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For: Jones DT, Buchan DWA, Cozzetto D, Pontil M. PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. ACTA ACUST UNITED AC 2011;28:184-90. [PMID: 22101153 DOI: 10.1093/bioinformatics/btr638] [Citation(s) in RCA: 535] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
101
Bisardi M, Rodriguez-Rivas J, Zamponi F, Weigt M. Modeling sequence-space exploration and emergence of epistatic signals in protein evolution. Mol Biol Evol 2021;39:6424001. [PMID: 34751386 PMCID: PMC8789065 DOI: 10.1093/molbev/msab321] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
102
Munro LJ, Kell DB. Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021;478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
103
Sanchez-Pulido L, Ponting CP. Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction. J Mol Biol 2021;433:167106. [PMID: 34139218 PMCID: PMC8527833 DOI: 10.1016/j.jmb.2021.167106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022]
104
Barrat-Charlaix P, Muntoni AP, Shimagaki K, Weigt M, Zamponi F. Sparse generative modeling via parameter reduction of Boltzmann machines: Application to protein-sequence families. Phys Rev E 2021;104:024407. [PMID: 34525554 DOI: 10.1103/physreve.104.024407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/19/2021] [Indexed: 11/07/2022]
105
Laine E, Eismann S, Elofsson A, Grudinin S. Protein sequence-to-structure learning: Is this the end(-to-end revolution)? Proteins 2021;89:1770-1786. [PMID: 34519095 DOI: 10.1002/prot.26235] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/16/2021] [Accepted: 09/03/2021] [Indexed: 01/08/2023]
106
Shen T, Wu J, Lan H, Zheng L, Pei J, Wang S, Liu W, Huang J. When homologous sequences meet structural decoys: Accurate contact prediction by tFold in CASP14-(tFold for CASP14 contact prediction). Proteins 2021;89:1901-1910. [PMID: 34473376 DOI: 10.1002/prot.26232] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/29/2022]
107
Yan Y, Huang SY. Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes. Brief Bioinform 2021;22:bbab038. [PMID: 33693482 PMCID: PMC8425427 DOI: 10.1093/bib/bbab038] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/09/2021] [Indexed: 12/14/2022]  Open
108
Wu H, Ling H, Gao L, Fu Q, Lu W, Ding Y, Jiang M, Li H. Empirical Potential Energy Function Toward ab Initio Folding G Protein-Coupled Receptors. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:1752-1762. [PMID: 32750885 DOI: 10.1109/tcbb.2020.3008014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
109
Mortuza SM, Zheng W, Zhang C, Li Y, Pearce R, Zhang Y. Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nat Commun 2021;12:5011. [PMID: 34408149 PMCID: PMC8373938 DOI: 10.1038/s41467-021-25316-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 08/04/2021] [Indexed: 11/28/2022]  Open
110
Holcomb D, Hamasaki-Katagiri N, Laurie K, Katneni U, Kames J, Alexaki A, Bar H, Kimchi-Sarfaty C. New approaches to predict the effect of co-occurring variants on protein characteristics. Am J Hum Genet 2021;108:1502-1511. [PMID: 34256028 DOI: 10.1016/j.ajhg.2021.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022]  Open
111
Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A, Romera-Paredes B, Nikolov S, Jain R, Adler J, Back T, Petersen S, Reiman D, Clancy E, Zielinski M, Steinegger M, Pacholska M, Berghammer T, Bodenstein S, Silver D, Vinyals O, Senior AW, Kavukcuoglu K, Kohli P, Hassabis D. Highly accurate protein structure prediction with AlphaFold. Nature 2021;596:583-589. [PMID: 34265844 PMCID: PMC8371605 DOI: 10.1038/s41586-021-03819-2] [Citation(s) in RCA: 21380] [Impact Index Per Article: 5345.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
112
