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For: Skwark MJ, Abdel-Rehim A, Elofsson A. PconsC: combination of direct information methods and alignments improves contact prediction. ACTA ACUST UNITED AC 2013;29:1815-6. [PMID: 23658418 DOI: 10.1093/bioinformatics/btt259] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [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)
1
Aldossari RM, Ali A, Rehman MU, Rashid S, Ahmad SB. Computational Approaches for Identification of Potential Plant Bioactives as Novel G6PD Inhibitors Using Advanced Tools and Databases. Molecules 2023;28:molecules28073018. [PMID: 37049781 PMCID: PMC10096328 DOI: 10.3390/molecules28073018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/26/2023] [Accepted: 03/06/2023] [Indexed: 03/31/2023]  Open
2
Zhang H, Huang Y, Bei Z, Ju Z, Meng J, Hao M, Zhang J, Zhang H, Xi W. Inter-Residue Distance Prediction From Duet Deep Learning Models. Front Genet 2022;13:887491. [PMID: 35651930 PMCID: PMC9148999 DOI: 10.3389/fgene.2022.887491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/30/2022] [Indexed: 12/04/2022]  Open
3
Mehrabiani KM, Cheng RR, Onuchic JN. Expanding Direct Coupling Analysis to Identify Heterodimeric Interfaces from Limited Protein Sequence Data. J Phys Chem B 2021;125:11408-11417. [PMID: 34618469 DOI: 10.1021/acs.jpcb.1c07145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
4
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]
5
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
6
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
7
Roche R, Bhattacharya S, Bhattacharya D. Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins. PLoS Comput Biol 2021;17:e1008753. [PMID: 33621244 PMCID: PMC7935296 DOI: 10.1371/journal.pcbi.1008753] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 03/05/2021] [Accepted: 01/31/2021] [Indexed: 11/18/2022]  Open
8
Seffernick JT, Lindert S. Hybrid methods for combined experimental and computational determination of protein structure. J Chem Phys 2020;153:240901. [PMID: 33380110 PMCID: PMC7773420 DOI: 10.1063/5.0026025] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/10/2020] [Indexed: 02/04/2023]  Open
9
Zhang GJ, Wang XQ, Ma LF, Wang LJ, Hu J, Zhou XG. Two-Stage Distance Feature-based Optimization Algorithm for De novo Protein Structure Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:2119-2130. [PMID: 31107659 DOI: 10.1109/tcbb.2019.2917452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
10
Liu J, Zhou XG, Zhang Y, Zhang GJ. CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. Bioinformatics 2020;36:2443-2450. [PMID: 31860059 DOI: 10.1093/bioinformatics/btz943] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 12/27/2022]  Open
11
Baldessari F, Capelli R, Carloni P, Giorgetti A. Coevolutionary data-based interaction networks approach highlighting key residues across protein families: The case of the G-protein coupled receptors. Comput Struct Biotechnol J 2020;18:1153-1159. [PMID: 32489528 PMCID: PMC7260681 DOI: 10.1016/j.csbj.2020.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 12/26/2022]  Open
12
Zhang GJ, Ma LF, Wang XQ, Zhou XG. Secondary Structure and Contact Guided Differential Evolution for Protein Structure Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:1068-1081. [PMID: 30295627 DOI: 10.1109/tcbb.2018.2873691] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
13
Badaczewska-Dawid AE, Kolinski A, Kmiecik S. Computational reconstruction of atomistic protein structures from coarse-grained models. Comput Struct Biotechnol J 2019;18:162-176. [PMID: 31969975 PMCID: PMC6961067 DOI: 10.1016/j.csbj.2019.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 01/02/2023]  Open
14
Wozniak PP, Pelc J, Skrzypecki M, Vriend G, Kotulska M. Bio-knowledge-based filters improve residue-residue contact prediction accuracy. Bioinformatics 2019;34:3675-3683. [PMID: 29850768 DOI: 10.1093/bioinformatics/bty416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 05/19/2018] [Indexed: 11/13/2022]  Open
15
Vajdi A, Zarringhalam K, Haspel N. Patch-DCA: improved protein interface prediction by utilizing structural information and clustering DCA scores. Bioinformatics 2019;36:1460-1467. [DOI: 10.1093/bioinformatics/btz791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/30/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023]  Open
16
Accurate Classification of Biological and non-Biological Interfaces in Protein Crystal Structures using Subtle Covariation Signals. Sci Rep 2019;9:12603. [PMID: 31471543 PMCID: PMC6717244 DOI: 10.1038/s41598-019-48913-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 08/14/2019] [Indexed: 11/08/2022]  Open
