Search Results - "PROTEIN structure"

Boosting AlphaFold protein tertiary structure prediction through MSA engineering and extensive model sampling and ranking in CASP16.

Authors: Liu J Neupane P Cheng J

Source: Communications biology [Commun Biol] 2025 Nov 17; Vol. 8 (1), pp. 1587. Date of Electronic Publication: 2025 Nov 17.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group UK Country of Publication: England NLM ID: 101719179 Publication Model: Electronic Cited Medium: Internet ISSN: 2399-3642 (Electronic) Linking ISSN: 23993642 NLM ISO Abbreviation: Commun Biol Subsets: MEDLINE

MeSH Terms: Computational Biology*/methods , Protein Structure, Tertiary* , Proteins*/chemistry , Software*, Protein Folding ; Models, Molecular ; Sequence Alignment/methods ; Sequence Analysis, Protein/methods ; Algorithms

DCBLSTM-Deep Convolutional Bidirectional Long Short-Term Memory neural network for Q8 secondary protein structure prediction.

Authors: Banthia S McKenna A Tiwari SK et al.

Source: Computers in biology and medicine [Comput Biol Med] 2025 Sep; Vol. 195, pp. 110457. Date of Electronic Publication: 2025 Jun 23.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Country of Publication: United States NLM ID: 1250250 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-0534 (Electronic) Linking ISSN: 00104825 NLM ISO Abbreviation: Comput Biol Med Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Neural Networks, Computer* , Protein Structure, Secondary* , Computational Biology*/methods, Databases, Protein ; Humans

Combining knowledge distillation and neural networks to predict protein secondary structure.

Authors: Zhao L Li J Zhang B et al.

Source: Scientific reports [Sci Rep] 2025 Aug 31; Vol. 15 (1), pp. 32031. Date of Electronic Publication: 2025 Aug 31.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH Terms: Neural Networks, Computer* , Proteins*/chemistry , Protein Structure, Secondary*, Deep Learning ; Databases, Protein ; Computational Biology/methods

Prediction and quality assessment of protein quaternary structure models using the MultiFOLD2 and ModFOLDdock2 servers.

Authors: McGuffin LJ Alhaddad SN Behzadi B et al.

Source: Nucleic acids research [Nucleic Acids Res] 2025 Jul 07; Vol. 53 (W1), pp. W472-W477.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

MeSH Terms: Software* , Models, Molecular* , Protein Structure, Quaternary* , Proteins*/chemistry , Computational Biology*/methods, Internet

A hybrid variational autoencoder and WGAN with gradient penalty for tertiary protein structure generation.

Authors: Sehsah AI Mousa A Farouk G

Source: Scientific reports [Sci Rep] 2025 Apr 23; Vol. 15 (1), pp. 14191. Date of Electronic Publication: 2025 Apr 23.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Computational Biology*/methods , Neural Networks, Computer* , Protein Structure, Tertiary*, Algorithms ; Deep Learning ; Models, Molecular ; Autoencoder

A comprehensive guide for secondary structure and tertiary structure determination in peptides and proteins by circular dichroism spectrometer.

Authors: Kuril AK Vashi A Subbappa PK

Source: Journal of peptide science : an official publication of the European Peptide Society [J Pept Sci] 2025 Jan; Vol. 31 (1), pp. e3648. Date of Electronic Publication: 2024 Aug 12.

Publication Type: Journal Article; Review

Journal Info: Publisher: John Wiley & Sons Country of Publication: England NLM ID: 9506309 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1099-1387 (Electronic) Linking ISSN: 10752617 NLM ISO Abbreviation: J Pept Sci Subsets: MEDLINE

MeSH Terms: Circular Dichroism*/methods , Peptides*/chemistry , Protein Structure, Secondary* , Protein Structure, Tertiary* , Proteins*/chemistry

Hierarchical Analysis of Protein Structures: From Secondary Structures to Protein Units and Domains.

Authors: Perin C Cretin G Gelly JC

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2870, pp. 357-370.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Protein Structure, Secondary* , Protein Domains*, Protein Folding ; Databases, Protein ; Models, Molecular ; Computational Biology/methods ; Protein Conformation

Synthesis, characterization, and in vitro hypolipidemic mechanisms of sugar-SA triazole conjugates as potent pancreatic lipase inhibitors.