Zheng W, Zhang C, Li Y, Pearce R, Bell EW, Zhang Y. Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. CELL REPORTS METHODS 2021;1:100014. [PMID: 34355210 PMCID: PMC8336924 DOI: 10.1016/j.crmeth.2021.100014] [Citation(s) in RCA: 299] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022]
113
Multamäki E, Nanekar R, Morozov D, Lievonen T, Golonka D, Wahlgren WY, Stucki-Buchli B, Rossi J, Hytönen VP, Westenhoff S, Ihalainen JA, Möglich A, Takala H. Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling. Nat Commun 2021;12:4394. [PMID: 34285211 PMCID: PMC8292422 DOI: 10.1038/s41467-021-24676-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/30/2021] [Indexed: 02/06/2023]  Open
114
Mulnaes D, Golchin P, Koenig F, Gohlke H. TopDomain: Exhaustive Protein Domain Boundary Metaprediction Combining Multisource Information and Deep Learning. J Chem Theory Comput 2021;17:4599-4613. [PMID: 34161735 DOI: 10.1021/acs.jctc.1c00129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
115
Neuwald AF, Lanczycki CJ, Hodges TK, Marchler-Bauer A. Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021;2020:5850901. [PMID: 32500917 PMCID: PMC7297217 DOI: 10.1093/database/baaa042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 04/01/2020] [Accepted: 05/06/2020] [Indexed: 11/12/2022]
116
Pearce R, Zhang Y. Toward the solution of the protein structure prediction problem. J Biol Chem 2021;297:100870. [PMID: 34119522 PMCID: PMC8254035 DOI: 10.1016/j.jbc.2021.100870] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 11/20/2022]  Open
117
Reza MS, Zhang H, Hossain MT, Jin L, Feng S, Wei Y. COMTOP: Protein Residue-Residue Contact Prediction through Mixed Integer Linear Optimization. MEMBRANES 2021;11:membranes11070503. [PMID: 34209399 PMCID: PMC8305966 DOI: 10.3390/membranes11070503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022]
118
Davies JS, Currie MJ, Wright JD, Newton-Vesty MC, North RA, Mace PD, Allison JR, Dobson RCJ. Selective Nutrient Transport in Bacteria: Multicomponent Transporter Systems Reign Supreme. Front Mol Biosci 2021;8:699222. [PMID: 34268334 PMCID: PMC8276074 DOI: 10.3389/fmolb.2021.699222] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/02/2021] [Indexed: 11/24/2022]  Open
119
Corcoran D, Maltbie N, Sudalairaj S, Baker FN, Hirschfeld J, Porollo A. CoeViz 2: Protein Graphs Derived From Amino Acid Covariance. FRONTIERS IN BIOINFORMATICS 2021;1. [PMID: 35694032 PMCID: PMC9187035 DOI: 10.3389/fbinf.2021.653681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
120
Mukherjee I, Chakrabarti S. Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes. Comput Struct Biotechnol J 2021;19:3779-3795. [PMID: 34285778 PMCID: PMC8271121 DOI: 10.1016/j.csbj.2021.06.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 11/16/2022]  Open
121
DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning. Sci Rep 2021;11:12295. [PMID: 34112907 PMCID: PMC8192766 DOI: 10.1038/s41598-021-91827-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022]  Open
122
Li Y, Golding GB, Ilie L. DELPHI: accurate deep ensemble model for protein interaction sites prediction. Bioinformatics 2021;37:896-904. [PMID: 32840562 DOI: 10.1093/bioinformatics/btaa750] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022]  Open
123
Bottino GF, Ferrari AJR, Gozzo FC, Martínez L. Structural discrimination analysis for constraint selection in protein modeling. Bioinformatics 2021;37:3766-3773. [PMID: 34086840 DOI: 10.1093/bioinformatics/btab425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/07/2021] [Accepted: 06/03/2021] [Indexed: 11/12/2022]  Open
124
Suh D, Lee JW, Choi S, Lee Y. Recent Applications of Deep Learning Methods on Evolution- and Contact-Based Protein Structure Prediction. Int J Mol Sci 2021;22:6032. [PMID: 34199677 PMCID: PMC8199773 DOI: 10.3390/ijms22116032] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/29/2021] [Accepted: 05/29/2021] [Indexed: 01/23/2023]  Open
125
