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For: Kosciolek T, Jones DT. Accurate contact predictions using covariation techniques and machine learning. Proteins 2015. [PMID: 26205532 PMCID: PMC5042084 DOI: 10.1002/prot.24863] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Number Cited by Other Article(s)
1
Alcalá-Santiago Á, García-Villanova B, Ruíz-López MD, Gil Á, Rodriguez-Barranco M, Sánchez MJ, Molina-Montes E. Dietary and lifestyle determinants of vitamin D status in the UK Biobank Cohort study for predictive modeling. J Nutr Biochem 2025;142:109919. [PMID: 40221106 DOI: 10.1016/j.jnutbio.2025.109919] [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: 05/27/2024] [Revised: 10/31/2024] [Accepted: 04/08/2025] [Indexed: 04/14/2025]
2
Bryant P, Kelkar A, Guljas A, Clementi C, Noé F. Structure prediction of protein-ligand complexes from sequence information with Umol. Nat Commun 2024;15:4536. [PMID: 38806453 PMCID: PMC11133481 DOI: 10.1038/s41467-024-48837-6] [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: 03/19/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024]  Open
3
Oda T. Improving protein structure prediction with extended sequence similarity searches and deep-learning-based refinement in CASP15. Proteins 2023;91:1712-1723. [PMID: 37485822 DOI: 10.1002/prot.26551] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/25/2023]
4
Elnaggar A, Heinzinger M, Dallago C, Rehawi G, Wang Y, Jones L, Gibbs T, Feher T, Angerer C, Steinegger M, Bhowmik D, Rost B. ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2022;44:7112-7127. [PMID: 34232869 DOI: 10.1109/tpami.2021.3095381] [Citation(s) in RCA: 694] [Impact Index Per Article: 231.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
5
Elnaggar A, Heinzinger M, Dallago C, Rehawi G, Wang Y, Jones L, Gibbs T, Feher T, Angerer C, Steinegger M, Bhowmik D, Rost B. ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2022. [PMID: 34232869 DOI: 10.1101/2020.07.12.199554] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
6
Improved prediction of protein-protein interactions using AlphaFold2. Nat Commun 2022;13:1265. [PMID: 35273146 PMCID: PMC8913741 DOI: 10.1038/s41467-022-28865-w] [Citation(s) in RCA: 492] [Impact Index Per Article: 164.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/11/2022] [Indexed: 01/02/2023]  Open
7
Zhang H, Shan G, Yang B. Optimized Elastic Network Models With Direct Characterization of Inter-Residue Cooperativity for Protein Dynamics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:1064-1074. [PMID: 32915744 DOI: 10.1109/tcbb.2020.3023147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
8
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]
9
Ruiz-Serra V, Pontes C, Milanetti E, Kryshtafovych A, Lepore R, Valencia A. Assessing the accuracy of contact and distance predictions in CASP14. Proteins 2021;89:1888-1900. [PMID: 34595772 DOI: 10.1002/prot.26248] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/06/2021] [Accepted: 09/21/2021] [Indexed: 12/26/2022]
10
Adiyaman R, McGuffin LJ. ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts. Nucleic Acids Res 2021;49:W589-W596. [PMID: 34009387 PMCID: PMC8218204 DOI: 10.1093/nar/gkab300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/23/2021] [Accepted: 04/16/2021] [Indexed: 12/16/2022]  Open
11
Adhikari B. A fully open-source framework for deep learning protein real-valued distances. Sci Rep 2020;10:13374. [PMID: 32770096 PMCID: PMC7414848 DOI: 10.1038/s41598-020-70181-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/23/2020] [Indexed: 11/12/2022]  Open
12
Hong SH, Joo K, Lee J. ConDo: protein domain boundary prediction using coevolutionary information. Bioinformatics 2020;35:2411-2417. [PMID: 30500873 DOI: 10.1093/bioinformatics/bty973] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 11/15/2018] [Accepted: 11/29/2018] [Indexed: 11/13/2022]  Open
13
Wei M, Wang Z, Wang X, Peng J, Song Y. Prediction of TBM penetration rate based on Monte Carlo-BP neural network. Neural Comput Appl 2020. [DOI: 10.1007/s00521-020-04993-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
14
Baryakova TH, Ritter SC, Tresnak DT, Hackel BJ. Computationally Aided Discovery of LysEFm5 Variants with Improved Catalytic Activity and Stability. Appl Environ Microbiol 2020;86:e02051-19. [PMID: 31811034 PMCID: PMC6997734 DOI: 10.1128/aem.02051-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/30/2019] [Indexed: 01/21/2023]  Open
15
Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure 2019;27:1745-1759. [PMID: 31780431 DOI: 10.1016/j.str.2019.11.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/31/2019] [Accepted: 11/06/2019] [Indexed: 12/23/2022]
16
Dos Santos RN, Bottino GF, Gozzo FC, Morcos F, Martínez L. Structural complementarity of distance constraints obtained from chemical cross-linking and amino acid coevolution. Proteins 2019;88:625-632. [PMID: 31693206 DOI: 10.1002/prot.25843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/07/2019] [Accepted: 11/03/2019] [Indexed: 12/11/2022]
17
Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XIII. Proteins 2019;87:1011-1020. [PMID: 31589781 DOI: 10.1002/prot.25823] [Citation(s) in RCA: 313] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/24/2022]
18
Kandathil SM, Greener JG, Jones DT. Prediction of interresidue contacts with DeepMetaPSICOV in CASP13. Proteins 2019;87:1092-1099. [PMID: 31298436 PMCID: PMC6899903 DOI: 10.1002/prot.25779] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/25/2019] [Accepted: 07/06/2019] [Indexed: 12/28/2022]
19
