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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)
501
Nemoto W, Saito A, Oikawa H. Recent advances in functional region prediction by using structural and evolutionary information - Remaining problems and future extensions. Comput Struct Biotechnol J 2013;8:e201308007. [PMID: 24688747 PMCID: PMC3962155 DOI: 10.5936/csbj.201308007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/12/2013] [Accepted: 11/13/2013] [Indexed: 11/22/2022]  Open
502
Coevolutionary signals across protein lineages help capture multiple protein conformations. Proc Natl Acad Sci U S A 2013;110:20533-8. [PMID: 24297889 DOI: 10.1073/pnas.1315625110] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
503
Khoury GA, Smadbeck J, Kieslich CA, Floudas CA. Protein folding and de novo protein design for biotechnological applications. Trends Biotechnol 2013;32:99-109. [PMID: 24268901 DOI: 10.1016/j.tibtech.2013.10.008] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/10/2013] [Accepted: 10/18/2013] [Indexed: 11/19/2022]
504
Abergel C. Molecular replacement: tricks and treats. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013;69:2167-73. [PMID: 24189227 PMCID: PMC3817689 DOI: 10.1107/s0907444913015291] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/02/2013] [Indexed: 11/16/2022]
505
Valentin JB, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J, Frellsen J, Mardia KV, Tian P, Hamelryck T. Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method. Proteins 2013;82:288-99. [PMID: 23934827 DOI: 10.1002/prot.24386] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/02/2013] [Accepted: 07/18/2013] [Indexed: 01/10/2023]
506
Eickholt J, Cheng J. A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks. BMC Bioinformatics 2013;14 Suppl 14:S12. [PMID: 24267585 PMCID: PMC3850995 DOI: 10.1186/1471-2105-14-s14-s12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
507
Savojardo C, Fariselli P, Martelli PL, Casadio R. BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming. ACTA ACUST UNITED AC 2013;29:3151-7. [PMID: 24064422 DOI: 10.1093/bioinformatics/btt555] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
508
Nugent T, Jones DT. Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics 2013;14:276. [PMID: 24047460 PMCID: PMC3852961 DOI: 10.1186/1471-2105-14-276] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 09/05/2013] [Indexed: 01/09/2023]  Open
509
Kim DE, Dimaio F, Yu-Ruei Wang R, Song Y, Baker D. One contact for every twelve residues allows robust and accurate topology-level protein structure modeling. Proteins 2013;82 Suppl 2:208-18. [PMID: 23900763 DOI: 10.1002/prot.24374] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/12/2013] [Accepted: 06/21/2013] [Indexed: 12/19/2022]
510
Proton-dependent gating and proton uptake by Wzx support O-antigen-subunit antiport across the bacterial inner membrane. mBio 2013;4:e00678-13. [PMID: 24023388 PMCID: PMC3774195 DOI: 10.1128/mbio.00678-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
511
Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Proc Natl Acad Sci U S A 2013;110:15674-9. [PMID: 24009338 DOI: 10.1073/pnas.1314045110] [Citation(s) in RCA: 485] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
512
Gleichmann T, Diensthuber RP, Möglich A. Charting the signal trajectory in a light-oxygen-voltage photoreceptor by random mutagenesis and covariance analysis. J Biol Chem 2013;288:29345-55. [PMID: 24003219 DOI: 10.1074/jbc.m113.506139] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
513
Monastyrskyy B, D'Andrea D, Fidelis K, Tramontano A, Kryshtafovych A. Evaluation of residue-residue contact prediction in CASP10. Proteins 2013;82 Suppl 2:138-53. [PMID: 23760879 DOI: 10.1002/prot.24340] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 05/14/2013] [Accepted: 05/21/2013] [Indexed: 12/13/2022]
514
From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol 2013;9:e1003176. [PMID: 23990764 PMCID: PMC3749948 DOI: 10.1371/journal.pcbi.1003176] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 06/24/2013] [Indexed: 11/19/2022]  Open
515
Yang J, Jang R, Zhang Y, Shen HB. High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling. ACTA ACUST UNITED AC 2013;29:2579-87. [PMID: 23946502 DOI: 10.1093/bioinformatics/btt440] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
516
Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis. Genetics 2013;195:443-55. [PMID: 23934888 DOI: 10.1534/genetics.113.155861] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
517
Feizi S, Marbach D, Médard M, Kellis M. Network deconvolution as a general method to distinguish direct dependencies in networks. Nat Biotechnol 2013;31:726-33. [PMID: 23851448 PMCID: PMC3773370 DOI: 10.1038/nbt.2635] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 06/11/2013] [Indexed: 01/08/2023]
518
Taylor WR, Hamilton RS, Sadowski MI. Prediction of contacts from correlated sequence substitutions. Curr Opin Struct Biol 2013;23:473-9. [PMID: 23680395 DOI: 10.1016/j.sbi.2013.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/12/2013] [Accepted: 04/02/2013] [Indexed: 11/26/2022]
519
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] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
