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For: Uziela K, Wallner B. ProQ2: estimation of model accuracy implemented in Rosetta. Bioinformatics 2016;32:1411-3. [PMID: 26733453 PMCID: PMC4848402 DOI: 10.1093/bioinformatics/btv767] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/23/2015] [Indexed: 11/24/2022]  Open
Number Cited by Other Article(s)
1
Powell HR, Islam SA, David A, Sternberg MJE. Phyre2.2: A Community Resource for Template-based Protein Structure Prediction. J Mol Biol 2025:168960. [PMID: 40133783 PMCID: PMC7617537 DOI: 10.1016/j.jmb.2025.168960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 01/17/2025] [Accepted: 01/20/2025] [Indexed: 03/27/2025]
2
Liang F, Sun M, Xie L, Zhao X, Liu D, Zhao K, Zhang G. Recent advances and challenges in protein complex model accuracy estimation. Comput Struct Biotechnol J 2024;23:1824-1832. [PMID: 38707538 PMCID: PMC11066466 DOI: 10.1016/j.csbj.2024.04.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024]  Open
3
Liu D, Zhang B, Liu J, Li H, Song L, Zhang G. Assessing protein model quality based on deep graph coupled networks using protein language model. Brief Bioinform 2023;25:bbad420. [PMID: 38018909 PMCID: PMC10685403 DOI: 10.1093/bib/bbad420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/19/2023] [Accepted: 10/31/2023] [Indexed: 11/30/2023]  Open
4
Chen X, Morehead A, Liu J, Cheng J. A gated graph transformer for protein complex structure quality assessment and its performance in CASP15. Bioinformatics 2023;39:i308-i317. [PMID: 37387159 PMCID: PMC10311325 DOI: 10.1093/bioinformatics/btad203] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]  Open
5
Maghrabi AHA, Aldowsari FMF, McGuffin LJ. Quality Estimates for 3D Protein Models. Methods Mol Biol 2023;2627:101-118. [PMID: 36959444 DOI: 10.1007/978-1-0716-2974-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
6
Adiyaman R, McGuffin LJ. Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategy. Methods Mol Biol 2023;2627:119-140. [PMID: 36959445 DOI: 10.1007/978-1-0716-2974-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
7
Zhao C, Liu T, Wang Z. Predicting residue-specific qualities of individual protein models using residual neural networks and graph neural networks. Proteins 2022;90:2091-2102. [PMID: 35842895 PMCID: PMC9796650 DOI: 10.1002/prot.26400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/24/2022] [Accepted: 07/08/2022] [Indexed: 01/02/2023]
8
Kaushik R, Zhang KY. An Integrated Protein Structure Fitness Scoring Approach for Identifying Native-Like Model Structures. Comput Struct Biotechnol J 2022;20:6467-6472. [DOI: 10.1016/j.csbj.2022.11.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]  Open
9
Bitton M, Keasar C. Estimation of model accuracy by a unique set of features and tree-based regressor. Sci Rep 2022;12:14074. [PMID: 35982086 PMCID: PMC9388490 DOI: 10.1038/s41598-022-17097-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/20/2022] [Indexed: 11/26/2022]  Open
10
Akhter N, Kabir KL, Chennupati G, Vangara R, Alexandrov BS, Djidjev H, Shehu A. Improved Protein Decoy Selection via Non-Negative Matrix Factorization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:1670-1682. [PMID: 33400654 DOI: 10.1109/tcbb.2020.3049088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
11
Kaushik R, Zhang KYJ. ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures. Bioinformatics 2022;38:369-376. [PMID: 34542606 DOI: 10.1093/bioinformatics/btab666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/06/2021] [Accepted: 09/16/2021] [Indexed: 02/03/2023]  Open
12
Ye L, Wu P, Peng Z, Gao J, Liu J, Yang J. Improved estimation of model quality using predicted inter-residue distance. Bioinformatics 2021;37:3752-3759. [PMID: 34473228 DOI: 10.1093/bioinformatics/btab632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022]  Open
13
McGuffin LJ, Aldowsari FMF, Alharbi SMA, Adiyaman R. ModFOLD8: accurate global and local quality estimates for 3D protein models. Nucleic Acids Res 2021;49:W425-W430. [PMID: 33963867 PMCID: PMC8218196 DOI: 10.1093/nar/gkab321] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 11/26/2022]  Open
14
Postic G, Janel N, Moroy G. Representations of protein structure for exploring the conformational space: A speed-accuracy trade-off. Comput Struct Biotechnol J 2021;19:2618-2625. [PMID: 34025948 PMCID: PMC8120936 DOI: 10.1016/j.csbj.2021.04.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/25/2022]  Open
15
