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For: Zuo YC, Chen W, Fan GL, Li QZ. A similarity distance of diversity measure for discriminating mesophilic and thermophilic proteins. Amino Acids 2012;44:573-80. [PMID: 22851052 DOI: 10.1007/s00726-012-1374-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 07/17/2012] [Indexed: 11/25/2022]
Number Cited by Other Article(s)
1
Yu H, Luo X. ThermoFinder: A sequence-based thermophilic proteins prediction framework. Int J Biol Macromol 2024;270:132469. [PMID: 38761901 DOI: 10.1016/j.ijbiomac.2024.132469] [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: 03/17/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024]
2
Huang A, Chen Z, Wu X, Yan W, Lu F, Liu F. Improving the thermal stability and catalytic activity of ulvan lyase by the combination of FoldX and KnowVolution campaign. Int J Biol Macromol 2024;257:128577. [PMID: 38070809 DOI: 10.1016/j.ijbiomac.2023.128577] [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: 08/09/2023] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 01/26/2024]
3
Li J, He X, Gao S, Liang Y, Qi Z, Xi Q, Zuo Y, Xing Y. The Metal-binding Protein Atlas (MbPA): an integrated database for curating metalloproteins in all aspects. J Mol Biol 2023:168117. [PMID: 37086947 DOI: 10.1016/j.jmb.2023.168117] [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: 10/29/2022] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/24/2023]
4
Converting the genomic knowledge base to build protein specific machine learning prediction models; a classification study on thermophilic serine protease. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01214-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
5
SAPPHIRE: A stacking-based ensemble learning framework for accurate prediction of thermophilic proteins. Comput Biol Med 2022;146:105704. [PMID: 35690478 DOI: 10.1016/j.compbiomed.2022.105704] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/15/2022] [Accepted: 06/04/2022] [Indexed: 11/22/2022]
6
Charoenkwan P, Schaduangrat N, Hasan MM, Moni MA, Lió P, Shoombuatong W. Empirical comparison and analysis of machine learning-based predictors for predicting and analyzing of thermophilic proteins. EXCLI JOURNAL 2022;21:554-570. [PMID: 35651661 PMCID: PMC9150013 DOI: 10.17179/excli2022-4723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/21/2022] [Indexed: 12/15/2022]
7
Ahmed Z, Zulfiqar H, Khan AA, Gul I, Dao FY, Zhang ZY, Yu XL, Tang L. iThermo: A Sequence-Based Model for Identifying Thermophilic Proteins Using a Multi-Feature Fusion Strategy. Front Microbiol 2022;13:790063. [PMID: 35273581 PMCID: PMC8902591 DOI: 10.3389/fmicb.2022.790063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/10/2022] [Indexed: 01/20/2023]  Open
8
Charoenkwan P, Chotpatiwetchkul W, Lee VS, Nantasenamat C, Shoombuatong W. A novel sequence-based predictor for identifying and characterizing thermophilic proteins using estimated propensity scores of dipeptides. Sci Rep 2021;11:23782. [PMID: 34893688 PMCID: PMC8664844 DOI: 10.1038/s41598-021-03293-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/01/2021] [Indexed: 02/08/2023]  Open
9
Wang H, Xi Q, Liang P, Zheng L, Hong Y, Zuo Y. IHEC_RAAC: a online platform for identifying human enzyme classes via reduced amino acid cluster strategy. Amino Acids 2021;53:239-251. [PMID: 33486591 DOI: 10.1007/s00726-021-02941-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/11/2021] [Indexed: 12/18/2022]
10
Wang XF, Gao P, Liu YF, Li HF, Lu F. Predicting Thermophilic Proteins by Machine Learning. Curr Bioinform 2020. [DOI: 10.2174/1574893615666200207094357] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
11
Sun Z, Huang S, Zheng L, Liang P, Yang W, Zuo Y. ICTC-RAAC: An improved web predictor for identifying the types of ion channel-targeted conotoxins by using reduced amino acid cluster descriptors. Comput Biol Chem 2020;89:107371. [PMID: 32950852 DOI: 10.1016/j.compbiolchem.2020.107371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/27/2022]
12
Wu L, Hu Y, Zhang X, Chen W, Yu ASL, Kellum JA, Waitman LR, Liu M. Changing relative risk of clinical factors for hospital-acquired acute kidney injury across age groups: a retrospective cohort study. BMC Nephrol 2020;21:321. [PMID: 32741377 PMCID: PMC7397647 DOI: 10.1186/s12882-020-01980-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022]  Open
13