Authors: Cao R Li J Sun Y et al.

Source: Food chemistry [Food Chem] 2025 Oct 01; Vol. 488, pp. 144876. Date of Electronic Publication: 2025 May 22.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Applied Science Publishers Country of Publication: England NLM ID: 7702639 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-7072 (Electronic) Linking ISSN: 03088146 NLM ISO Abbreviation: Food Chem Subsets: MEDLINE

MeSH Terms: Hypolipidemic Agents*/chemical synthesis , Hypolipidemic Agents*/chemistry , Hypolipidemic Agents*/pharmacology , Lipase*/antagonists & inhibitors , Lipase*/chemistry , Enzyme Inhibitors*/chemical synthesis , Enzyme Inhibitors*/chemistry , Enzyme Inhibitors*/pharmacology , Triazoles*/chemical synthesis , Triazoles*/chemistry , Triazoles*/pharmacology , Gallic Acid*/chemistry , Gallic Acid*/pharmacology , Gallic Acid*/analogs & derivatives , Glycoconjugates*/chemical synthesis , Glycoconjugates*/chemistry , Glycoconjugates*/pharmacology, Click Chemistry/methods ; Solubility ; Cholesterol/chemistry ; Bile Acids and Salts/chemistry ; Glucose/chemistry ; Hydrophobic and Hydrophilic Interactions ; Molecular Docking Simulation ; Protein Structure, Secondary ; Protein Structure, Tertiary

CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary structure.

Authors: Chivot L Mathieux N Cosson A et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Mar 29; Vol. 41 (4).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH Terms: Algorithms* , Proteins*/chemistry , Protein Structure, Tertiary* , Software* , Computational Biology*/methods, Models, Molecular

TransConv: convolution-infused transformer for protein secondary structure prediction.

Authors: Das S Ghosh S Jana ND

Source: Journal of molecular modeling [J Mol Model] 2025 Jan 08; Vol. 31 (2), pp. 37. Date of Electronic Publication: 2025 Jan 08.

Publication Type: Journal Article

Journal Info: Publisher: Springer Country of Publication: Germany NLM ID: 9806569 Publication Model: Electronic Cited Medium: Internet ISSN: 0948-5023 (Electronic) Linking ISSN: 09485023 NLM ISO Abbreviation: J Mol Model Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Protein Structure, Secondary* , Computational Biology*/methods, Algorithms ; Models, Molecular ; Hydrogen Bonding ; Databases, Protein ; Amino Acid Sequence

Recent Advances in Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences.

Authors: Zhang J Qian J Zou Q et al.

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2870, pp. 1-19.

Publication Type: Journal Article; Review

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Computational Biology*/methods , Protein Structure, Secondary*, Software ; Databases, Protein ; Amino Acid Sequence ; Machine Learning ; Sequence Analysis, Protein/methods ; Neural Networks, Computer

Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field.

Authors: Lubecka EA Czaplewski C Sieradzan AK et al.

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2867, pp. 19-41.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Thermodynamics* , Protein Structure, Secondary* , Molecular Dynamics Simulation*, Computational Biology/methods ; Models, Molecular

Strategy for improving circular dichroism spectra deconvolution accuracy for macrocyclic peptides in drug discovery.

Authors: Guo W Makarov AA Buevich AV et al.

Source: Journal of pharmaceutical and biomedical analysis [J Pharm Biomed Anal] 2025 Jan 01; Vol. 252, pp. 116476. Date of Electronic Publication: 2024 Sep 16.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Science Country of Publication: England NLM ID: 8309336 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-264X (Electronic) Linking ISSN: 07317085 NLM ISO Abbreviation: J Pharm Biomed Anal Subsets: MEDLINE

MeSH Terms: Circular Dichroism*/methods , Drug Discovery*/methods , Peptides, Cyclic*/chemistry , Protein Structure, Secondary*, Calibration ; Magnetic Resonance Spectroscopy/methods ; Crystallography, X-Ray/methods

Improving Protein Secondary Structure Prediction by Deep Language Models and Transformer Networks.