Alam FF, Shehu A. Unsupervised multi-instance learning for protein structure determination. J Bioinform Comput Biol 2021;19:2140002. [PMID: 33568002 DOI: 10.1142/s0219720021400023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
16
Akhter N, Chennupati G, Djidjev H, Shehu A. Decoy selection for protein structure prediction via extreme gradient boosting and ranking. BMC Bioinformatics 2020;21:189. [PMID: 33297949 PMCID: PMC7724862 DOI: 10.1186/s12859-020-3523-9] [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: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 11/10/2022]  Open
17
Abbass J, Nebel JC. Rosetta and the Journey to Predict Proteins’ Structures, 20 Years on. Curr Bioinform 2020. [DOI: 10.2174/1574893615999200504103643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
18
Liu T, Wang Z. MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials. BMC Bioinformatics 2020;21:246. [PMID: 32631256 PMCID: PMC7336608 DOI: 10.1186/s12859-020-3383-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 11/10/2022]  Open
19
Abbass J, Nebel JC. Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure. BMC Bioinformatics 2020;21:170. [PMID: 32357827 PMCID: PMC7195757 DOI: 10.1186/s12859-020-3491-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/13/2020] [Indexed: 11/10/2022]  Open
20
Tadepalli S, Akhter N, Barbara D, Shehu A. Anomaly Detection-Based Recognition of Near-Native Protein Structures. IEEE Trans Nanobioscience 2020;19:562-570. [PMID: 32340957 DOI: 10.1109/tnb.2020.2990642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
21
Tenorio CA, Longo LM, Parker JB, Lee J, Blaber M. Ab initio folding of a trefoil-fold motif reveals structural similarity with a β-propeller blade motif. Protein Sci 2020;29:1172-1185. [PMID: 32142181 DOI: 10.1002/pro.3850] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 01/05/2023]
22
Wallner B. Estimating local protein model quality: prospects for molecular replacement. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020;76:285-290. [PMID: 32133992 PMCID: PMC7057213 DOI: 10.1107/s2059798320000972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/24/2020] [Indexed: 11/10/2022]
23
Maghrabi AHA, McGuffin LJ. Estimating the Quality of 3D Protein Models Using the ModFOLD7 Server. Methods Mol Biol 2020;2165:69-81. [PMID: 32621219 DOI: 10.1007/978-1-0716-0708-4_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
24
Akhter N, Chennupati G, Kabir KL, Djidjev H, Shehu A. Unsupervised and Supervised Learning over theEnergy Landscape for Protein Decoy Selection. Biomolecules 2019;9:E607. [PMID: 31615116 PMCID: PMC6843838 DOI: 10.3390/biom9100607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 11/17/2022]  Open
25
Akhter N, Hassan L, Rajabi Z, Barbará D, Shehu A. Learning Organizations of Protein Energy Landscapes: An Application on Decoy Selection in Template-Free Protein Structure Prediction. Methods Mol Biol 2019;1958:147-171. [PMID: 30945218 DOI: 10.1007/978-1-4939-9161-7_8] [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] [Indexed: 03/31/2023]
26
Cheng J, Choe MH, Elofsson A, Han KS, Hou J, Maghrabi AHA, McGuffin LJ, Menéndez-Hurtado D, Olechnovič K, Schwede T, Studer G, Uziela K, Venclovas Č, Wallner B. Estimation of model accuracy in CASP13. Proteins 2019;87:1361-1377. [PMID: 31265154 DOI: 10.1002/prot.25767] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/04/2019] [Accepted: 06/15/2019] [Indexed: 12/28/2022]
27
Maghrabi AHA, McGuffin LJ. ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models. Nucleic Acids Res 2019;45:W416-W421. [PMID: 28460136 PMCID: PMC5570241 DOI: 10.1093/nar/gkx332] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/21/2017] [Indexed: 11/24/2022]  Open
28
Methods for the Refinement of Protein Structure 3D Models. Int J Mol Sci 2019;20:ijms20092301. [PMID: 31075942 PMCID: PMC6539982 DOI: 10.3390/ijms20092301] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/24/2019] [Accepted: 05/07/2019] [Indexed: 12/25/2022]  Open
29
Kabir KL, Hassan L, Rajabi Z, Akhter N, Shehu A. Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure Prediction. MOLECULES (BASEL, SWITZERLAND) 2019;24:molecules24050854. [PMID: 30823390 PMCID: PMC6429114 DOI: 10.3390/molecules24050854] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/14/2019] [Accepted: 02/22/2019] [Indexed: 11/30/2022]
30
In silico prediction of prolactin molecules as a tool for equine genomics reproduction. Mol Divers 2019;23:1019-1028. [PMID: 30740642 DOI: 10.1007/s11030-018-09914-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/31/2018] [Indexed: 10/27/2022]
