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Authors:
Source: Scientific Reports, Vol 15, Iss 1, Pp 1-22 (2025)
Subject Terms: HTTPS traffic classification, Encrypted traffic, Network security, Network traffic classification, Deep learning, Ensemble learning, Medicine, Science
File Description: electronic resource
Relation: https://doaj.org/toc/2045-2322
Access URL:
https ://doaj.org/article/cd8f8e99ded44ac2b23fc0de09acc54e -
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Authors: et al.
Index Terms: Computer Science - Cryptography and Security, Computer Science - Networking and Internet Architecture, text
URL:
http://arxiv.org/abs/2405.17737 -
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Authors: et al.
Subject Terms: Biochemistry, Genetics, Molecular Biology, Biotechnology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, target proteins via, molecules remain underdeveloped, https :// bailab, generative artificial intelligence, garnered significant attention, demonstrate superior performance, based partitioned datasets, based model built, https :// github, exceptional generalization ability, drug design due, experimental synthetic data, protac synthetic accessibility, synthetic accessibility, github repository, web server, test set, targeting chimeras, protac synthesis, prediction accuracy, novel compounds, house dataset, essential tool, driven approach
Relation: https://figshare.com/articles/journal_contribution/DeepPSA_A_Geometric_Deep_Learning_Model_for_PROTAC_Synthetic_Accessibility_Prediction/29403711
Availability: https://doi.org/10.1021/acs.jcim.5c00366.s001
https://figshare.com/articles/journal_contribution/DeepPSA_A_Geometric_Deep_Learning_Model_for_PROTAC_Synthetic_Accessibility_Prediction/29403711 -
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Authors: et al.
Subject Terms: Biophysics, Biochemistry, Cell Biology, Biotechnology, Hematology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, thereby promoting accessible, secondary structure probability, residue distance matrices, quality graphical outputs, packages often lack, ligand occupancy maps, https :// pypi, generate interactive plots, different temperatures illustrates, comparative tests performed, amyloid peptide simulations, online web server, principal component analysis, descriptive statistical analysis, based software package, web platform designed, https :// github, https :// dynamispectra, reproducible md analysis, reproducible analysis tools, python software package, web platform
Relation: https://figshare.com/articles/journal_contribution/DynamiSpectra_A_Python_Software_Package_and_Web_Platform_for_Molecular_Dynamics_Data_Analysis_in_Computational_Biology/29955677
Availability: https://doi.org/10.1021/acs.jcim.5c01270.s001
https://figshare.com/articles/journal_contribution/DynamiSpectra_A_Python_Software_Package_and_Web_Platform_for_Molecular_Dynamics_Data_Analysis_in_Computational_Biology/29955677 -
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Authors:
Subject Terms: Biochemistry, Biotechnology, Mental Health, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, transformer encoder architecture, substantially outperforming msbert, reasonable spectral embeddings, quality spectral embeddings, offered new solutions, mtbls1572 data set, mona data set, https :// huggingface, https :// github, gnps training subset, gnps test subset, dimensional vector representations, 1 hit ratio, experimental results show, specembedding significantly enhances, employs replicated spectra, experimental conditions, widely applied, web service, specembedding achieves, source code, recent advancements, publicly available
Relation: https://figshare.com/articles/journal_contribution/Supervised_Contrastive_Learning_Leads_to_More_Reasonable_Spectral_Embeddings/30118561
Availability: https://doi.org/10.1021/acs.analchem.5c02655.s001
https://figshare.com/articles/journal_contribution/Supervised_Contrastive_Learning_Leads_to_More_Reasonable_Spectral_Embeddings/30118561 -
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Authors: et al.
