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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)
251
Wuyun Q, Zheng W, Peng Z, Yang J. A large-scale comparative assessment of methods for residue-residue contact prediction. Brief Bioinform 2019;19:219-230. [PMID: 27802931 DOI: 10.1093/bib/bbw106] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 11/14/2022]  Open
252
Téletchéa S, Santuz H, Léonard S, Etchebest C. Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE). PLoS One 2019;14:e0211043. [PMID: 30794542 PMCID: PMC6386447 DOI: 10.1371/journal.pone.0211043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 01/07/2019] [Indexed: 12/25/2022]  Open
253
Figliuzzi M, Barrat-Charlaix P, Weigt M. How Pairwise Coevolutionary Models Capture the Collective Residue Variability in Proteins? Mol Biol Evol 2019;35:1018-1027. [PMID: 29351669 DOI: 10.1093/molbev/msy007] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
254
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
255
Malinverni D, Barducci A. Coevolutionary Analysis of Protein Sequences for Molecular Modeling. Methods Mol Biol 2019;2022:379-397. [PMID: 31396912 DOI: 10.1007/978-1-4939-9608-7_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
256
Dehghani T, Naghibzadeh M, Eghdami M. BetaDL: A protein beta-sheet predictor utilizing a deep learning model and independent set solution. Comput Biol Med 2019;104:241-249. [PMID: 30530227 DOI: 10.1016/j.compbiomed.2018.11.021] [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: 08/27/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022]
257
MacCarthy E, Perry D, Kc DB. Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction. Methods Mol Biol 2019;1958:15-45. [PMID: 30945212 DOI: 10.1007/978-1-4939-9161-7_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
258
Wan C. Background on Biology of Ageing and Bioinformatics. ADVANCED INFORMATION AND KNOWLEDGE PROCESSING 2019:25-43. [DOI: 10.1007/978-3-319-97919-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
259
Schmidt M, Hamacher K. hoDCA: higher order direct-coupling analysis. BMC Bioinformatics 2018;19:546. [PMID: 30594145 PMCID: PMC6311078 DOI: 10.1186/s12859-018-2583-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 12/12/2018] [Indexed: 11/30/2022]  Open
260
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
261
Huang YJ, Brock KP, Ishida Y, Swapna GVT, Inouye M, Marks DS, Sander C, Montelione GT. Combining Evolutionary Covariance and NMR Data for Protein Structure Determination. Methods Enzymol 2018;614:363-392. [PMID: 30611430 PMCID: PMC6640129 DOI: 10.1016/bs.mie.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
262
Neuwald AF, Altschul SF. Statistical investigations of protein residue direct couplings. PLoS Comput Biol 2018;14:e1006237. [PMID: 30596639 PMCID: PMC6329532 DOI: 10.1371/journal.pcbi.1006237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 01/11/2019] [Accepted: 11/23/2018] [Indexed: 12/12/2022]  Open
263
Butler BM, Kazan IC, Kumar A, Ozkan SB. Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs. PLoS Comput Biol 2018;14:e1006626. [PMID: 30496278 PMCID: PMC6289467 DOI: 10.1371/journal.pcbi.1006626] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/11/2018] [Accepted: 11/09/2018] [Indexed: 11/18/2022]  Open
264
Cheung NJ, Yu W. De novo protein structure prediction using ultra-fast molecular dynamics simulation. PLoS One 2018;13:e0205819. [PMID: 30458007 PMCID: PMC6245515 DOI: 10.1371/journal.pone.0205819] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 10/02/2018] [Indexed: 11/19/2022]  Open
265
Ding W, Mao W, Shao D, Zhang W, Gong H. DeepConPred2: An Improved Method for the Prediction of Protein Residue Contacts. Comput Struct Biotechnol J 2018;16:503-510. [PMID: 30505403 PMCID: PMC6247404 DOI: 10.1016/j.csbj.2018.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/16/2018] [Accepted: 10/18/2018] [Indexed: 12/18/2022]  Open
266
Vorberg S, Seemayer S, Söding J. Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction. PLoS Comput Biol 2018;14:e1006526. [PMID: 30395601 PMCID: PMC6237422 DOI: 10.1371/journal.pcbi.1006526] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/15/2018] [Accepted: 09/24/2018] [Indexed: 12/01/2022]  Open
267
Bitbol AF. Inferring interaction partners from protein sequences using mutual information. PLoS Comput Biol 2018;14:e1006401. [PMID: 30422978 PMCID: PMC6258550 DOI: 10.1371/journal.pcbi.1006401] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/27/2018] [Accepted: 10/27/2018] [Indexed: 11/30/2022]  Open