31
An Energy Landscape Treatment of Decoy Selection in Template-Free Protein Structure Prediction. COMPUTATION 2018. [DOI: 10.3390/computation6020039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
32
Cassidy CK, Himes BA, Luthey-Schulten Z, Zhang P. CryoEM-based hybrid modeling approaches for structure determination. Curr Opin Microbiol 2018;43:14-23. [PMID: 29107896 PMCID: PMC5934336 DOI: 10.1016/j.mib.2017.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/04/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022]
33
Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A. Improved protein model quality assessments by changing the target function. Proteins 2018. [PMID: 29524250 DOI: 10.1002/prot.25492] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
34
Manavalan B, Lee J. SVMQA: support-vector-machine-based protein single-model quality assessment. Bioinformatics 2018;33:2496-2503. [PMID: 28419290 DOI: 10.1093/bioinformatics/btx222] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/12/2017] [Indexed: 01/03/2023]  Open
35
Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A. ProQ3D: improved model quality assessments using deep learning. Bioinformatics 2018;33:1578-1580. [PMID: 28052925 DOI: 10.1093/bioinformatics/btw819] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/20/2016] [Indexed: 11/14/2022]  Open
36
Haas J, Barbato A, Behringer D, Studer G, Roth S, Bertoni M, Mostaguir K, Gumienny R, Schwede T. Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12. Proteins 2017;86 Suppl 1:387-398. [PMID: 29178137 DOI: 10.1002/prot.25431] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/10/2017] [Accepted: 11/22/2017] [Indexed: 12/22/2022]
37
Cao R, Adhikari B, Bhattacharya D, Sun M, Hou J, Cheng J. QAcon: single model quality assessment using protein structural and contact information with machine learning techniques. Bioinformatics 2017;33:586-588. [PMID: 28035027 DOI: 10.1093/bioinformatics/btw694] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 11/01/2016] [Indexed: 11/14/2022]  Open
38
Elofsson A, Joo K, Keasar C, Lee J, Maghrabi AHA, Manavalan B, McGuffin LJ, Ménendez Hurtado D, Mirabello C, Pilstål R, Sidi T, Uziela K, Wallner B. Methods for estimation of model accuracy in CASP12. Proteins 2017;86 Suppl 1:361-373. [DOI: 10.1002/prot.25395] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/25/2017] [Accepted: 10/03/2017] [Indexed: 12/28/2022]
39
McGuffin LJ, Shuid AN, Kempster R, Maghrabi AH, Nealon JO, Salehe BR, Atkins JD, Roche DB. Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods. Proteins 2017;86 Suppl 1:335-344. [DOI: 10.1002/prot.25360] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/12/2017] [Accepted: 07/25/2017] [Indexed: 11/05/2022]
40
Basu S, Wallner B. Finding correct protein-protein docking models using ProQDock. Bioinformatics 2017;32:i262-i270. [PMID: 27307625 PMCID: PMC4908341 DOI: 10.1093/bioinformatics/btw257] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
41
Jing X, Dong Q. MQAPRank: improved global protein model quality assessment by learning-to-rank. BMC Bioinformatics 2017;18:275. [PMID: 28545390 PMCID: PMC5445322 DOI: 10.1186/s12859-017-1691-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 05/16/2017] [Indexed: 11/10/2022]  Open
42
Olechnovič K, Venclovas Č. VoroMQA: Assessment of protein structure quality using interatomic contact areas. Proteins 2017;85:1131-1145. [DOI: 10.1002/prot.25278] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/13/2017] [Accepted: 02/21/2017] [Indexed: 12/14/2022]
43
Cao R, Bhattacharya D, Hou J, Cheng J. DeepQA: improving the estimation of single protein model quality with deep belief networks. BMC Bioinformatics 2016;17:495. [PMID: 27919220 PMCID: PMC5139030 DOI: 10.1186/s12859-016-1405-y] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/01/2016] [Indexed: 01/02/2023]  Open
44
ProQ3: Improved model quality assessments using Rosetta energy terms. Sci Rep 2016;6:33509. [PMID: 27698390 PMCID: PMC5048106 DOI: 10.1038/srep33509] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/26/2016] [Indexed: 01/17/2023]  Open
45
Jing X, Wang K, Lu R, Dong Q. Sorting protein decoys by machine-learning-to-rank. Sci Rep 2016;6:31571. [PMID: 27530967 PMCID: PMC4987638 DOI: 10.1038/srep31571] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/26/2016] [Indexed: 11/18/2022]  Open
46
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
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