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For: Ding Y, Cai Y, Zhang G, Xu W. The influence of dipeptide composition on protein thermostability. FEBS Lett 2004;569:284-8. [PMID: 15225649 DOI: 10.1016/j.febslet.2004.06.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Accepted: 06/03/2004] [Indexed: 11/15/2022]
Number Cited by Other Article(s)
1
Teimouri H, Medvedeva A, Kolomeisky AB. Unraveling the role of physicochemical differences in predicting protein-protein interactions. J Chem Phys 2024;161:045102. [PMID: 39051836 DOI: 10.1063/5.0219501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024]  Open
2
Rodella C, Lazaridi S, Lemmin T. TemBERTure: advancing protein thermostability prediction with deep learning and attention mechanisms. BIOINFORMATICS ADVANCES 2024;4:vbae103. [PMID: 39040220 PMCID: PMC11262459 DOI: 10.1093/bioadv/vbae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/14/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024]
3
Karim T, Shaon MSH, Sultan MF, Hasan MZ, Kafy AA. ANNprob-ACPs: A novel anticancer peptide identifier based on probabilistic feature fusion approach. Comput Biol Med 2024;169:107915. [PMID: 38171261 DOI: 10.1016/j.compbiomed.2023.107915] [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: 08/20/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024]
4
Yang B, Wang L, Bao W. Identify Diabetes-related Targets based on ForgeNet_GPC. Curr Comput Aided Drug Des 2024;20:1042-1054. [PMID: 38173214 DOI: 10.2174/0115734099258183230929173855] [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: 05/15/2023] [Revised: 08/06/2023] [Accepted: 08/15/2023] [Indexed: 01/05/2024]
5
Yan J, Zhang B, Zhou M, Campbell-Valois FX, Siu SWI. A deep learning method for predicting the minimum inhibitory concentration of antimicrobial peptides against Escherichia coli using Multi-Branch-CNN and Attention. mSystems 2023;8:e0034523. [PMID: 37431995 PMCID: PMC10506472 DOI: 10.1128/msystems.00345-23] [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: 04/19/2023] [Accepted: 05/31/2023] [Indexed: 07/12/2023]  Open
6
El-Behery H, Attia AF, El-Fishawy N, Torkey H. An ensemble-based drug-target interaction prediction approach using multiple feature information with data balancing. J Biol Eng 2022;16:21. [PMID: 35941686 PMCID: PMC9361677 DOI: 10.1186/s13036-022-00296-7] [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: 02/02/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022]  Open
7
Yan J, Zhang B, Zhou M, Kwok HF, Siu SWI. Multi-Branch-CNN: Classification of ion channel interacting peptides using multi-branch convolutional neural network. Comput Biol Med 2022;147:105717. [PMID: 35752114 DOI: 10.1016/j.compbiomed.2022.105717] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 05/18/2022] [Accepted: 06/05/2022] [Indexed: 11/03/2022]
8
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: 20] [Impact Index Per Article: 6.7] [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
9
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: 31] [Impact Index Per Article: 7.8] [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
10
Chen YZ, Wang ZZ, Wang Y, Ying G, Chen Z, Song J. nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. Brief Bioinform 2021;22:6277413. [PMID: 34002774 DOI: 10.1093/bib/bbab146] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022]  Open
11
Abdel-Naby MA, El-Wafa WMA, Salem GEM. Molecular characterization, catalytic, kinetic and thermodynamic properties of protease produced by a mutant of Bacillus cereus-S6-3. Int J Biol Macromol 2020;160:695-702. [PMID: 32485254 DOI: 10.1016/j.ijbiomac.2020.05.241] [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: 01/29/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/19/2023]
12
Wang L, Wang M, Shi X, Yang J, Qian C, Liu Q, Zong L, Liu X, Zhu Z, Tang D, Zhang X. Investigation into archaeal extremophilic lifestyles through comparative proteogenomic analysis. J Biomol Struct Dyn 2020;39:7080-7092. [PMID: 32820705 DOI: 10.1080/07391102.2020.1808531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
13
Yu Z, Shi D, Liu W, Meng Y, Meng F. Metabolome responses of Enterococcus faecium to acid shock and nitrite stress. Biotechnol Bioeng 2020;117:3559-3571. [PMID: 32662876 DOI: 10.1002/bit.27497] [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: 04/25/2020] [Revised: 06/26/2020] [Accepted: 07/08/2020] [Indexed: 01/21/2023]
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: 17] [Impact Index Per Article: 3.4] [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
Manavalan B, Subramaniyam S, Shin TH, Kim MO, Lee G. Machine-Learning-Based Prediction of Cell-Penetrating Peptides and Their Uptake Efficiency with Improved Accuracy. J Proteome Res 2018;17:2715-2726. [PMID: 29893128 DOI: 10.1021/acs.jproteome.8b00148] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
16
A novel strategy to improve the thermostability of Penicillium camembertii mono- and di-acylglycerol lipase. Biochem Biophys Res Commun 2018;500:639-644. [DOI: 10.1016/j.bbrc.2018.04.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 04/14/2018] [Indexed: 01/24/2023]
17