Jernigan R, Jia K, Ren Z, Zhou W. Large-scale multiple inference of collective dependence with applications to protein function. Ann Appl Stat 2021;15:902-924. [DOI: 10.1214/20-aoas1431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
126
Pearce R, Zhang Y. Deep learning techniques have significantly impacted protein structure prediction and protein design. Curr Opin Struct Biol 2021;68:194-207. [PMID: 33639355 PMCID: PMC8222070 DOI: 10.1016/j.sbi.2021.01.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/09/2021] [Accepted: 01/18/2021] [Indexed: 12/26/2022]
127
Mulligan VK. Current directions in combining simulation-based macromolecular modeling approaches with deep learning. Expert Opin Drug Discov 2021;16:1025-1044. [PMID: 33993816 DOI: 10.1080/17460441.2021.1918097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
128
On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins. PLoS Comput Biol 2021;17:e1008957. [PMID: 34029316 PMCID: PMC8177639 DOI: 10.1371/journal.pcbi.1008957] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 06/04/2021] [Accepted: 04/09/2021] [Indexed: 12/04/2022]  Open
129
Zhang H, Bei Z, Xi W, Hao M, Ju Z, Saravanan KM, Zhang H, Guo N, Wei Y. Evaluation of residue-residue contact prediction methods: From retrospective to prospective. PLoS Comput Biol 2021;17:e1009027. [PMID: 34029314 PMCID: PMC8177648 DOI: 10.1371/journal.pcbi.1009027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/04/2021] [Accepted: 04/28/2021] [Indexed: 12/31/2022]  Open
130
Zhang T, Singh J, Litfin T, Zhan J, Paliwal K, Zhou Y. RNAcmap: A Fully Automatic Pipeline for Predicting Contact Maps of RNAs by Evolutionary Coupling Analysis. Bioinformatics 2021;37:3494-3500. [PMID: 34021744 DOI: 10.1093/bioinformatics/btab391] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/27/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022]  Open
131
AlphaFold and the amyloid landscape. J Mol Biol 2021;433:167059. [PMID: 34023402 DOI: 10.1016/j.jmb.2021.167059] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023]
132
Sequeiros-Borja CE, Surpeta B, Brezovsky J. Recent advances in user-friendly computational tools to engineer protein function. Brief Bioinform 2021;22:bbaa150. [PMID: 32743637 PMCID: PMC8138880 DOI: 10.1093/bib/bbaa150] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/03/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022]  Open
133
Schmidt M, Hamacher K. Identification of biophysical interaction patterns in direct coupling analysis. Phys Rev E 2021;103:042418. [PMID: 34005861 DOI: 10.1103/physreve.103.042418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 03/27/2021] [Indexed: 11/07/2022]
134
Machine learning in protein structure prediction. Curr Opin Chem Biol 2021;65:1-8. [PMID: 34015749 DOI: 10.1016/j.cbpa.2021.04.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/10/2021] [Indexed: 12/31/2022]
135
Neuwald AF, Kolaczkowski BD, Altschul SF. eCOMPASS: evaluative comparison of multiple protein alignments by statistical score. Bioinformatics 2021;37:3456-3463. [PMID: 33983436 PMCID: PMC8545322 DOI: 10.1093/bioinformatics/btab374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/31/2021] [Accepted: 05/12/2021] [Indexed: 11/21/2022]  Open
136
Ju F, Zhu J, Shao B, Kong L, Liu TY, Zheng WM, Bu D. CopulaNet: Learning residue co-evolution directly from multiple sequence alignment for protein structure prediction. Nat Commun 2021;12:2535. [PMID: 33953201 PMCID: PMC8100175 DOI: 10.1038/s41467-021-22869-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/28/2021] [Indexed: 11/29/2022]  Open
137
Fleishman SJ, Horovitz A. Extending the New Generation of Structure Predictors to Account for Dynamics and Allostery. J Mol Biol 2021;433:167007. [PMID: 33901536 DOI: 10.1016/j.jmb.2021.167007] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
138