520
Protein structure prediction from sequence variation. Nat Biotechnol 2013;30:1072-80. [PMID: 23138306 DOI: 10.1038/nbt.2419] [Citation(s) in RCA: 450] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 10/15/2012] [Indexed: 02/07/2023]
521
de Juan D, Pazos F, Valencia A. Emerging methods in protein co-evolution. Nat Rev Genet 2013;14:249-61. [PMID: 23458856 DOI: 10.1038/nrg3414] [Citation(s) in RCA: 436] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
522
Yu DJ, Hu J, Tang ZM, Shen HB, Yang J, Yang JY. Improving protein-ATP binding residues prediction by boosting SVMs with random under-sampling. Neurocomputing 2013. [DOI: 10.1016/j.neucom.2012.10.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
523
Sadowski MI. Prediction of protein domain boundaries from inverse covariances. Proteins 2013;81:253-60. [PMID: 22987736 PMCID: PMC3563215 DOI: 10.1002/prot.24181] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 08/10/2012] [Accepted: 09/04/2012] [Indexed: 01/04/2023]
524
Savojardo C, Fariselli P, Martelli PL, Casadio R. Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations. BMC Bioinformatics 2013;14 Suppl 1:S10. [PMID: 23368835 PMCID: PMC3548674 DOI: 10.1186/1471-2105-14-s1-s10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
525
Ekeberg M, Lövkvist C, Lan Y, Weigt M, Aurell E. Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013;87:012707. [PMID: 23410359 DOI: 10.1103/physreve.87.012707] [Citation(s) in RCA: 411] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Indexed: 05/24/2023]
526
Sadowski MI, Taylor WR. Prediction of protein contacts from correlated sequence substitutions. Sci Prog 2013;96:33-42. [PMID: 23738436 PMCID: PMC10365419 DOI: 10.3184/003685013x13612883013639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
527
Dill KA, MacCallum JL. The Protein-Folding Problem, 50 Years On. Science 2012. [PMID: 23180855 DOI: 10.1126/science.1219021] [Citation(s) in RCA: 1011] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
528
Accurate simulation and detection of coevolution signals in multiple sequence alignments. PLoS One 2012;7:e47108. [PMID: 23091608 PMCID: PMC3473043 DOI: 10.1371/journal.pone.0047108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 09/10/2012] [Indexed: 11/19/2022]  Open
529
Eickholt J, Cheng J. Predicting protein residue-residue contacts using deep networks and boosting. Bioinformatics 2012;28:3066-72. [PMID: 23047561 DOI: 10.1093/bioinformatics/bts598] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]  Open
530
Evolutionary decision rules for predicting protein contact maps. Pattern Anal Appl 2012. [DOI: 10.1007/s10044-012-0297-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
531
Kalinina OV, Oberwinkler H, Glass B, Kräusslich HG, Russell RB, Briggs JAG. Computational identification of novel amino-acid interactions in HIV Gag via correlated evolution. PLoS One 2012;7:e42468. [PMID: 22879995 PMCID: PMC3411748 DOI: 10.1371/journal.pone.0042468] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/09/2012] [Indexed: 12/31/2022]  Open
532
Di Lena P, Nagata K, Baldi P. Deep architectures for protein contact map prediction. ACTA ACUST UNITED AC 2012;28:2449-57. [PMID: 22847931 DOI: 10.1093/bioinformatics/bts475] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
533
Deciphering membrane protein structures from protein sequences. Genome Biol 2012;13:160. [PMID: 22738306 PMCID: PMC3446308 DOI: 10.1186/gb-2012-13-6-160] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
534
Shang L, Xu W, Ozer S, Gutell RR. Structural constraints identified with covariation analysis in ribosomal RNA. PLoS One 2012;7:e39383. [PMID: 22724009 PMCID: PMC3378556 DOI: 10.1371/journal.pone.0039383] [Citation(s) in RCA: 21] [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: 12/13/2011] [Accepted: 05/24/2012] [Indexed: 11/19/2022]  Open
535
Kozma D, Simon I, Tusnády GE. CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods. Nucleic Acids Res 2012;40:W329-33. [PMID: 22669913 PMCID: PMC3394325 DOI: 10.1093/nar/gks488] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
536
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proc Natl Acad Sci U S A 2012;109:E1540-7. [PMID: 22645369 DOI: 10.1073/pnas.1120036109] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
537
Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS. Three-dimensional structures of membrane proteins from genomic sequencing. Cell 2012;149:1607-21. [PMID: 22579045 DOI: 10.1016/j.cell.2012.04.012] [Citation(s) in RCA: 389] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 04/12/2012] [Accepted: 04/23/2012] [Indexed: 01/21/2023]
538
Amino acid coevolution induces an evolutionary Stokes shift. Proc Natl Acad Sci U S A 2012;109:E1352-9. [PMID: 22547823 DOI: 10.1073/pnas.1120084109] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
539
Taylor WR, Jones DT, Sadowski MI. Protein topology from predicted residue contacts. Protein Sci 2011;21:299-305. [PMID: 22102360 DOI: 10.1002/pro.2002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 11/08/2011] [Accepted: 11/10/2011] [Indexed: 11/12/2022]
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