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For: Geng H, Lu T, Lin X, Liu Y, Yan F. Prediction of Protein-Protein Interaction Sites Based on Naive Bayes Classifier. Biochem Res Int 2015;2015:978193. [PMID: 26697220 DOI: 10.1155/2015/978193] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/05/2015] [Accepted: 11/12/2015] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Pratiwi NKC, Tayara H, Chong KT. An Ensemble Classifiers for Improved Prediction of Native-Non-Native Protein-Protein Interaction. Int J Mol Sci 2024;25:5957. [PMID: 38892144 PMCID: PMC11172808 DOI: 10.3390/ijms25115957] [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] [Received: 04/22/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024]  Open
2
Nikam R, Yugandhar K, Gromiha MM. DeepBSRPred: deep learning-based binding site residue prediction for proteins. Amino Acids 2023;55:1305-1316. [PMID: 36574037 DOI: 10.1007/s00726-022-03228-3] [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: 06/09/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022]
3
Nedyalkova M, Vasighi M, Azmoon A, Naneva L, Simeonov V. Sequence-Based Prediction of Plant Allergenic Proteins: Machine Learning Classification Approach. ACS OMEGA 2023;8:3698-3704. [PMID: 36743013 PMCID: PMC9893444 DOI: 10.1021/acsomega.2c02842] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/21/2022] [Indexed: 06/18/2023]
4
Jung Y, Geng C, Bonvin AMJJ, Xue LC, Honavar VG. MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations. Biomolecules 2023;13:121. [PMID: 36671507 PMCID: PMC9855734 DOI: 10.3390/biom13010121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023]  Open
5
Zhang F, Li M, Zhang J, Shi W, Kurgan L. DeepPRObind: Modular Deep Learner that Accurately Predicts Structure and Disorder-Annotated Protein Binding Residues. J Mol Biol 2023:167945. [PMID: 36621533 DOI: 10.1016/j.jmb.2023.167945] [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: 09/19/2022] [Revised: 12/15/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023]
6
Li M, Wu Z, Wang W, Lu K, Zhang J, Zhou Y, Chen Z, Li D, Zheng S, Chen P, Wang B. Protein-Protein Interaction Sites Prediction Based on an Under-Sampling Strategy and Random Forest Algorithm. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3646-3654. [PMID: 34705656 DOI: 10.1109/tcbb.2021.3123269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
7
Robin V, Bodein A, Scott-Boyer MP, Leclercq M, Périn O, Droit A. Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context. Front Mol Biosci 2022;9:962799. [PMID: 36158572 PMCID: PMC9494275 DOI: 10.3389/fmolb.2022.962799] [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: 06/06/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022]  Open
8
Bioinformatic Analyses of Peroxiredoxins and RF-Prx: A Random Forest-Based Predictor and Classifier for Prxs. Methods Mol Biol 2022;2499:155-176. [PMID: 35696080 PMCID: PMC9844236 DOI: 10.1007/978-1-0716-2317-6_8] [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: 01/19/2023]
9
Tang M, Wu L, Yu X, Chu Z, Jin S, Liu J. Prediction of Protein-Protein Interaction Sites Based on Stratified Attentional Mechanisms. Front Genet 2021;12:784863. [PMID: 34880910 PMCID: PMC8647646 DOI: 10.3389/fgene.2021.784863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/08/2021] [Indexed: 11/19/2022]  Open
10
Li Y, Golding GB, Ilie L. DELPHI: accurate deep ensemble model for protein interaction sites prediction. Bioinformatics 2021;37:896-904. [PMID: 32840562 DOI: 10.1093/bioinformatics/btaa750] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022]  Open
11
Islam MM, Alam MJ, Ahmed FF, Hasan MM, Mollah MNH. Improved Prediction of Protein-Protein Interaction Mapping on Homo Sapiens by Using Amino Acid Sequence Features in a Supervised Learning Framework. Protein Pept Lett 2021;28:74-83. [PMID: 32520672 DOI: 10.2174/0929866527666200610141258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023]
12
Zhang J, Ghadermarzi S, Kurgan L. Prediction of protein-binding residues: dichotomy of sequence-based methods developed using structured complexes versus disordered proteins. Bioinformatics 2021;36:4729-4738. [PMID: 32860044 DOI: 10.1093/bioinformatics/btaa573] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/22/2020] [Accepted: 06/10/2020] [Indexed: 01/08/2023]  Open
13
Zhang F, Shi W, Zhang J, Zeng M, Li M, Kurgan L. PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection. Bioinformatics 2020;36:i735-i744. [DOI: 10.1093/bioinformatics/btaa806] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 12/13/2022]  Open
14
Zhang J, Kurgan L. SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences. Bioinformatics 2020;35:i343-i353. [PMID: 31510679 PMCID: PMC6612887 DOI: 10.1093/bioinformatics/btz324] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
15
Arian R, Hariri A, Mehridehnavi A, Fassihi A, Ghasemi F. Protein kinase inhibitors' classification using K-Nearest neighbor algorithm. Comput Biol Chem 2020;86:107269. [PMID: 32413830 DOI: 10.1016/j.compbiolchem.2020.107269] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 03/15/2020] [Accepted: 04/20/2020] [Indexed: 10/24/2022]
16
RF-MaloSite and DL-Malosite: Methods based on random forest and deep learning to identify malonylation sites. Comput Struct Biotechnol J 2020;18:852-860. [PMID: 32322367 PMCID: PMC7160427 DOI: 10.1016/j.csbj.2020.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/27/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]  Open
17
Xie Z, Deng X, Shu K. Prediction of Protein-Protein Interaction Sites Using Convolutional Neural Network and Improved Data Sets. Int J Mol Sci 2020;21:E467. [PMID: 31940793 PMCID: PMC7013409 DOI: 10.3390/ijms21020467] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/23/2019] [Accepted: 01/08/2020] [Indexed: 12/20/2022]  Open
18
Meruelo AD, Jacobus J, Idy E, Nguyen-Louie T, Brown G, Tapert SF. Early adolescent brain markers of late adolescent academic functioning. Brain Imaging Behav 2020;13:945-952. [PMID: 29911279 DOI: 10.1007/s11682-018-9912-2] [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] [Indexed: 11/29/2022]
19
Using Naive Bayes Classifier to predict osteonecrosis of the femoral head with cannulated screw fixation. Injury 2018;49:1865-1870. [PMID: 30097310 DOI: 10.1016/j.injury.2018.07.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 07/03/2018] [Accepted: 07/26/2018] [Indexed: 02/02/2023]
20
Zhang J, Kurgan L. Review and comparative assessment of sequence-based predictors of protein-binding residues. Brief Bioinform 2017;19:821-837. [DOI: 10.1093/bib/bbx022] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Indexed: 12/31/2022]  Open
21
Cai Y, Liao Z, Ju Y, Liu J, Mao Y, Liu X. Resistance gene identification from Larimichthys crocea with machine learning techniques. Sci Rep 2016;6:38367. [PMID: 27922074 PMCID: PMC5138596 DOI: 10.1038/srep38367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/08/2016] [Indexed: 12/11/2022]  Open
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