Authors: Wu T Cheng W Cheng J

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2867, pp. 43-53.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Protein Structure, Secondary* , Computational Biology*/methods, Deep Learning ; Software ; Databases, Protein ; Sequence Alignment/methods ; Algorithms ; Amino Acid Sequence

Importance of Secondary Structure Data in Large Scale Protein Modeling Using Low-Resolution SURPASS Method.

Authors: Badaczewska-Dawid AE Kolinski A

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2867, pp. 55-78.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Protein Structure, Secondary*, Monte Carlo Method ; Protein Folding ; Models, Molecular ; Computational Biology/methods ; Molecular Dynamics Simulation ; Algorithms ; Protein Conformation

dRama: Differential Ramachandran Plot as a Tool to Analyze Subtle Changes in Protein Secondary Structure.

Authors: Batys P Krzemień L Barbasz J

Source: Proteomics. Clinical applications [Proteomics Clin Appl] 2025 Jan; Vol. 19 (1), pp. e202400087. Date of Electronic Publication: 2024 Nov 24.

Publication Type: Journal Article

Journal Info: Publisher: Wiley-VCH Country of Publication: Germany NLM ID: 101298608 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1862-8354 (Electronic) Linking ISSN: 18628346 NLM ISO Abbreviation: Proteomics Clin Appl Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Protein Structure, Secondary* , Software*, Molecular Dynamics Simulation

Protein Secondary Structure and DNA/RNA Detection for Cryo-EM and Cryo-ET Using Emap2sec and Emap2sec ^.

Authors: Baghirov J Zhu H Wang X et al.

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2867, pp. 105-120.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Cryoelectron Microscopy*/methods , Software* , RNA*/chemistry , DNA*/chemistry , Protein Structure, Secondary*, Proteins/chemistry ; Models, Molecular ; Nucleic Acid Conformation

Structural Variability of Pfam Domains Based on Alphafold2 Predictions.

Authors: Poretsky E Andorf CM Sen TZ

Source: Proteins [Proteins] 2025 Dec; Vol. 93 (12), pp. 2182-2192. Date of Electronic Publication: 2025 Jul 22.

Publication Type: Journal Article

Journal Info: Publisher: Wiley-Liss Country of Publication: United States NLM ID: 8700181 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1097-0134 (Electronic) Linking ISSN: 08873585 NLM ISO Abbreviation: Proteins Subsets: MEDLINE

MeSH Terms: Computational Biology*/methods , Proteins*/chemistry, Databases, Protein ; Protein Domains ; Humans ; Models, Molecular ; Proteome/chemistry ; Amino Acid Sequence ; Software ; Protein Structure, Secondary ; Protein Folding ; Animals ; Sequence Analysis, Protein

Porter 6: Protein Secondary Structure Prediction by Leveraging Pre-Trained Language Models (PLMs).

Authors: Alanazi W Meng D Pollastri G

Source: International journal of molecular sciences [Int J Mol Sci] 2024 Dec 27; Vol. 26 (1). Date of Electronic Publication: 2024 Dec 27.

Publication Type: Journal Article

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

MeSH Terms: Natural Language Processing* , Proteins*/chemistry , Protein Structure, Secondary* , Computational Biology*/methods , Software*, Deep Learning ; Algorithms

Transient Tertiary Structures of Disordered Dynein Intermediate Chain Regulate its Interactions with Multiple Partners.

Authors: Morgan JL Yeager A Estelle AB et al.

Source: Journal of molecular biology [J Mol Biol] 2021 Sep 03; Vol. 433 (18), pp. 167152. Date of Electronic Publication: 2021 Jul 14.

Publication Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.

Journal Info: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 2985088R Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1089-8638 (Electronic) Linking ISSN: 00222836 NLM ISO Abbreviation: J Mol Biol Subsets: MEDLINE

MeSH Terms: Protein Structure, Tertiary*, Carrier Proteins/*metabolism , Drosophila Proteins/*chemistry , Drosophila Proteins/*metabolism , Drosophila melanogaster/*metabolism , Dyneins/*chemistry , Dyneins/*metabolism, Animals ; Binding Sites ; Carrier Proteins/chemistry ; Molecular Dynamics Simulation ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Secondary