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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)
351
Perez A, Morrone JA, Dill KA. Accelerating physical simulations of proteins by leveraging external knowledge. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017;7. [PMID: 28959358 DOI: 10.1002/wcms.1309] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
352
Mandloi S, Chakrabarti S. Protein sites with more coevolutionary connections tend to evolve slower, while more variable protein families acquire higher coevolutionary connections. F1000Res 2017;6:453. [PMID: 28751967 PMCID: PMC5506539 DOI: 10.12688/f1000research.11251.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/05/2017] [Indexed: 11/20/2022]  Open
353
Uguzzoni G, John Lovis S, Oteri F, Schug A, Szurmant H, Weigt M. Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis. Proc Natl Acad Sci U S A 2017;114:E2662-E2671. [PMID: 28289198 PMCID: PMC5380090 DOI: 10.1073/pnas.1615068114] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
354
Skwark MJ, Croucher NJ, Puranen S, Chewapreecha C, Pesonen M, Xu YY, Turner P, Harris SR, Beres SB, Musser JM, Parkhill J, Bentley SD, Aurell E, Corander J. Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis. PLoS Genet 2017;13:e1006508. [PMID: 28207813 PMCID: PMC5312804 DOI: 10.1371/journal.pgen.1006508] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/24/2016] [Indexed: 12/05/2022]  Open
355
Várnai C, Burkoff NS, Wild DL. Improving protein-protein interaction prediction using evolutionary information from low-quality MSAs. PLoS One 2017;12:e0169356. [PMID: 28166227 PMCID: PMC5293240 DOI: 10.1371/journal.pone.0169356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 12/15/2016] [Indexed: 01/05/2023]  Open
356
Hopf TA, Ingraham JB, Poelwijk FJ, Schärfe CP, Springer M, Sander C, Marks DS. Mutation effects predicted from sequence co-variation. Nat Biotechnol 2017;35:128-135. [PMID: 28092658 PMCID: PMC5383098 DOI: 10.1038/nbt.3769] [Citation(s) in RCA: 448] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 12/09/2016] [Indexed: 01/09/2023]
357
Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D. Protein structure determination using metagenome sequence data. Science 2017;355:294-298. [PMID: 28104891 PMCID: PMC5493203 DOI: 10.1126/science.aah4043] [Citation(s) in RCA: 351] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/22/2016] [Indexed: 01/30/2023]
358
Lim K, Yamada KD, Frith MC, Tomii K. Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix. ACTA ACUST UNITED AC 2017;17:147-154. [PMID: 28083762 PMCID: PMC5274646 DOI: 10.1007/s10969-016-9210-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 12/05/2016] [Indexed: 12/28/2022]
359
da Fonseca NJ, Lima Afonso MQ, Pedersolli NG, de Oliveira LC, Andrade DS, Bleicher L. Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains. Biochem Biophys Res Commun 2017;492:565-571. [PMID: 28087275 DOI: 10.1016/j.bbrc.2017.01.041] [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: 12/02/2016] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
360
Wang S, Sun S, Li Z, Zhang R, Xu J. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. PLoS Comput Biol 2017;13:e1005324. [PMID: 28056090 PMCID: PMC5249242 DOI: 10.1371/journal.pcbi.1005324] [Citation(s) in RCA: 589] [Impact Index Per Article: 73.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 01/20/2017] [Accepted: 12/20/2016] [Indexed: 12/02/2022]  Open
361
Wei Q, La D, Kihara D. BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns. Methods Mol Biol 2017;1529:279-289. [PMID: 27914057 DOI: 10.1007/978-1-4939-6637-0_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
362
Vaitinadapoule A, Etchebest C. Molecular Modeling of Transporters: From Low Resolution Cryo-Electron Microscopy Map to Conformational Exploration. The Example of TSPO. Methods Mol Biol 2017;1635:383-416. [PMID: 28755381 DOI: 10.1007/978-1-4939-7151-0_21] [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] [Indexed: 06/07/2023]
363
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
364
Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. Proc Natl Acad Sci U S A 2016;113:15018-15023. [PMID: 27965389 DOI: 10.1073/pnas.1611861114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
365