268
Schelling M, Hopf TA, Rost B. Evolutionary couplings and sequence variation effect predict protein binding sites. Proteins 2018;86:1064-1074. [DOI: 10.1002/prot.25585] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 06/14/2018] [Accepted: 07/04/2018] [Indexed: 01/16/2023]
269
Dhar A, Davidsen K, Matsen FA, Minin VN. Predicting B cell receptor substitution profiles using public repertoire data. PLoS Comput Biol 2018;14:e1006388. [PMID: 30332400 PMCID: PMC6205660 DOI: 10.1371/journal.pcbi.1006388] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 10/29/2018] [Accepted: 07/22/2018] [Indexed: 12/31/2022]  Open
270
Rouse SL, Matthews SJ, Dueholm MS. Ecology and Biogenesis of Functional Amyloids in Pseudomonas. J Mol Biol 2018;430:3685-3695. [PMID: 29753779 PMCID: PMC6173800 DOI: 10.1016/j.jmb.2018.05.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 12/02/2022]
271
How is structural divergence related to evolutionary information? Mol Phylogenet Evol 2018;127:859-866. [DOI: 10.1016/j.ympev.2018.06.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 06/01/2018] [Accepted: 06/19/2018] [Indexed: 12/15/2022]
272
Jones DT, Kandathil SM. High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features. Bioinformatics 2018;34:3308-3315. [PMID: 29718112 PMCID: PMC6157083 DOI: 10.1093/bioinformatics/bty341] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/06/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022]  Open
273
Nerli S, Sgourakis NG. CS-ROSETTA. Methods Enzymol 2018;614:321-362. [PMID: 30611429 DOI: 10.1016/bs.mie.2018.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
274
Wu H, Cao C, Xia X, Lu Q. Unified Deep Learning Architecture for Modeling Biology Sequence. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:1445-1452. [PMID: 28991751 DOI: 10.1109/tcbb.2017.2760832] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
275
Jakubec D, Kratochvíl M, Vymĕtal J, Vondrášek J. Widespread evolutionary crosstalk among protein domains in the context of multi-domain proteins. PLoS One 2018;13:e0203085. [PMID: 30169546 PMCID: PMC6118372 DOI: 10.1371/journal.pone.0203085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/14/2018] [Indexed: 11/20/2022]  Open
276
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
277
Khan S, Guo TW, Misra S. A coevolution-guided model for the rotor of the bacterial flagellar motor. Sci Rep 2018;8:11754. [PMID: 30082903 PMCID: PMC6079021 DOI: 10.1038/s41598-018-30293-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/19/2018] [Indexed: 01/17/2023]  Open
278
Kassem MM, Christoffersen LB, Cavalli A, Lindorff-Larsen K. Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts. Sci Rep 2018;8:11112. [PMID: 30042380 PMCID: PMC6057941 DOI: 10.1038/s41598-018-29357-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/10/2018] [Indexed: 11/29/2022]  Open
279
Delarue M, Koehl P. Combined approaches from physics, statistics, and computer science for ab initio protein structure prediction: ex unitate vires (unity is strength)? F1000Res 2018;7. [PMID: 30079234 PMCID: PMC6058471 DOI: 10.12688/f1000research.14870.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/19/2018] [Indexed: 11/20/2022]  Open
280
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
281
Baldi P. Deep Learning in Biomedical Data Science. Annu Rev Biomed Data Sci 2018. [DOI: 10.1146/annurev-biodatasci-080917-013343] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
282
Holland J, Pan Q, Grigoryan G. Contact prediction is hardest for the most informative contacts, but improves with the incorporation of contact potentials. PLoS One 2018;13:e0199585. [PMID: 29953468 PMCID: PMC6023208 DOI: 10.1371/journal.pone.0199585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 06/11/2018] [Indexed: 11/18/2022]  Open
283
Nerli S, McShan AC, Sgourakis NG. Chemical shift-based methods in NMR structure determination. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018;106-107:1-25. [PMID: 31047599 PMCID: PMC6788782 DOI: 10.1016/j.pnmrs.2018.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 05/08/2023]
284
Szurmant H, Weigt M. Inter-residue, inter-protein and inter-family coevolution: bridging the scales. Curr Opin Struct Biol 2018;50:26-32. [PMID: 29101847 PMCID: PMC5940578 DOI: 10.1016/j.sbi.2017.10.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/12/2017] [Accepted: 10/13/2017] [Indexed: 10/18/2022]
