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For: Zhong WZ, Zhou SF. Molecular science for drug development and biomedicine. Int J Mol Sci 2014;15:20072-8. [PMID: 25375190 PMCID: PMC4264156 DOI: 10.3390/ijms151120072] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 10/24/2014] [Indexed: 01/21/2023]  Open
Number Cited by Other Article(s)
1
Sarma H, Upadhyaya M, Gogoi B, Phukan M, Kashyap P, Das B, Devi R, Sharma HK. Cardiovascular Drugs: an Insight of In Silico Drug Design Tools. J Pharm Innov 2021. [DOI: 10.1007/s12247-021-09587-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
2
Rahman CR, Amin R, Shatabda S, Toaha MSI. A convolution based computational approach towards DNA N6-methyladenine site identification and motif extraction in rice genome. Sci Rep 2021;11:10357. [PMID: 33990665 PMCID: PMC8121938 DOI: 10.1038/s41598-021-89850-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 05/04/2021] [Indexed: 12/23/2022]  Open
3
Recent Advances in Predicting Protein S-Nitrosylation Sites. BIOMED RESEARCH INTERNATIONAL 2021;2021:5542224. [PMID: 33628788 PMCID: PMC7892234 DOI: 10.1155/2021/5542224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 01/09/2023]
4
Khan YD, Alzahrani E, Alghamdi W, Ullah MZ. Sequence-based Identification of Allergen Proteins Developed by Integration of PseAAC and Statistical Moments via 5-Step Rule. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200424085947] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
5
Shechter S, Thomas DR, Jans DA. Application of In Silico and HTS Approaches to Identify Nuclear Import Inhibitors for Venezuelan Equine Encephalitis Virus Capsid Protein: A Case Study. Front Chem 2020;8:573121. [PMID: 33505952 PMCID: PMC7832173 DOI: 10.3389/fchem.2020.573121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/12/2020] [Indexed: 01/16/2023]  Open
6
Progresses in Predicting Post-translational Modification. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09893-5
https://link.springer.com/article/10.1007%2fs10989-019-09893-5
] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
7
Some illuminating remarks on molecular genetics and genomics as well as drug development. Mol Genet Genomics 2020;295:261-274. [PMID: 31894399 DOI: 10.1007/s00438-019-01634-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
8
Chou KC. Advances in Predicting Subcellular Localization of Multi-label Proteins and its Implication for Developing Multi-target Drugs. Curr Med Chem 2019;26:4918-4943. [PMID: 31060481 DOI: 10.2174/0929867326666190507082559] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/16/2022]
9
Chou KC. Advances in Predicting Subcellular Localization of Multi-label Proteins and its Implication for Developing Multi-target Drugs. Curr Med Chem 2019. [DOI: 10.2174/0929867326666190507082559
http://www.eurekaselect.com/172010/article
] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
10
Chou KC. Progresses in Predicting Post-translational Modification. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09893-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
11
Cheng X, Xiao X, Chou KC. pLoc_bal-mGneg: Predict subcellular localization of Gram-negative bacterial proteins by quasi-balancing training dataset and general PseAAC. J Theor Biol 2018;458:92-102. [DOI: 10.1016/j.jtbi.2018.09.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 01/03/2023]
12
Ning Q, Zhao X, Bao L, Ma Z, Zhao X. Detecting Succinylation sites from protein sequences using ensemble support vector machine. BMC Bioinformatics 2018;19:237. [PMID: 29940836 PMCID: PMC6016146 DOI: 10.1186/s12859-018-2249-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 06/14/2018] [Indexed: 12/14/2022]  Open
13
Chen W, Feng P, Yang H, Ding H, Lin H, Chou KC. iRNA-3typeA: Identifying Three Types of Modification at RNA's Adenosine Sites. MOLECULAR THERAPY. NUCLEIC ACIDS 2018;11:468-474. [PMID: 29858081 PMCID: PMC5992483 DOI: 10.1016/j.omtn.2018.03.012] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/25/2018] [Accepted: 03/27/2018] [Indexed: 01/09/2023]