Rives A, Meier J, Sercu T, Goyal S, Lin Z, Liu J, Guo D, Ott M, Zitnick CL, Ma J, Fergus R. Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. Proc Natl Acad Sci U S A 2021;118:e2016239118. [PMID: 33876751 PMCID: PMC8053943 DOI: 10.1073/pnas.2016239118] [Citation(s) in RCA: 1079] [Impact Index Per Article: 269.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
139
Jain A, Terashi G, Kagaya Y, Maddhuri Venkata Subramaniya SR, Christoffer C, Kihara D. Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction. Sci Rep 2021;11:7574. [PMID: 33828153 PMCID: PMC8027171 DOI: 10.1038/s41598-021-87204-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022]  Open
140
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLoS Comput Biol 2021;17:e1008865. [PMID: 33770072 PMCID: PMC8026059 DOI: 10.1371/journal.pcbi.1008865] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 04/07/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022]  Open
141
Rivas E. Evolutionary conservation of RNA sequence and structure. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021;12:e1649. [PMID: 33754485 PMCID: PMC8250186 DOI: 10.1002/wrna.1649] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/22/2022]
142
Chen C, Wu T, Guo Z, Cheng J. Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction. Proteins 2021;89:697-707. [PMID: 33538038 PMCID: PMC8089057 DOI: 10.1002/prot.26052] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/22/2020] [Accepted: 01/31/2021] [Indexed: 12/17/2022]
143
Akand EH, Murray JM. NGlyAlign: an automated library building tool to align highly divergent HIV envelope sequences. BMC Bioinformatics 2021;22:54. [PMID: 33557755 PMCID: PMC7869453 DOI: 10.1186/s12859-020-03901-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/23/2020] [Indexed: 08/29/2023]  Open
144
Liu Y, Zhu YH, Song X, Song J, Yu DJ. Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation. Brief Bioinform 2021;22:6127449. [PMID: 33537753 DOI: 10.1093/bib/bbab001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/20/2020] [Accepted: 01/01/2021] [Indexed: 01/26/2023]  Open
145
Hawkins-Hooker A, Depardieu F, Baur S, Couairon G, Chen A, Bikard D. Generating functional protein variants with variational autoencoders. PLoS Comput Biol 2021;17:e1008736. [PMID: 33635868 PMCID: PMC7946179 DOI: 10.1371/journal.pcbi.1008736] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/10/2021] [Accepted: 01/25/2021] [Indexed: 11/20/2022]  Open
146
Wu T, Guo Z, Hou J, Cheng J. DeepDist: real-value inter-residue distance prediction with deep residual convolutional network. BMC Bioinformatics 2021;22:30. [PMID: 33494711 PMCID: PMC7831258 DOI: 10.1186/s12859-021-03960-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/06/2021] [Indexed: 11/10/2022]  Open
147
Neverov AD, Popova AV, Fedonin GG, Cheremukhin EA, Klink GV, Bazykin GA. Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins. PLoS Genet 2021;17:e1008711. [PMID: 33493156 PMCID: PMC7861529 DOI: 10.1371/journal.pgen.1008711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 02/04/2021] [Accepted: 12/07/2020] [Indexed: 11/19/2022]  Open
148
Jia K, Jernigan RL. New amino acid substitution matrix brings sequence alignments into agreement with structure matches. Proteins 2021;89:671-682. [PMID: 33469973 PMCID: PMC8641535 DOI: 10.1002/prot.26050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 12/27/2022]
149
Schmitz S, Ertelt M, Merkl R, Meiler J. Rosetta design with co-evolutionary information retains protein function. PLoS Comput Biol 2021;17:e1008568. [PMID: 33465067 PMCID: PMC7815116 DOI: 10.1371/journal.pcbi.1008568] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/28/2020] [Indexed: 12/14/2022]  Open
150
Slater O, Miller B, Kontoyianni M. Decoding Protein-protein Interactions: An Overview. Curr Top Med Chem 2021;20:855-882. [PMID: 32101126 DOI: 10.2174/1568026620666200226105312] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022]
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