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For: Wang Z, Xu J. Predicting protein contact map using evolutionary and physical constraints by integer programming. Bioinformatics 2013;29:i266-73. [PMID: 23812992 PMCID: PMC3694661 DOI: 10.1093/bioinformatics/btt211] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
51
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]
52
Sharma A, Hussain A, Mun BG, Imran QM, Falak N, Lee SU, Kim JY, Hong JK, Loake GJ, Ali A, Yun BW. Comprehensive analysis of plant rapid alkalization factor (RALF) genes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016;106:82-90. [PMID: 27155375 DOI: 10.1016/j.plaphy.2016.03.037] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/14/2016] [Accepted: 03/27/2016] [Indexed: 05/04/2023]
53
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]
54
Taylor WR. An algorithm to parse segment packing in predicted protein contact maps. Algorithms Mol Biol 2016;11:17. [PMID: 27330543 PMCID: PMC4912788 DOI: 10.1186/s13015-016-0080-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/24/2016] [Indexed: 11/30/2022]  Open
55
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
56
Yang J, Jin QY, Zhang B, Shen HB. R2C: improving ab initio residue contact map prediction using dynamic fusion strategy and Gaussian noise filter. ACTA ACUST UNITED AC 2016;32:2435-43. [PMID: 27153618 DOI: 10.1093/bioinformatics/btw181] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/03/2016] [Indexed: 11/12/2022]
57
Zhang H, Gao Y, Deng M, Wang C, Zhu J, Li SC, Zheng WM, Bu D. Improving residue-residue contact prediction via low-rank and sparse decomposition of residue correlation matrix. Biochem Biophys Res Commun 2016;472:217-22. [PMID: 26920058 DOI: 10.1016/j.bbrc.2016.01.188] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 01/30/2016] [Indexed: 10/22/2022]
58
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]
59
De novo protein conformational sampling using a probabilistic graphical model. Sci Rep 2015;5:16332. [PMID: 26541939 PMCID: PMC4635387 DOI: 10.1038/srep16332] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 10/13/2015] [Indexed: 11/08/2022]  Open
60
Márquez-Chamorro AE, Asencio-Cortés G, Santiesteban-Toca CE, Aguilar-Ruiz JS. Soft computing methods for the prediction of protein tertiary structures: A survey. Appl Soft Comput 2015. [DOI: 10.1016/j.asoc.2015.06.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
61
Raval A, Piana S, Eastwood MP, Shaw DE. Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations. Protein Sci 2015;25:19-29. [PMID: 26266489 PMCID: PMC4815320 DOI: 10.1002/pro.2770] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 08/07/2015] [Accepted: 08/11/2015] [Indexed: 12/15/2022]
62
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
63
Adhikari B, Bhattacharya D, Cao R, Cheng J. CONFOLD: Residue-residue contact-guided ab initio protein folding. Proteins 2015;83:1436-49. [PMID: 25974172 PMCID: PMC4509844 DOI: 10.1002/prot.24829] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/11/2015] [Accepted: 05/02/2015] [Indexed: 12/20/2022]
64
Kozma D, Tusnády GE. TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool. BMC Bioinformatics 2015;16:201. [PMID: 26123059 PMCID: PMC4486421 DOI: 10.1186/s12859-015-0638-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/06/2015] [Indexed: 12/26/2022]  Open
65
Andreani J, Söding J. bbcontacts: prediction of β-strand pairing from direct coupling patterns. ACTA ACUST UNITED AC 2015;31:1729-37. [PMID: 25618863 DOI: 10.1093/bioinformatics/btv041] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/17/2015] [Indexed: 01/08/2023]
66
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
67
Ma C, Zhang HH, Wang X. Machine learning for Big Data analytics in plants. TRENDS IN PLANT SCIENCE 2014;19:798-808. [PMID: 25223304 DOI: 10.1016/j.tplants.2014.08.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/30/2014] [Accepted: 08/20/2014] [Indexed: 05/19/2023]
68
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
69
Schneider M, Brock O. Combining physicochemical and evolutionary information for protein contact prediction. PLoS One 2014;9:e108438. [PMID: 25338092 PMCID: PMC4206277 DOI: 10.1371/journal.pone.0108438] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/28/2014] [Indexed: 11/18/2022]  Open
70
Chen Y, Shang Y, Xu D. Multi-Dimensional Scaling and MODELLER-Based Evolutionary Algorithms for Protein Model Refinement. PROCEEDINGS OF THE ... CONGRESS ON EVOLUTIONARY COMPUTATION. CONGRESS ON EVOLUTIONARY COMPUTATION 2014;2014:1038-1045. [PMID: 25844403 PMCID: PMC4380876 DOI: 10.1109/cec.2014.6900443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
71
Ma J, Wang S, Wang Z, Xu J. MRFalign: protein homology detection through alignment of Markov random fields. PLoS Comput Biol 2014;10:e1003500. [PMID: 24675572 PMCID: PMC3967925 DOI: 10.1371/journal.pcbi.1003500] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 01/08/2014] [Indexed: 11/24/2022]  Open
72
Kaján L, Hopf TA, Kalaš M, Marks DS, Rost B. FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics 2014;15:85. [PMID: 24669753 PMCID: PMC3987048 DOI: 10.1186/1471-2105-15-85] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/18/2014] [Indexed: 11/10/2022]  Open
73
Ma J, Wang S. Algorithms, Applications, and Challenges of Protein Structure Alignment. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014;94:121-75. [DOI: 10.1016/b978-0-12-800168-4.00005-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
74
Zhang H, Kurgan L. Sequence-based Gaussian network model for protein dynamics. ACTA ACUST UNITED AC 2013;30:497-505. [PMID: 24336646 PMCID: PMC3928524 DOI: 10.1093/bioinformatics/btt716] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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