Subject Terms: Microbiology, Biotechnology, Inorganic Chemistry, Science Policy, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, supporting rational decision, source code provided, minimal input requirements, microaerobic production stage, maximizing bioprocess efficiency, https :// github, https :// chemnettools, exponential feeding strategies, friendly web tool, batch fermentation strategies, arrested production stage, aid process design, extensive modeling expertise, demonstrate fedbatchdesigner ’, process ’, friendly dashboard, batch processes, arrested fed, saccharomyces cerevisiae, present fedbatchdesigner, optimizing fed, nitrogen starvation, mit license, mathematical modeling
Availability: https://doi.org/10.1021/acssynbio.5c00357.s002
https://figshare.com/articles/journal_contribution/Fedbatchdesigner_A_User-Friendly_Dashboard_for_Modeling_and_Optimizing_Growth-Arrested_Fed-Batch_Processes/29614871 -
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Authors: et al.
Subject Terms: Biophysics, Molecular Biology, Cancer, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, within ± 0, vertical transition energies, rydberg transitions occurring, many computational methods, https :// github, deemed chemically accurate, corresponding data associated, associated github repository, quest also includes, accurate excitation energies, quest database, excitation character, vast majority, various single, states characterized, state methodologies, significant list, reported values, pvtz estimate, popular excited, particularly challenging, large number, hydrogen atoms
Availability: https://doi.org/10.1021/acs.jctc.5c00975.s001
https://figshare.com/articles/journal_contribution/QUEST_Database_of_Highly-Accurate_Excitation_Energies/29865870 -
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Authors: et al.
Subject Terms: Biophysics, Biochemistry, Medicine, Hematology, Computational Biology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, one specific challenge, extensive human input, demo data sets, attracted increasing interest, cryptic site region, 93 cryptic pockets, studied cryptic sites, cryptic sites studies, cryptosite data set, 84 protein systems, procedure dynamically identifies, two cryptic sites, https :// github, dynamic pocket transitions, conformational dynamics capturing, based pocket characterization, wbc method outperforms, md simulation results, cryptic sites, two well
Availability: https://doi.org/10.1021/acs.jctc.5c01019.s001
https://figshare.com/articles/journal_contribution/Identification_of_Protein_Cryptic_Sites_via_Conformational_Dynamics_Capturing_and_Water-Based_Pocket_Characterization_in_Molecular_Dynamics_Simulations/30005528 -
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Authors: et al.
Subject Terms: Biophysics, Biochemistry, Biotechnology, Immunology, Cancer, Hematology, Infectious Diseases, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, specific databases often, reference experimental complexes, provide molecular descriptors, machine learning applications, incorrect quality based, corresponding molecular descriptors, accompanying scripts hosted, protein data bank, publicly available via, generate structural variants, https :// github, curated dataset comprising, standardized data set, 000 antibody structures, data sets, structural similarity, decoy set, available structures, zenodo repository, therapeutic antibodies
Relation: https://figshare.com/articles/journal_contribution/AbSet_A_Standardized_Data_Set_of_Antibody_Structures_for_Machine_Learning_Applications/29031922
Availability: https://doi.org/10.1021/acs.jcim.5c00410.s002
https://figshare.com/articles/journal_contribution/AbSet_A_Standardized_Data_Set_of_Antibody_Structures_for_Machine_Learning_Applications/29031922 -
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Authors: et al.
Subject Terms: Biochemistry, Sociology, Science Policy, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, specific experimental conditions, resulting physicochemical properties, ms data challenges, adaptability allows researchers, synthetic peptide library, peptide identification due, offering high performance, improving predictive capacity, https :// github, deep learning model, peptide detectability prediction, peptide detectability, detectability prediction, peptide sequences, peptide sequence, improving accuracy, high variability, subsequently fine, strongly related, species datasets, reliable state, protein abundance, outperforming state, negative impact, mass spectrometry
Relation: https://figshare.com/articles/journal_contribution/To_Fly_or_Not_to_Fly_That_Is_the_Question_A_Deep_Learning_Model_for_Peptide_Detectability_Prediction_in_Mass_Spectrometry/28996342
Availability: https://doi.org/10.1021/acs.jproteome.4c00973.s001
https://figshare.com/articles/journal_contribution/To_Fly_or_Not_to_Fly_That_Is_the_Question_A_Deep_Learning_Model_for_Peptide_Detectability_Prediction_in_Mass_Spectrometry/28996342 -
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Authors:
Contributors:
Subject Terms: Ajax, Andrea Hauser, Basel, Browser, Firefox, GitHub, Google, Hardening, HTML, HTTP, Javascript, Master, Microsoft, Penetration Test, Policy, Report, Request, Research, Shop, Tool, Twitter, West
Relation: https://zenodo.org/records/3521919; oai:zenodo.org:3521919; https://doi.org/10.5281/zenodo.3521919
Availability: https://doi.org/10.5281/zenodo.3521919
https://zenodo.org/records/3521919 -
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Authors: et al.