Adhikari B, Nowotny J, Bhattacharya D, Hou J, Cheng J. ConEVA: a toolbox for comprehensive assessment of protein contacts. BMC Bioinformatics 2016;17:517. [PMID: 27923350 PMCID: PMC5142288 DOI: 10.1186/s12859-016-1404-z] [Citation(s) in RCA: 21] [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: 07/01/2016] [Accepted: 12/01/2016] [Indexed: 12/31/2022]  Open
366
Alcock F, Stansfeld PJ, Basit H, Habersetzer J, Baker MA, Palmer T, Wallace MI, Berks BC. Assembling the Tat protein translocase. eLife 2016;5. [PMID: 27914200 PMCID: PMC5201420 DOI: 10.7554/elife.20718] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/29/2016] [Indexed: 12/18/2022]  Open
367
Levy RM, Haldane A, Flynn WF. Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness. Curr Opin Struct Biol 2016;43:55-62. [PMID: 27870991 DOI: 10.1016/j.sbi.2016.11.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/03/2016] [Indexed: 11/17/2022]
368
Orlando G, Raimondi D, Vranken WF. Observation selection bias in contact prediction and its implications for structural bioinformatics. Sci Rep 2016;6:36679. [PMID: 27857150 PMCID: PMC5114557 DOI: 10.1038/srep36679] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/18/2016] [Indexed: 01/14/2023]  Open
369
Taylor WR, Matthews-Palmer TRS, Beeby M. Molecular Models for the Core Components of the Flagellar Type-III Secretion Complex. PLoS One 2016;11:e0164047. [PMID: 27855178 PMCID: PMC5113899 DOI: 10.1371/journal.pone.0164047] [Citation(s) in RCA: 10] [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: 03/29/2016] [Accepted: 09/19/2016] [Indexed: 01/10/2023]  Open
370
Jacquin H, Rançon A. Resummed mean-field inference for strongly coupled data. Phys Rev E 2016;94:042118. [PMID: 27841631 DOI: 10.1103/physreve.94.042118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Indexed: 11/07/2022]
371
Coucke A, Uguzzoni G, Oteri F, Cocco S, Monasson R, Weigt M. Direct coevolutionary couplings reflect biophysical residue interactions in proteins. J Chem Phys 2016;145:174102. [DOI: 10.1063/1.4966156] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
372
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]
373
Yu J, Andreani J, Ochsenbein F, Guerois R. Lessons from (co-)evolution in the docking of proteins and peptides for CAPRI Rounds 28-35. Proteins 2016;85:378-390. [PMID: 27701780 DOI: 10.1002/prot.25180] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/25/2016] [Accepted: 08/25/2016] [Indexed: 11/06/2022]
374
Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis. Proc Natl Acad Sci U S A 2016;113:12186-12191. [PMID: 27729520 DOI: 10.1073/pnas.1607570113] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
375
Inferring interaction partners from protein sequences. Proc Natl Acad Sci U S A 2016;113:12180-12185. [PMID: 27663738 DOI: 10.1073/pnas.1606762113] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
376
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]
377
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
378
Zhang L, Wang H, Yan L, Su L, Xu D. OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method. J Comput Biol 2016;24:217-228. [PMID: 27513917 DOI: 10.1089/cmb.2015.0236] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
379
A novel algorithm for detecting multiple covariance and clustering of biological sequences. Sci Rep 2016;6:30425. [PMID: 27451921 PMCID: PMC4958985 DOI: 10.1038/srep30425] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 07/05/2016] [Indexed: 12/14/2022]  Open
380
Baker JA, Simkovic F, Taylor HMC, Rigden DJ. Potential DNA binding and nuclease functions of ComEC domains characterized in silico. Proteins 2016;84:1431-42. [PMID: 27318187 PMCID: PMC5031224 DOI: 10.1002/prot.25088] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/25/2016] [Accepted: 06/13/2016] [Indexed: 12/15/2022]
381
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]
382
Haldane A, Flynn WF, He P, Vijayan RSK, Levy RM. Structural propensities of kinase family proteins from a Potts model of residue co-variation. Protein Sci 2016;25:1378-84. [PMID: 27241634 DOI: 10.1002/pro.2954] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 12/23/2022]
383
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
384
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
385
Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction: Progress and new directions in round XI. Proteins 2016;84 Suppl 1:4-14. [PMID: 27171127 DOI: 10.1002/prot.25064] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/29/2016] [Accepted: 05/08/2016] [Indexed: 12/15/2022]
386
Pandini A, Kleinjung J, Taylor WR, Junge W, Khan S. The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance. Biophys J 2016;109:975-87. [PMID: 26331255 PMCID: PMC4564677 DOI: 10.1016/j.bpj.2015.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/20/2015] [Accepted: 07/09/2015] [Indexed: 12/28/2022]  Open
387
Champeimont R, Laine E, Hu SW, Penin F, Carbone A. Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins. Sci Rep 2016;6:26401. [PMID: 27198619 PMCID: PMC4873791 DOI: 10.1038/srep26401] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 05/03/2016] [Indexed: 12/20/2022]  Open
388
Neuwald AF. Gleaning structural and functional information from correlations in protein multiple sequence alignments. Curr Opin Struct Biol 2016;38:1-8. [PMID: 27179293 DOI: 10.1016/j.sbi.2016.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/28/2016] [Accepted: 04/29/2016] [Indexed: 10/24/2022]
389
van Nimwegen E. Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? PLoS Comput Biol 2016;12:e1004726. [PMID: 27171220 PMCID: PMC4865087 DOI: 10.1371/journal.pcbi.1004726] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]  Open
390
Wang S, Li W, Zhang R, Liu S, Xu J. CoinFold: a web server for protein contact prediction and contact-assisted protein folding. Nucleic Acids Res 2016;44:W361-6. [PMID: 27112569 PMCID: PMC4987891 DOI: 10.1093/nar/gkw307] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 04/12/2016] [Indexed: 12/14/2022]  Open
391
Kurczynska M, Kania E, Konopka BM, Kotulska M. Applying PyRosetta molecular energies to separate properly oriented protein models from mirror models, obtained from contact maps. J Mol Model 2016;22:111. [PMID: 27107578 PMCID: PMC4842210 DOI: 10.1007/s00894-016-2975-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/05/2016] [Indexed: 11/30/2022]
392
Kinjo AR. A unified statistical model of protein multiple sequence alignment integrating direct coupling and insertions. Biophys Physicobiol 2016;13:45-62. [PMID: 27924257 PMCID: PMC5042171 DOI: 10.2142/biophysico.13.0_45] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/18/2016] [Indexed: 12/01/2022]  Open
393
Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev 2016;116:6370-90. [PMID: 27074285 PMCID: PMC4901368 DOI: 10.1021/acs.chemrev.5b00631] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
394
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]
395
Asti L, Uguzzoni G, Marcatili P, Pagnani A. Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity. PLoS Comput Biol 2016;12:e1004870. [PMID: 27074145 PMCID: PMC4830580 DOI: 10.1371/journal.pcbi.1004870] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/15/2016] [Indexed: 11/18/2022]  Open
396
Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation. Proc Natl Acad Sci U S A 2016;113:3539-44. [PMID: 26979958 DOI: 10.1073/pnas.1516579113] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
397
Bywater RP. Comparison of Algorithms for Prediction of Protein Structural Features from Evolutionary Data. PLoS One 2016;11:e0150769. [PMID: 26963911 PMCID: PMC4786192 DOI: 10.1371/journal.pone.0150769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/17/2016] [Indexed: 11/18/2022]  Open
398
Morrill GA, Kostellow AB, Liu L, Gupta RK, Askari A. Evolution of the α-Subunit of Na/K-ATPase from Paramecium to Homo sapiens: Invariance of Transmembrane Helix Topology. J Mol Evol 2016;82:183-98. [PMID: 26961431 PMCID: PMC4866997 DOI: 10.1007/s00239-016-9732-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/03/2016] [Indexed: 12/01/2022]
399
Baker FN, Porollo A. CoeViz: a web-based tool for coevolution analysis of protein residues. BMC Bioinformatics 2016;17:119. [PMID: 26956673 PMCID: PMC4782369 DOI: 10.1186/s12859-016-0975-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 03/01/2016] [Indexed: 11/30/2022]  Open
400
Belsom A, Schneider M, Fischer L, Brock O, Rappsilber J. Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology. Mol Cell Proteomics 2016;15:1105-16. [PMID: 26385339 PMCID: PMC4813692 DOI: 10.1074/mcp.m115.048504] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 09/16/2015] [Indexed: 01/12/2023]  Open
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