14
Khan YD, Rasool N, Hussain W, Khan SA, Chou KC. iPhosT-PseAAC: Identify phosphothreonine sites by incorporating sequence statistical moments into PseAAC. Anal Biochem 2018;550:109-116. [DOI: 10.1016/j.ab.2018.04.021] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/19/2018] [Accepted: 04/21/2018] [Indexed: 01/29/2023]
15
Yang H, Qiu WR, Liu G, Guo FB, Chen W, Chou KC, Lin H. iRSpot-Pse6NC: Identifying recombination spots in Saccharomyces cerevisiae by incorporating hexamer composition into general PseKNC. Int J Biol Sci 2018;14:883-891. [PMID: 29989083 PMCID: PMC6036749 DOI: 10.7150/ijbs.24616] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/04/2018] [Indexed: 02/06/2023]  Open
16
Song J, Li F, Takemoto K, Haffari G, Akutsu T, Chou KC, Webb GI. PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework. J Theor Biol 2018;443:125-137. [DOI: 10.1016/j.jtbi.2018.01.023] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/17/2018] [Accepted: 01/18/2018] [Indexed: 10/18/2022]
17
Xu L, Liang G, Wang L, Liao C. A Novel Hybrid Sequence-Based Model for Identifying Anticancer Peptides. Genes (Basel) 2018. [PMID: 29534013 PMCID: PMC5867879 DOI: 10.3390/genes9030158] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
18
Qiu WR, Sun BQ, Xiao X, Xu ZC, Chou KC. iHyd-PseCp: Identify hydroxyproline and hydroxylysine in proteins by incorporating sequence-coupled effects into general PseAAC. Oncotarget 2018;7:44310-44321. [PMID: 27322424 PMCID: PMC5190098 DOI: 10.18632/oncotarget.10027] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/29/2016] [Indexed: 12/30/2022]  Open
19
iOri-Human: identify human origin of replication by incorporating dinucleotide physicochemical properties into pseudo nucleotide composition. Oncotarget 2018;7:69783-69793. [PMID: 27626500 PMCID: PMC5342515 DOI: 10.18632/oncotarget.11975] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/06/2016] [Indexed: 02/07/2023]  Open
20
Pan G, Jiang L, Tang J, Guo F. A Novel Computational Method for Detecting DNA Methylation Sites with DNA Sequence Information and Physicochemical Properties. Int J Mol Sci 2018;19:ijms19020511. [PMID: 29419752 PMCID: PMC5855733 DOI: 10.3390/ijms19020511] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 02/06/2023]  Open
21
Qiu WR, Xiao X, Xu ZC, Chou KC. iPhos-PseEn: identifying phosphorylation sites in proteins by fusing different pseudo components into an ensemble classifier. Oncotarget 2018;7:51270-51283. [PMID: 27323404 PMCID: PMC5239474 DOI: 10.18632/oncotarget.9987] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/23/2016] [Indexed: 11/26/2022]  Open
22
Feng P, Yang H, Ding H, Lin H, Chen W, Chou KC. iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC. Genomics 2018;111:96-102. [PMID: 29360500 DOI: 10.1016/j.ygeno.2018.01.005] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/24/2017] [Accepted: 01/07/2018] [Indexed: 11/29/2022]
23
Jia J, Liu Z, Xiao X, Liu B, Chou KC. iCar-PseCp: identify carbonylation sites in proteins by Monte Carlo sampling and incorporating sequence coupled effects into general PseAAC. Oncotarget 2018;7:34558-70. [PMID: 27153555 PMCID: PMC5085176 DOI: 10.18632/oncotarget.9148] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 04/09/2016] [Indexed: 01/22/2023]  Open
24
iACP: a sequence-based tool for identifying anticancer peptides. Oncotarget 2017;7:16895-909. [PMID: 26942877 PMCID: PMC4941358 DOI: 10.18632/oncotarget.7815] [Citation(s) in RCA: 312] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/11/2016] [Indexed: 02/07/2023]  Open
25
Cheng X, Xiao X, Chou KC. pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information. Bioinformatics 2017;34:1448-1456. [DOI: 10.1093/bioinformatics/btx711] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/31/2017] [Indexed: 01/19/2023]  Open
26