Subject Terms: Biochemistry, Genetics, Pharmacology, Biotechnology, Cancer, Computational Biology, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, significantly attenuate fibrosis, screen active compounds, presents significant challenges, https :// github, 8 å ), drug discovery community, discover critical targets, accelerating drug discovery, structurally relevant targets, 50 sub, relevant targets, therapeutic discovery, would benefit, source software, revealed retinoid, ray crystallography, prioritize disease, murine models, findings demonstrated, fibrotic cascades
Availability: https://doi.org/10.1021/acs.jmedchem.5c01682.s001
https://figshare.com/articles/journal_contribution/ComplexDnet_A_Network-Based_Strategy_to_Discover_Critical_Targets_and_Screen_Active_Compounds_for_Complex_Diseases/30053034 -
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Authors:
Subject Terms: Biophysics, Biochemistry, Medicine, Microbiology, Genetics, Molecular Biology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, throughput screening due, needs without requiring, https :// github, automate microbial handling, recombinant protein production, source opentrons ot, 7 – 17, produce recombinant proteins, generating recombinant proteins, automated heterologous expression, automated protein expression, 2 hardware setup, protein expression, automated pipeline, minimal ot, 7 kb, time consumption
Relation: https://figshare.com/articles/journal_contribution/APEX_Automated_Protein_EXpression_in_Escherichia_coli/30037939
Availability: https://doi.org/10.1021/acssynbio.5c00189.s002
https://figshare.com/articles/journal_contribution/APEX_Automated_Protein_EXpression_in_Escherichia_coli/30037939 -
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Authors:
Subject Terms: Biochemistry, Medicine, Immunology, Computational Biology, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, uncover distinct regions, tunable solvation properties, new geometric measure, negligible vapor pressure, machine learning prediction, https :// github, dimensionality reduction techniques, dilution activity coefficients, analysis reveals many, traditional il selection, design space exploration, >- 125 ), develop machine learning, refrigerant separation involving, il design space, >- 410a separation, >- 125 solubility, >- 125, >- 410a, refrigerant mixtures, >- 32, widely used
Relation: https://figshare.com/articles/journal_contribution/Design_Space_Exploration_and_Machine_Learning_Prediction_of_Hydrofluorocarbon_Solubility_in_Ionic_Liquids_for_Refrigerant_Separation/29977765
Availability: https://doi.org/10.1021/acs.jcim.5c01216.s001
https://figshare.com/articles/journal_contribution/Design_Space_Exploration_and_Machine_Learning_Prediction_of_Hydrofluorocarbon_Solubility_in_Ionic_Liquids_for_Refrigerant_Separation/29977765 -
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Authors:
Subject Terms: Biophysics, Genetics, Biotechnology, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, https :// github, disk space compared, artificial neural network, thus facilitating storage, large protein complexes, intrinsically disordered proteins, including folded proteins, bound protein systems, biomolecular simulation studies, compress md trajectories, simulation trajectories, biomolecular systems, share large, optimal storage, simulation programs, larger systems, composite systems, tested across, scientific community, remarkable stride, publicly available, practical solution, phospholipid bilayers
Relation: https://figshare.com/articles/journal_contribution/Employing_Artificial_Neural_Networks_for_Optimal_Storage_and_Facile_Sharing_of_Molecular_Dynamics_Simulation_Trajectories/29930872
Availability: https://doi.org/10.1021/acs.jcim.5c01294.s001
https://figshare.com/articles/journal_contribution/Employing_Artificial_Neural_Networks_for_Optimal_Storage_and_Facile_Sharing_of_Molecular_Dynamics_Simulation_Trajectories/29930872 -
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Authors: Alison Felipe Alencar Chaves