Meher PK, Sahu TK, Mohanty J, Gahoi S, Purru S, Grover M, Rao AR. nifPred: Proteome-Wide Identification and Categorization of Nitrogen-Fixation Proteins of Diaztrophs Based on Composition-Transition-Distribution Features Using Support Vector Machine. Front Microbiol 2018;9:1100. [PMID: 29896173 PMCID: PMC5986947 DOI: 10.3389/fmicb.2018.01100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/08/2018] [Indexed: 11/13/2022]  Open
18
Wang S, Yue Y. Protein subnuclear localization based on a new effective representation and intelligent kernel linear discriminant analysis by dichotomous greedy genetic algorithm. PLoS One 2018;13:e0195636. [PMID: 29649330 PMCID: PMC5896989 DOI: 10.1371/journal.pone.0195636] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/26/2018] [Indexed: 01/03/2023]  Open
19
Meher PK, Sahu TK, Gahoi S, Rao AR. ir-HSP: Improved Recognition of Heat Shock Proteins, Their Families and Sub-types Based On g-Spaced Di-peptide Features and Support Vector Machine. Front Genet 2018;8:235. [PMID: 29379521 PMCID: PMC5770798 DOI: 10.3389/fgene.2017.00235] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/27/2017] [Indexed: 12/24/2022]  Open
20
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: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
21
Meher PK, Sahu TK, Banchariya A, Rao AR. DIRProt: a computational approach for discriminating insecticide resistant proteins from non-resistant proteins. BMC Bioinformatics 2017;18:190. [PMID: 28340571 PMCID: PMC5364559 DOI: 10.1186/s12859-017-1587-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/09/2017] [Indexed: 02/06/2023]  Open
22
Protein Sub-Nuclear Localization Based on Effective Fusion Representations and Dimension Reduction Algorithm LDA. Int J Mol Sci 2015;16:30343-61. [PMID: 26703574 PMCID: PMC4691178 DOI: 10.3390/ijms161226237] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/07/2015] [Accepted: 12/11/2015] [Indexed: 01/01/2023]  Open
23
Govindan G, Nair AS. Bagging with CTD--a novel signature for the hierarchical prediction of secreted protein trafficking in eukaryotes. GENOMICS PROTEOMICS & BIOINFORMATICS 2013;11:385-90. [PMID: 24316328 PMCID: PMC4357838 DOI: 10.1016/j.gpb.2013.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 07/01/2013] [Accepted: 07/17/2013] [Indexed: 11/19/2022]
24
Support vector machine with a Pearson VII function kernel for discriminating halophilic and non-halophilic proteins. Comput Biol Chem 2013;46:16-22. [DOI: 10.1016/j.compbiolchem.2013.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 04/24/2013] [Accepted: 05/03/2013] [Indexed: 01/15/2023]
25
Determination of amino acids and dipeptides is correlated significantly with optimum temperatures of microbial lipases. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-012-0475-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]  Open
26
Van Damme P, Hole K, Pimenta-Marques A, Helsens K, Vandekerckhove J, Martinho RG, Gevaert K, Arnesen T. NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation. PLoS Genet 2011;7:e1002169. [PMID: 21750686 PMCID: PMC3131286 DOI: 10.1371/journal.pgen.1002169] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 05/20/2011] [Indexed: 01/31/2023]  Open
27
Ma X, Guo J, Wu J, Liu H, Yu J, Xie J, Sun X. Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature. Proteins 2011;79:1230-9. [DOI: 10.1002/prot.22958] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 11/02/2010] [Accepted: 11/24/2010] [Indexed: 11/10/2022]
28
New Feature Vector for Apoptosis Protein Subcellular Localization Prediction. ADVANCES IN COMPUTING AND COMMUNICATIONS 2011. [DOI: 10.1007/978-3-642-22709-7_30] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
29
Chakravorty D, Parameswaran S, Dubey VK, Patra S. In silico characterization of thermostable lipases. Extremophiles 2010;15:89-103. [PMID: 21153672 DOI: 10.1007/s00792-010-0337-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 11/15/2010] [Indexed: 11/28/2022]
30
Lin H, Chen W. Prediction of thermophilic proteins using feature selection technique. J Microbiol Methods 2010;84:67-70. [PMID: 21044646 DOI: 10.1016/j.mimet.2010.10.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/15/2010] [Accepted: 10/19/2010] [Indexed: 11/16/2022]
31
Wang J, Wang J, Gong X, Zheng G. A novel esterase Sso2518 from Sulfolobus solfataricus with a much lower temperature optimum than the growth temperature. Biotechnol Lett 2010;32:1103-8. [DOI: 10.1007/s10529-010-0261-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 03/23/2010] [Indexed: 10/19/2022]
32
Gromiha MM, Suresh MX. Discrimination of mesophilic and thermophilic proteins using machine learning algorithms. Proteins 2008;70:1274-9. [PMID: 17876820 DOI: 10.1002/prot.21616] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
33
Zhang G, Fang B. The influence of dipeptide composition on optimum temperature of alcohol dehydrogenase. Enzyme Microb Technol 2006. [DOI: 10.1016/j.enzmictec.2006.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
34
Zhang G, Fang B. Application of amino acid distribution along the sequence for discriminating mesophilic and thermophilic proteins. Process Biochem 2006. [DOI: 10.1016/j.procbio.2006.03.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
35
Liu L, Dong H, Wang S, Chen H, Shao W. Computational analysis of di-peptides correlated with the optimal temperature in G/11 xylanase. Process Biochem 2006. [DOI: 10.1016/j.procbio.2005.06.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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