Jing X, Dong Q, Lu R, Dong Q. Protein Inter-Residue Contacts Prediction: Methods, Performances and Applications. Curr Bioinform 2019. [DOI: 10.2174/1574893613666181109130430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
20
Adhikari B, Hou J, Cheng J. DNCON2: improved protein contact prediction using two-level deep convolutional neural networks. Bioinformatics 2019;34:1466-1472. [PMID: 29228185 PMCID: PMC5925776 DOI: 10.1093/bioinformatics/btx781] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/07/2017] [Indexed: 12/14/2022]  Open
21
Koehl P, Orland H, Delarue M. Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments. Molecules 2018;24:E104. [PMID: 30597916 PMCID: PMC6337344 DOI: 10.3390/molecules24010104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 11/17/2022]  Open
22
Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings. Int J Mol Sci 2018;19:ijms19113315. [PMID: 30366362 PMCID: PMC6274761 DOI: 10.3390/ijms19113315] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 12/22/2022]  Open
23
Kc DB. Recent advances in sequence-based protein structure prediction. Brief Bioinform 2018;18:1021-1032. [PMID: 27562963 DOI: 10.1093/bib/bbw070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Indexed: 11/13/2022]  Open
24
Li B, Fooksa M, Heinze S, Meiler J. Finding the needle in the haystack: towards solving the protein-folding problem computationally. Crit Rev Biochem Mol Biol 2018;53:1-28. [PMID: 28976219 PMCID: PMC6790072 DOI: 10.1080/10409238.2017.1380596] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/22/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022]
25
Adhikari B, Cheng J. CONFOLD2: improved contact-driven ab initio protein structure modeling. BMC Bioinformatics 2018;19:22. [PMID: 29370750 PMCID: PMC5784681 DOI: 10.1186/s12859-018-2032-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 01/17/2018] [Indexed: 12/31/2022]  Open
26
Prediction of Structures and Interactions from Genome Information. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018;1105:123-152. [DOI: 10.1007/978-981-13-2200-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
27
Adhikari B, Hou J, Cheng J. Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning. Proteins 2017;86 Suppl 1:84-96. [PMID: 29047157 DOI: 10.1002/prot.25405] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/08/2017] [Accepted: 10/16/2017] [Indexed: 12/14/2022]
28
Buchan DWA, Jones DT. Improved protein contact predictions with the MetaPSICOV2 server in CASP12. Proteins 2017;86 Suppl 1:78-83. [PMID: 28901583 PMCID: PMC5836854 DOI: 10.1002/prot.25379] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/18/2017] [Accepted: 09/10/2017] [Indexed: 12/26/2022]
29
Jing X, Dong Q, Lu R. RRCRank: a fusion method using rank strategy for residue-residue contact prediction. BMC Bioinformatics 2017;18:390. [PMID: 28865433 PMCID: PMC5581475 DOI: 10.1186/s12859-017-1811-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/28/2017] [Indexed: 11/10/2022]  Open
30
Adhikari B, Cheng J. Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts. BMC Bioinformatics 2017;18:380. [PMID: 28851269 PMCID: PMC5576353 DOI: 10.1186/s12859-017-1807-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/22/2017] [Indexed: 11/12/2022]  Open
31
Lam SD, Das S, Sillitoe I, Orengo C. An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. Acta Crystallogr D Struct Biol 2017;73:628-640. [PMID: 28777078 PMCID: PMC5571743 DOI: 10.1107/s2059798317008920] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 06/14/2017] [Indexed: 12/02/2022]  Open
32
Kosciolek T, Buchan DWA, Jones DT. Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment-Based Protein Structure Predictions. Sci Rep 2017;7:6999. [PMID: 28765603 PMCID: PMC5539115 DOI: 10.1038/s41598-017-07156-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/23/2017] [Indexed: 11/08/2022]  Open
33
Xiong D, Zeng J, Gong H. A deep learning framework for improving long-range residue–residue contact prediction using a hierarchical strategy. Bioinformatics 2017;33:2675-2683. [DOI: 10.1093/bioinformatics/btx296] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 05/02/2017] [Indexed: 12/31/2022]  Open
34
Simkovic F, Ovchinnikov S, Baker D, Rigden DJ. Applications of contact predictions to structural biology. IUCRJ 2017;4:291-300. [PMID: 28512576 PMCID: PMC5414403 DOI: 10.1107/s2052252517005115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
35
Monastyrskyy B, D'Andrea D, Fidelis K, Tramontano A, Kryshtafovych A. New encouraging developments in contact prediction: Assessment of the CASP11 results. Proteins 2016;84 Suppl 1:131-44. [PMID: 26474083 PMCID: PMC4834069 DOI: 10.1002/prot.24943] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/15/2015] [Accepted: 10/11/2015] [Indexed: 12/27/2022]
36
Li Q, Dahl DB, Vannucci M, Joo H, Tsai JW. KScons: a Bayesian approach for protein residue contact prediction using the knob-socket model of protein tertiary structure. Bioinformatics 2016;32:3774-3781. [PMID: 27559156 DOI: 10.1093/bioinformatics/btw553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/15/2016] [Accepted: 08/18/2016] [Indexed: 11/13/2022]  Open
37
Simkovic F, Thomas JMH, Keegan RM, Winn MD, Mayans O, Rigden DJ. Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds. IUCRJ 2016;3:259-70. [PMID: 27437113 PMCID: PMC4937781 DOI: 10.1107/s2052252516008113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/18/2016] [Indexed: 05/05/2023]
38
Bhattacharya D, Cao R, Cheng J. UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling. Bioinformatics 2016;32:2791-9. [PMID: 27259540 PMCID: PMC5018369 DOI: 10.1093/bioinformatics/btw316] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/15/2016] [Indexed: 12/20/2022]  Open
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