285
Dutta S, Eckmann JP, Libchaber A, Tlusty T. Green function of correlated genes in a minimal mechanical model of protein evolution. Proc Natl Acad Sci U S A 2018;115:E4559-E4568. [PMID: 29712824 PMCID: PMC5960285 DOI: 10.1073/pnas.1716215115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
286
Simkovic F, Thomas JMH, Rigden DJ. ConKit: a python interface to contact predictions. Bioinformatics 2018;33:2209-2211. [PMID: 28369168 PMCID: PMC5870551 DOI: 10.1093/bioinformatics/btx148] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/14/2017] [Indexed: 11/19/2022]  Open
287
Fonseca-Júnior NJ, Afonso MQ, Oliveira LC, Bleicher L. PFstats: A Network-Based Open Tool for Protein Family Analysis. J Comput Biol 2018;25:480-486. [DOI: 10.1089/cmb.2017.0181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
288
Raimondi D, Orlando G, Moreau Y, Vranken WF. Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping. Bioinformatics 2018;34:3118-3125. [DOI: 10.1093/bioinformatics/bty309] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/18/2018] [Indexed: 11/14/2022]  Open
289
Mao W, Wang T, Zhang W, Gong H. Identification of residue pairing in interacting β-strands from a predicted residue contact map. BMC Bioinformatics 2018;19:146. [PMID: 29673311 PMCID: PMC5907701 DOI: 10.1186/s12859-018-2150-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/09/2018] [Indexed: 12/04/2022]  Open
290
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
291
de Oliveira SHP, Law EC, Shi J, Deane CM. Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction. Bioinformatics 2018;34:1132-1140. [PMID: 29136098 PMCID: PMC6030820 DOI: 10.1093/bioinformatics/btx722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 09/22/2017] [Accepted: 11/04/2017] [Indexed: 01/12/2023]  Open
292
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]
293
He B, Mortuza SM, Wang Y, Shen HB, Zhang Y. NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers. Bioinformatics 2018;33:2296-2306. [PMID: 28369334 DOI: 10.1093/bioinformatics/btx164] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/21/2017] [Indexed: 12/12/2022]  Open
294
Douam F, Fusil F, Enguehard M, Dib L, Nadalin F, Schwaller L, Hrebikova G, Mancip J, Mailly L, Montserret R, Ding Q, Maisse C, Carlot E, Xu K, Verhoeyen E, Baumert TF, Ploss A, Carbone A, Cosset FL, Lavillette D. A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism. PLoS Pathog 2018;14:e1006908. [PMID: 29505618 PMCID: PMC5854445 DOI: 10.1371/journal.ppat.1006908] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 03/15/2018] [Accepted: 01/26/2018] [Indexed: 12/15/2022]  Open
295
Cocco S, Feinauer C, Figliuzzi M, Monasson R, Weigt M. Inverse statistical physics of protein sequences: a key issues review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018;81:032601. [PMID: 29120346 DOI: 10.1088/1361-6633/aa9965] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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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]
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Garrido-Martín D, Pazos F. Effect of the sequence data deluge on the performance of methods for detecting protein functional residues. BMC Bioinformatics 2018;19:67. [PMID: 29482506 PMCID: PMC5827975 DOI: 10.1186/s12859-018-2084-7] [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: 11/07/2017] [Accepted: 02/21/2018] [Indexed: 11/10/2022]  Open
298
Le Q, Sievers F, Higgins DG. Protein multiple sequence alignment benchmarking through secondary structure prediction. Bioinformatics 2018;33:1331-1337. [PMID: 28093407 PMCID: PMC5408826 DOI: 10.1093/bioinformatics/btw840] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/10/2017] [Indexed: 12/26/2022]  Open
299
Barrat-Charlaix P, Weigt M. [From sequence variability to structural and functional prediction: modeling of homologous protein families]. Biol Aujourdhui 2018;211:239-244. [PMID: 29412135 DOI: 10.1051/jbio/2017030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Indexed: 06/08/2023]
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Cortés Cabrera Á, Sánchez-Murcia PA, Gago F. Making sense of the past: hyperstability of ancestral thioredoxins explained by free energy simulations. Phys Chem Chem Phys 2018;19:23239-23246. [PMID: 28825743 DOI: 10.1039/c7cp03659k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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