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For: He Y, Maisuradze GG, Yin Y, Kachlishvili K, Rackovsky S, Scheraga HA. Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins. Proc Natl Acad Sci U S A 2017;114:1578-83. [PMID: 28143938 DOI: 10.1073/pnas.1621344114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Xie X, Deng X, Chen L, Yuan J, Chen H, Wei C, Feng C, Liu X, Qiu G. From Gene to Structure: Unraveling Genomic Dark Matter in Ca. Accumulibacter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39699575 DOI: 10.1021/acs.est.4c09948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2024]
2
Song S, Li T, Stevens AO, Shorty T, He Y. Molecular Dynamics Reveal Key Steps in BAR-Related Membrane Remodeling. Pathogens 2024;13:902. [PMID: 39452773 PMCID: PMC11510478 DOI: 10.3390/pathogens13100902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 10/08/2024] [Accepted: 10/13/2024] [Indexed: 10/26/2024]  Open
3
Sabsay KR, te Velthuis AJW. Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships. Virus Evol 2024;10:veae058. [PMID: 39129834 PMCID: PMC11315766 DOI: 10.1093/ve/veae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 05/21/2024] [Accepted: 07/19/2024] [Indexed: 08/13/2024]  Open
4
Dong Y, Quan H, Ma C, Shan L, Deng L. TGC-ARG: Anticipating Antibiotic Resistance via Transformer-Based Modeling and Contrastive Learning. Int J Mol Sci 2024;25:7228. [PMID: 39000335 PMCID: PMC11241484 DOI: 10.3390/ijms25137228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024]  Open
5
Chen Z, Wang R, Guo J, Wang X. The role and future prospects of artificial intelligence algorithms in peptide drug development. Biomed Pharmacother 2024;175:116709. [PMID: 38713945 DOI: 10.1016/j.biopha.2024.116709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]  Open
6
Sabsay KR, te Velthuis AJ. Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580771. [PMID: 38405982 PMCID: PMC10888975 DOI: 10.1101/2024.02.16.580771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
7
Wu C, Guo D. Identification of Two Flip-Over Genes in Grass Family as Potential Signature of C4 Photosynthesis Evolution. Int J Mol Sci 2023;24:14165. [PMID: 37762466 PMCID: PMC10531853 DOI: 10.3390/ijms241814165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]  Open
8
Rappoport D, Jinich A. Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves. J Chem Inf Model 2023;63:1637-1648. [PMID: 36802628 DOI: 10.1021/acs.jcim.3c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
9
In Search of a Dynamical Vocabulary: A Pipeline to Construct a Basis of Shared Traits in Large-Scale Motions of Proteins. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12147157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
10
Toopaang W, Bunnak W, Srisuksam C, Wattananukit W, Tanticharoen M, Yang YL, Amnuaykanjanasin A. Microbial polyketides and their roles in insect virulence: from genomics to biological functions. Nat Prod Rep 2022;39:2008-2029. [PMID: 35822627 DOI: 10.1039/d1np00058f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
11
George MW, Abreu BL, Boufroura H, Moore JC, Poliakoff M. Telescoped Continuous Flow Synthesis of 2-Substituted 1,4-Benzoquinones via Oxidative Dearomatisation of para-Substituted Phenols Using Singlet Oxygen in Supercritical CO2. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0041-1737413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
12
Zhao W, Luo S, Wu H, Jiang X, He T, Hu X. A multi-label learning framework for predicting antibiotic resistance genes via dual-view modeling. Brief Bioinform 2022;23:6546259. [PMID: 35272349 DOI: 10.1093/bib/bbac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022]  Open
13
Wei L, Ye X, Xue Y, Sakurai T, Wei L. ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism. Brief Bioinform 2021;22:6209691. [PMID: 33822870 DOI: 10.1093/bib/bbab041] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/11/2021] [Accepted: 01/28/2021] [Indexed: 12/13/2022]  Open
14
The structure of protein dynamic space. Proc Natl Acad Sci U S A 2020;117:19938-19942. [PMID: 32759212 DOI: 10.1073/pnas.2008873117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
15
Paul S, Ainavarapu SRK, Venkatramani R. Variance of Atomic Coordinates as a Dynamical Metric to Distinguish Proteins and Protein-Protein Interactions in Molecular Dynamics Simulations. J Phys Chem B 2020;124:4247-4262. [PMID: 32281802 DOI: 10.1021/acs.jpcb.0c01191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
16
Beyond Supersecondary Structure: Physics-Based Sequence Alignment. Methods Mol Biol 2019. [PMID: 30945228 DOI: 10.1007/978-1-4939-9161-7_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
17
Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019;119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 313] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
18
Ng ML, Rahmat ZB, Bin Omar MSS. Molecular Modeling and Simulation of Transketolase from Orthosiphon stamineus. Curr Comput Aided Drug Des 2018;15:308-317. [PMID: 30345923 DOI: 10.2174/1573409914666181022141753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/21/2018] [Accepted: 10/17/2018] [Indexed: 11/22/2022]
19
Cao K, Li N, Wang H, Cao X, He J, Zhang B, He QY, Zhang G, Sun X. Two zinc-binding domains in the transporter AdcA from Streptococcus pyogenes facilitate high-affinity binding and fast transport of zinc. J Biol Chem 2018;293:6075-6089. [PMID: 29491141 DOI: 10.1074/jbc.m117.818997] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 02/25/2018] [Indexed: 11/06/2022]  Open
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