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Number Cited by Other Article(s)
1
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]
2
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: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
3
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]
4
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: 0.8] [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
5
Khor S. Folding with a protein's native shortcut network. Proteins 2019;86:924-934. [PMID: 29790602 DOI: 10.1002/prot.25524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 04/13/2018] [Accepted: 05/14/2018] [Indexed: 11/09/2022]
6
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: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
7
Gadiyaram V, Vishveshwara S, Vishveshwara S. From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses. J Chem Inf Model 2019;59:1715-1727. [DOI: 10.1021/acs.jcim.9b00002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
8
Pražnikar J, Tomić M, Turk D. Validation and quality assessment of macromolecular structures using complex network analysis. Sci Rep 2019;9:1678. [PMID: 30737447 PMCID: PMC6368557 DOI: 10.1038/s41598-019-38658-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 01/07/2019] [Indexed: 02/06/2023]  Open
9
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: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
10
Ghosh S, Vishveshwara S. Ranking the quality of protein structure models using sidechain based network properties. F1000Res 2014;3:17. [PMID: 25580218 PMCID: PMC4038323 DOI: 10.12688/f1000research.3-17.v1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2014] [Indexed: 01/31/2023]  Open
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