Gado JE, Beckham GT, Payne CM. Improving Enzyme Optimum Temperature Prediction with Resampling Strategies and Ensemble Learning. J Chem Inf Model 2020;60:4098-4107. [DOI: 10.1021/acs.jcim.0c00489] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
14
Feng C, Ma Z, Yang D, Li X, Zhang J, Li Y. A Method for Prediction of Thermophilic Protein Based on Reduced Amino Acids and Mixed Features. Front Bioeng Biotechnol 2020;8:285. [PMID: 32432088 PMCID: PMC7214540 DOI: 10.3389/fbioe.2020.00285] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/18/2020] [Indexed: 11/13/2022]  Open
15
Fu X, Yang Y. WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning. QUANTITATIVE BIOLOGY 2019. [DOI: 10.1007/s40484-019-0184-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
16
Fang X, Huang J, Zhang R, Wang F, Zhang Q, Li G, Yan J, Zhang H, Yan Y, Xu L. Convolution Neural Network-Based Prediction of Protein Thermostability. J Chem Inf Model 2019;59:4833-4843. [PMID: 31657922 DOI: 10.1021/acs.jcim.9b00220] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
17
Zuo Y, Chang Y, Huang S, Zheng L, Yang L, Cao G. iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor. Evol Bioinform Online 2019;15:1176934319867088. [PMID: 31391777 PMCID: PMC6669840 DOI: 10.1177/1176934319867088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/08/2019] [Indexed: 11/18/2022]  Open
18
Pan Z, Zhang H, Liang C, Li G, Xiao Q, Ding P, Luo J. Self-Weighted Multi-Kernel Multi-Label Learning for Potential miRNA-Disease Association Prediction. MOLECULAR THERAPY-NUCLEIC ACIDS 2019;17:414-423. [PMID: 31319245 PMCID: PMC6637211 DOI: 10.1016/j.omtn.2019.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/22/2019] [Accepted: 06/12/2019] [Indexed: 11/23/2022]
19
Panja AS, Nag A, Bandopadhyay B, Maiti S. Protein Stability Determination (PSD): A Tool for Proteomics Analysis. Curr Bioinform 2018. [DOI: 10.2174/1574893613666180315121614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
20
Lai HY, Chen XX, Chen W, Tang H, Lin H. Sequence-based predictive modeling to identify cancerlectins. Oncotarget 2018;8:28169-28175. [PMID: 28423655 PMCID: PMC5438640 DOI: 10.18632/oncotarget.15963] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/24/2017] [Indexed: 11/25/2022]  Open
21
Tang H, Cao RZ, Wang W, Liu TS, Wang LM, He CM. A two-step discriminated method to identify thermophilic proteins. INT J BIOMATH 2017. [DOI: 10.1142/s1793524517500504] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
22
Fan GL, Liu YL, Wang H. Identification of thermophilic proteins by incorporating evolutionary and acid dissociation information into Chou's general pseudo amino acid composition. J Theor Biol 2016;407:138-142. [DOI: 10.1016/j.jtbi.2016.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/24/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
23
iDPF-PseRAAAC: A Web-Server for Identifying the Defensin Peptide Family and Subfamily Using Pseudo Reduced Amino Acid Alphabet Composition. PLoS One 2015;10:e0145541. [PMID: 26713618 PMCID: PMC4694767 DOI: 10.1371/journal.pone.0145541] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/04/2015] [Indexed: 11/29/2022]  Open
24
Zuo YC, Su WX, Zhang SH, Wang SS, Wu CY, Yang L, Li GP. Discrimination of membrane transporter protein types using K-nearest neighbor method derived from the similarity distance of total diversity measure. MOLECULAR BIOSYSTEMS 2015;11:950-7. [PMID: 25607774 DOI: 10.1039/c4mb00681j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
25
Zuo YC, Peng Y, Liu L, Chen W, Yang L, Fan GL. Predicting peroxidase subcellular location by hybridizing different descriptors of Chou’ pseudo amino acid patterns. Anal Biochem 2014;458:14-9. [DOI: 10.1016/j.ab.2014.04.032] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 04/22/2014] [Accepted: 04/25/2014] [Indexed: 11/28/2022]
26
Wang L, Li C. Optimal subset selection of primary sequence features using the genetic algorithm for thermophilic proteins identification. Biotechnol Lett 2014;36:1963-9. [PMID: 24930111 DOI: 10.1007/s10529-014-1577-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2022]
27
Human proteins characterization with subcellular localizations. J Theor Biol 2014;358:61-73. [PMID: 24862400 DOI: 10.1016/j.jtbi.2014.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 05/04/2014] [Accepted: 05/05/2014] [Indexed: 11/20/2022]
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