17
The role of coevolutionary signatures in protein interaction dynamics, complex inference, molecular recognition, and mutational landscapes. Curr Opin Struct Biol 2019;56:179-186. [PMID: 31029927 DOI: 10.1016/j.sbi.2019.03.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 11/22/2022]
18
Haldane A, Levy RM. Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation. Phys Rev E 2019;99:032405. [PMID: 30999494 PMCID: PMC6508952 DOI: 10.1103/physreve.99.032405] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Indexed: 02/02/2023]
19
Ji S, Oruç T, Mead L, Rehman MF, Thomas CM, Butterworth S, Winn PJ. DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure. PLoS One 2019;14:e0205214. [PMID: 30620738 PMCID: PMC6324825 DOI: 10.1371/journal.pone.0205214] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/13/2018] [Indexed: 11/28/2022]  Open
20
Coevolutionary Signals and Structure-Based Models for the Prediction of Protein Native Conformations. Methods Mol Biol 2019;1851:83-103. [PMID: 30298393 DOI: 10.1007/978-1-4939-8736-8_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
21
de Oliveira SHP, Shi J, Deane CM. Comparing co-evolution methods and their application to template-free protein structure prediction. Bioinformatics 2018;33:373-381. [PMID: 28171606 PMCID: PMC5860252 DOI: 10.1093/bioinformatics/btw618] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 09/19/2016] [Accepted: 09/22/2016] [Indexed: 02/01/2023]  Open
22
dos Santos RN, Khan S, Morcos F. Characterization of C-ring component assembly in flagellar motors from amino acid coevolution. ROYAL SOCIETY OPEN SCIENCE 2018;5:171854. [PMID: 29892378 PMCID: PMC5990795 DOI: 10.1098/rsos.171854] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
23
Gil N, Fiser A. Identifying functionally informative evolutionary sequence profiles. Bioinformatics 2018;34:1278-1286. [PMID: 29211823 PMCID: PMC5905606 DOI: 10.1093/bioinformatics/btx779] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/29/2017] [Indexed: 01/06/2023]  Open
24
Michel M, Menéndez Hurtado D, Uziela K, Elofsson A. Large-scale structure prediction by improved contact predictions and model quality assessment. Bioinformatics 2018;33:i23-i29. [PMID: 28881974 PMCID: PMC5870574 DOI: 10.1093/bioinformatics/btx239] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
25
Nicoludis JM, Gaudet R. Applications of sequence coevolution in membrane protein biochemistry. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018;1860:895-908. [PMID: 28993150 PMCID: PMC5807202 DOI: 10.1016/j.bbamem.2017.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/28/2017] [Accepted: 10/02/2017] [Indexed: 12/22/2022]
26
Schaarschmidt J, Monastyrskyy B, Kryshtafovych A, Bonvin AM. Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age. Proteins 2018;86 Suppl 1:51-66. [PMID: 29071738 PMCID: PMC5820169 DOI: 10.1002/prot.25407] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/06/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022]
27
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]
28
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]
29
Wozniak PP, Konopka BM, Xu J, Vriend G, Kotulska M. Forecasting residue-residue contact prediction accuracy. Bioinformatics 2017;33:3405-3414. [PMID: 29036497 DOI: 10.1093/bioinformatics/btx416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/22/2017] [Indexed: 11/14/2022]  Open
30
de Oliveira S, Deane C. Co-evolution techniques are reshaping the way we do structural bioinformatics. F1000Res 2017;6:1224. [PMID: 28781768 PMCID: PMC5531156 DOI: 10.12688/f1000research.11543.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2017] [Indexed: 11/20/2022]  Open
31
Teixeira PL, Mendenhall JL, Heinze S, Weiner B, Skwark MJ, Meiler J. Membrane protein contact and structure prediction using co-evolution in conjunction with machine learning. PLoS One 2017;12:e0177866. [PMID: 28542325 PMCID: PMC5443516 DOI: 10.1371/journal.pone.0177866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 05/04/2017] [Indexed: 11/18/2022]  Open
32
Garcia-Garcia J, Valls-Comamala V, Guney E, Andreu D, Muñoz FJ, Fernandez-Fuentes N, Oliva B. iFrag: A Protein–Protein Interface Prediction Server Based on Sequence Fragments. J Mol Biol 2017;429:382-389. [DOI: 10.1016/j.jmb.2016.11.034] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/27/2016] [Accepted: 11/30/2016] [Indexed: 01/08/2023]
33
