/bioinformatics/btx536
– ident: e_1_2_7_184_1
  doi: 10.1101/gr.235028.118.29
– ident: e_1_2_7_263_1
  doi: 10.2147/dddt.s236788
– ident: e_1_2_7_187_1
  doi: 10.1093/bioinformatics/17.9.847
– ident: e_1_2_7_94_1
  doi: 10.1093/nar/gkq936
– ident: e_1_2_7_36_1
  doi: 10.1016/j.str.2007.09.024
– ident: e_1_2_7_99_1
  doi: 10.1093/nar/gki385
– ident: e_1_2_7_17_1
  doi: 10.33545/27076636.2022.v3.i1a.33
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Snippet ABSTRACT The field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de...
The field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de novo protein...
ABSTRACT The field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de...
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SubjectTerms Accuracy
Algorithms
Amino acids
Artificial intelligence
Bioinformatics
Biomedical materials
Datasets
Design
Energy
Engineering
Machine learning
Mutagenesis
Mutation
Neural networks
NMR
Nuclear magnetic resonance
protein computational resources
protein design
protein engineering
protein engineering tools
Proteins
Research methodology
Software
Stability
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Title Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and Engineering
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