Subject Terms: Biochemistry, Biotechnology, Developmental Biology, Inorganic Chemistry, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, traditional spreadsheet formats, throughput sample analyses, samplewise similarity metrics, local r setup, intuitively assessing large, https :// github, free data visualization, fastest computational platforms, based r application, visual quality control, rapid quality control, quality control metrics, peptide length distributions, fragpipe results fragpipe, protein data visualization, protein abundance discrepancies, scale proteomics data, quality scores, fragpipe introduced, filter peptide, protein coverage, version 23, spectrum matches
Relation: https://figshare.com/articles/journal_contribution/PSManalyst_A_Dashboard_for_Visual_Quality_Control_of_FragPipe_Results/29922914
Availability: https://doi.org/10.1021/acs.jproteome.5c00557.s002
https://figshare.com/articles/journal_contribution/PSManalyst_A_Dashboard_for_Visual_Quality_Control_of_FragPipe_Results/29922914 -
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Authors: et al.
Subject Terms: Biochemistry, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, reverse spectral search, principle first introduced, multiple precursor ions, library matching remains, https :// github, annotation workflows face, untargeted metabolomics data, benchmark data sets, tandem mass spectrometry, computationally efficient solution, chimeric spectral annotation, nonchimeric reference spectra, mass spectra, chimeric spectra, data reuse, overlooked solution, composite spectra, source codes, simultaneous fragmentation, reannotation strategies, reaching billions, public repositories, metabolite annotations, largely overlooked, gold standard, gnps ecosystem
Relation: https://figshare.com/articles/journal_contribution/Reverse_Spectral_Search_Reimagined_A_Simple_but_Overlooked_Solution_for_Chimeric_Spectral_Annotation/29922804
Availability: https://doi.org/10.1021/acs.analchem.5c02047.s001
https://figshare.com/articles/journal_contribution/Reverse_Spectral_Search_Reimagined_A_Simple_but_Overlooked_Solution_for_Chimeric_Spectral_Annotation/29922804 -
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Authors: et al.
Subject Terms: Biochemistry, Medicine, Molecular Biology, Sociology, Cancer, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, various data sets, processing functional groups, identify functional group, https :// github, carbon backbone ), functional group level, specific molecular patterns, molecular structure comparison, accfg generates refined, molecular structures, molecular pairs, molecular modality, level differences, useful tool, tool designed, textual descriptors, results demonstrate, present accfg, molecules based, molecule ’, manual examination
Relation: https://figshare.com/articles/journal_contribution/AccFG_Accurate_Functional_Group_Extraction_and_Molecular_Structure_Comparison/29850026
Availability: https://doi.org/10.1021/acs.jcim.5c01317.s001
https://figshare.com/articles/journal_contribution/AccFG_Accurate_Functional_Group_Extraction_and_Molecular_Structure_Comparison/29850026 -
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Authors: et al.
Subject Terms: Biochemistry, Medicine, Pharmacology, Infectious Diseases, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, specific scoring matrices, localizing allosteric sites, identify allosteric sites, https :// github, evolutionary profiles derived, comprehensive results demonstrate, asd2023 data set, allosteric site prediction, 24 allosteric sites, modulating protein function, protein sequences, static structures, source code, promising strategy, promising method, modality features, language models, embedding representations, drug discovery, diverse features, crucial role, biochemical properties
Availability: https://doi.org/10.1021/acs.jcim.5c01033.s001
https://figshare.com/articles/journal_contribution/Allofusion_Allosteric_Site_Prediction_Based_on_Language_Models_and_Multi-Feature_Fusion/29802869
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