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For: Iqbal S, Hoque MT. Estimation of Position Specific Energy as a Feature of Protein Residues from Sequence Alone for Structural Classification. PLoS One 2016;11:e0161452. [PMID: 27588752 PMCID: PMC5010294 DOI: 10.1371/journal.pone.0161452] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/06/2016] [Indexed: 11/20/2022]  Open
Number Cited by Other Article(s)
1
Wang K, Hu G, Basu S, Kurgan L. flDPnn2: Accurate and Fast Predictor of Intrinsic Disorder in Proteins. J Mol Biol 2024;436:168605. [PMID: 39237195 DOI: 10.1016/j.jmb.2024.168605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/16/2024] [Accepted: 05/04/2024] [Indexed: 09/07/2024]
2
Kabir MWU, Alawad DM, Pokhrel P, Hoque MT. DRBpred: A sequence-based machine learning method to effectively predict DNA- and RNA-binding residues. Comput Biol Med 2024;170:108081. [PMID: 38295475 PMCID: PMC10922697 DOI: 10.1016/j.compbiomed.2024.108081] [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: 08/16/2023] [Revised: 01/12/2024] [Accepted: 01/27/2024] [Indexed: 02/02/2024]
3
Kabir MWU, Alawad DM, Mishra A, Hoque MT. TAFPred: Torsion Angle Fluctuations Prediction from Protein Sequences. BIOLOGY 2023;12:1020. [PMID: 37508449 PMCID: PMC10376102 DOI: 10.3390/biology12071020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
4
Gao M, Günther S. HyperCys: A Structure- and Sequence-Based Predictor of Hyper-Reactive Druggable Cysteines. Int J Mol Sci 2023;24:ijms24065960. [PMID: 36983037 PMCID: PMC10054327 DOI: 10.3390/ijms24065960] [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: 02/13/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]  Open
5
Arif M, Kabir M, Ahmed S, Khan A, Ge F, Khelifi A, Yu DJ. DeepCPPred: A Deep Learning Framework for the Discrimination of Cell-Penetrating Peptides and Their Uptake Efficiencies. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:2749-2759. [PMID: 34347603 DOI: 10.1109/tcbb.2021.3102133] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
6
Tamburrini KC, Pesce G, Nilsson J, Gondelaud F, Kajava AV, Berrin JG, Longhi S. Predicting Protein Conformational Disorder and Disordered Binding Sites. Methods Mol Biol 2022;2449:95-147. [PMID: 35507260 DOI: 10.1007/978-1-0716-2095-3_4] [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: 06/14/2023]
7
Zhao B, Kurgan L. Surveying over 100 predictors of intrinsic disorder in proteins. Expert Rev Proteomics 2021;18:1019-1029. [PMID: 34894985 DOI: 10.1080/14789450.2021.2018304] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
8
Mishra A, Kabir MWU, Hoque MT. diSBPred: A machine learning based approach for disulfide bond prediction. Comput Biol Chem 2021;91:107436. [PMID: 33550156 DOI: 10.1016/j.compbiolchem.2021.107436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/28/2020] [Accepted: 01/10/2021] [Indexed: 12/25/2022]
9
Flot M, Mishra A, Kuchi AS, Hoque MT. StackSSSPred: A Stacking-Based Prediction of Supersecondary Structure from Sequence. Methods Mol Biol 2019;1958:101-122. [PMID: 30945215 DOI: 10.1007/978-1-4939-9161-7_5] [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: 06/09/2023]
10
Mishra A, Pokhrel P, Hoque MT. StackDPPred: a stacking based prediction of DNA-binding protein from sequence. Bioinformatics 2018;35:433-441. [DOI: 10.1093/bioinformatics/bty653] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/18/2018] [Indexed: 12/12/2022]  Open
11
Iqbal S, Hoque MT. PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence. Bioinformatics 2018;34:3289-3299. [DOI: 10.1093/bioinformatics/bty352] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/29/2018] [Indexed: 01/10/2023]  Open
12
Tarafder S, Toukir Ahmed M, Iqbal S, Tamjidul Hoque M, Sohel Rahman M. RBSURFpred: Modeling protein accessible surface area in real and binary space using regularized and optimized regression. J Theor Biol 2018;441:44-57. [PMID: 29305182 DOI: 10.1016/j.jtbi.2017.12.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/11/2017] [Accepted: 12/28/2017] [Indexed: 01/04/2023]
13
Dosztányi Z. Prediction of protein disorder based on IUPred. Protein Sci 2017;27:331-340. [PMID: 29076577 DOI: 10.1002/pro.3334] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 12/19/2022]
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