Du QS, Wang SQ, Xie NZ, Wang QY, Huang RB, Chou KC. 2L-PCA: a two-level principal component analyzer for quantitative drug design and its applications. Oncotarget 2017;8:70564-70578. [PMID: 29050302 PMCID: PMC5642577 DOI: 10.18632/oncotarget.19757] [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: 04/26/2017] [Accepted: 06/30/2017] [Indexed: 01/25/2023]  Open
27
Highly accurate prediction of protein self-interactions by incorporating the average block and PSSM information into the general PseAAC. J Theor Biol 2017;432:80-86. [PMID: 28802824 DOI: 10.1016/j.jtbi.2017.08.009] [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] [Received: 05/12/2017] [Revised: 08/05/2017] [Accepted: 08/08/2017] [Indexed: 11/23/2022]
28
He L, Li Y, He RL, Yau SST. A novel alignment-free vector method to cluster protein sequences. J Theor Biol 2017;427:41-52. [DOI: 10.1016/j.jtbi.2017.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/04/2017] [Accepted: 06/02/2017] [Indexed: 11/29/2022]
29
Ju Z, He JJ. Prediction of lysine propionylation sites using biased SVM and incorporating four different sequence features into Chou's PseAAC. J Mol Graph Model 2017;76:356-363. [PMID: 28763688 DOI: 10.1016/j.jmgm.2017.07.022] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 12/21/2022]
30
Protein Sequence Comparison Based on Physicochemical Properties and the Position-Feature Energy Matrix. Sci Rep 2017;7:46237. [PMID: 28393857 PMCID: PMC5385872 DOI: 10.1038/srep46237] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/14/2017] [Indexed: 11/08/2022]  Open
31
Jiao YS, Du PF. Predicting protein submitochondrial locations by incorporating the positional-specific physicochemical properties into Chou's general pseudo-amino acid compositions. J Theor Biol 2017;416:81-87. [DOI: 10.1016/j.jtbi.2016.12.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/06/2016] [Accepted: 12/30/2016] [Indexed: 11/26/2022]
32
Zhou SF, Zhong WZ. Drug Design and Discovery: Principles and Applications. Molecules 2017;22:molecules22020279. [PMID: 28208821 PMCID: PMC6155886 DOI: 10.3390/molecules22020279] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 12/23/2022]  Open
33
OOgenesis_Pred: A sequence-based method for predicting oogenesis proteins by six different modes of Chou's pseudo amino acid composition. J Theor Biol 2017;414:128-136. [DOI: 10.1016/j.jtbi.2016.11.028] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 11/25/2016] [Accepted: 11/29/2016] [Indexed: 12/22/2022]
34
Xiao X, Cheng X, Su S, Mao Q, Chou KC. pLoc-mGpos: Incorporate Key Gene Ontology Information into General PseAAC for Predicting Subcellular Localization of Gram-Positive Bacterial Proteins. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/ns.2017.99032] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
35
Behbahani M, Mohabatkar H, Nosrati M. Analysis and comparison of lignin peroxidases between fungi and bacteria using three different modes of Chou’s general pseudo amino acid composition. J Theor Biol 2016;411:1-5. [DOI: 10.1016/j.jtbi.2016.09.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/27/2016] [Accepted: 09/01/2016] [Indexed: 02/02/2023]
36
Zuo Y, Li Y, Chen Y, Li G, Yan Z, Yang L. PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition. Bioinformatics 2016;33:122-124. [DOI: 10.1093/bioinformatics/btw564] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/11/2016] [Accepted: 08/24/2016] [Indexed: 11/14/2022]  Open
37
Xu C, Sun D, Liu S, Zhang Y. Protein sequence analysis by incorporating modified chaos game and physicochemical properties into Chou's general pseudo amino acid composition. J Theor Biol 2016;406:105-15. [PMID: 27375218 DOI: 10.1016/j.jtbi.2016.06.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 06/17/2016] [Accepted: 06/25/2016] [Indexed: 11/27/2022]
38
Jia J, Zhang L, Liu Z, Xiao X, Chou KC. pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC. Bioinformatics 2016;32:3133-3141. [DOI: 10.1093/bioinformatics/btw387] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/15/2016] [Indexed: 11/13/2022]  Open
39