Wozniak PP, Vriend G, Kotulska M. Correlated mutations select misfolded from properly folded proteins. Bioinformatics 2017;33:1497-1504. [PMID: 28203707 DOI: 10.1093/bioinformatics/btx013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/11/2017] [Indexed: 11/14/2022]  Open
34
Rawi R, Mall R, Kunji K, El Anbari M, Aupetit M, Ullah E, Bensmail H. COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator. BMC Bioinformatics 2016;17:533. [PMID: 27978812 PMCID: PMC5159955 DOI: 10.1186/s12859-016-1400-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/01/2016] [Indexed: 11/13/2022]  Open
35
Assessing Predicted Contacts for Building Protein Three-Dimensional Models. Methods Mol Biol 2016. [PMID: 27787823 DOI: 10.1007/978-1-4939-6406-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
36
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]
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
39
Zhang H, Huang Q, Bei Z, Wei Y, Floudas CA. COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming. Proteins 2016;84:332-48. [PMID: 26756402 DOI: 10.1002/prot.24979] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/19/2015] [Accepted: 12/10/2015] [Indexed: 12/28/2022]
40
Braun T, Koehler Leman J, Lange OF. Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction. PLoS Comput Biol 2015;11:e1004661. [PMID: 26713437 PMCID: PMC4694711 DOI: 10.1371/journal.pcbi.1004661] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 11/17/2015] [Indexed: 12/18/2022]  Open
41
Ma J, Wang S, Wang Z, Xu J. Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. Bioinformatics 2015;31:3506-13. [PMID: 26275894 DOI: 10.1093/bioinformatics/btv472] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 08/08/2015] [Indexed: 02/07/2023]  Open
42
Pietal MJ, Bujnicki JM, Kozlowski LP. GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function. Bioinformatics 2015;31:3499-505. [PMID: 26130575 DOI: 10.1093/bioinformatics/btv390] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 06/23/2015] [Indexed: 11/13/2022]  Open
43
Mao W, Kaya C, Dutta A, Horovitz A, Bahar I. Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution. Bioinformatics 2015;31:1929-37. [PMID: 25697822 PMCID: PMC4481699 DOI: 10.1093/bioinformatics/btv103] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 02/02/2015] [Indexed: 01/02/2023]  Open
44
Li G, Theys K, Verheyen J, Pineda-Peña AC, Khouri R, Piampongsant S, Eusébio M, Ramon J, Vandamme AM. A new ensemble coevolution system for detecting HIV-1 protein coevolution. Biol Direct 2015;10:1. [PMID: 25564011 PMCID: PMC4332441 DOI: 10.1186/s13062-014-0031-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/02/2014] [Indexed: 12/31/2022]  Open
45
Nugent T. De novo membrane protein structure prediction. Methods Mol Biol 2015;1215:331-50. [PMID: 25330970 DOI: 10.1007/978-1-4939-1465-4_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Jones DT, Singh T, Kosciolek T, Tetchner S. MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. ACTA ACUST UNITED AC 2014;31:999-1006. [PMID: 25431331 PMCID: PMC4382908 DOI: 10.1093/bioinformatics/btu791] [Citation(s) in RCA: 237] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/22/2014] [Indexed: 12/13/2022]
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Improved contact predictions using the recognition of protein like contact patterns. PLoS Comput Biol 2014;10:e1003889. [PMID: 25375897 PMCID: PMC4222596 DOI: 10.1371/journal.pcbi.1003889] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 09/03/2014] [Indexed: 11/23/2022]  Open
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Wozniak PP, Kotulska M. Characteristics of protein residue-residue contacts and their application in contact prediction. J Mol Model 2014;20:2497. [PMID: 25374390 PMCID: PMC4221654 DOI: 10.1007/s00894-014-2497-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 10/09/2014] [Indexed: 11/28/2022]
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Feinauer C, Skwark MJ, Pagnani A, Aurell E. Improving contact prediction along three dimensions. PLoS Comput Biol 2014;10:e1003847. [PMID: 25299132 PMCID: PMC4191875 DOI: 10.1371/journal.pcbi.1003847] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 08/07/2014] [Indexed: 11/18/2022]  Open
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Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A. PconsFold: improved contact predictions improve protein models. Bioinformatics 2014;30:i482-8. [PMID: 25161237 PMCID: PMC4147911 DOI: 10.1093/bioinformatics/btu458] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]  Open
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