Qiu WR, Sun BQ, Xiao X, Xu ZC, Chou KC. iPTM-mLys: identifying multiple lysine PTM sites and their different types. Bioinformatics 2016;32:3116-3123. [DOI: 10.1093/bioinformatics/btw380] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 06/13/2016] [Indexed: 11/13/2022]  Open
40
Application of Euclidean distance measurement and principal component analysis for gene identification. Gene 2016;583:112-120. [DOI: 10.1016/j.gene.2016.02.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/27/2015] [Accepted: 02/07/2016] [Indexed: 11/22/2022]
41
Qiu WR, Sun BQ, Xiao X, Xu D, Chou KC. iPhos-PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory. Mol Inform 2016;36. [DOI: 10.1002/minf.201600010] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/05/2016] [Indexed: 01/04/2023]
42
Antony EJ, Shibu A, Ramasamy S, Paulraj MS, Enoch IVMV. Loading of atorvastatin and linezolid in β-cyclodextrin-conjugated cadmium selenide/silica nanoparticles: A spectroscopic study. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016;65:194-8. [PMID: 27157743 DOI: 10.1016/j.msec.2016.04.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/12/2016] [Accepted: 04/11/2016] [Indexed: 11/25/2022]
43
Jia J, Liu Z, Xiao X, Liu B, Chou KC. pSuc-Lys: Predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach. J Theor Biol 2016;394:223-230. [DOI: 10.1016/j.jtbi.2016.01.020] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
44
iSuc-PseOpt: Identifying lysine succinylation sites in proteins by incorporating sequence-coupling effects into pseudo components and optimizing imbalanced training dataset. Anal Biochem 2016;497:48-56. [DOI: 10.1016/j.ab.2015.12.009] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/02/2015] [Accepted: 12/11/2015] [Indexed: 11/18/2022]
45
An estimator for local analysis of genome based on the minimal absent word. J Theor Biol 2016;395:23-30. [PMID: 26829314 DOI: 10.1016/j.jtbi.2016.01.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/17/2016] [Accepted: 01/19/2016] [Indexed: 11/22/2022]
46
iPPBS-Opt: A Sequence-Based Ensemble Classifier for Identifying Protein-Protein Binding Sites by Optimizing Imbalanced Training Datasets. Molecules 2016;21:E95. [PMID: 26797600 PMCID: PMC6274413 DOI: 10.3390/molecules21010095] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/18/2015] [Accepted: 01/07/2016] [Indexed: 12/25/2022]  Open
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Ju Z, Cao JZ, Gu H. iLM-2L: A two-level predictor for identifying protein lysine methylation sites and their methylation degrees by incorporating K-gap amino acid pairs into Chou׳s general PseAAC. J Theor Biol 2015;385:50-7. [DOI: 10.1016/j.jtbi.2015.07.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/06/2015] [Accepted: 07/23/2015] [Indexed: 10/23/2022]
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Ahmad S, Kabir M, Hayat M. Identification of Heat Shock Protein families and J-protein types by incorporating Dipeptide Composition into Chou's general PseAAC. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2015;122:165-174. [PMID: 26233307 DOI: 10.1016/j.cmpb.2015.07.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/21/2015] [Accepted: 07/13/2015] [Indexed: 06/04/2023]
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Jia J, Liu Z, Xiao X, Liu B, Chou KC. Identification of protein-protein binding sites by incorporating the physicochemical properties and stationary wavelet transforms into pseudo amino acid composition. J Biomol Struct Dyn 2015;34:1946-61. [PMID: 26375780 DOI: 10.1080/07391102.2015.1095116] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Fan GL, Zhang XY, Liu YL, Nang Y, Wang H. DSPMP: Discriminating secretory proteins of malaria parasite by hybridizing different descriptors of Chou's pseudo amino acid patterns. J Comput Chem 2015;36:2317-27. [PMID: 26484844 DOI: 10.1002/jcc.24210] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/20/2015] [Accepted: 08/23/2015] [Indexed: 12/28/2022]
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