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For: Lin HH, Han LY, Zhang HL, Zheng CJ, Xie B, Cao ZW, Chen YZ. Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach. BMC Bioinformatics 2006;7 Suppl 5:S13. [PMID: 17254297 PMCID: PMC1764469 DOI: 10.1186/1471-2105-7-s5-s13] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
Number Cited by Other Article(s)
1
Wu YT, Lu PW, Lin CA, Chang LY, Jaihao C, Peng TY, Lee WF, Teng NC, Lee SY, Dwivedi RP, Negi P, Yang JC. Development of a zinc chloride-based chemo-mechanical system for potential minimally invasive dental caries removal system. J Dent Sci 2024;19:919-928. [PMID: 38618085 PMCID: PMC11010630 DOI: 10.1016/j.jds.2023.08.004] [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: 07/07/2023] [Revised: 08/01/2023] [Indexed: 04/16/2024]  Open
2
Brix KV, Baken S, Poland CA, Blust R, Pope LJ, Tyler CR. Challenges and Recommendations in Assessing Potential Endocrine-Disrupting Properties of Metals in Aquatic Organisms. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023;42:2564-2579. [PMID: 37671843 DOI: 10.1002/etc.5741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/25/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023]
3
Zhang J, Zhou F, Liang X, Yang G. SCAMPER: Accurate Type-Specific Prediction of Calcium-Binding Residues Using Sequence-Derived Features. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:1406-1416. [PMID: 35536812 DOI: 10.1109/tcbb.2022.3173437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
4
Sun K, Hu X, Feng Z, Wang H, Lv H, Wang Z, Zhang G, Xu S, You X. Predicting Ca2+ and Mg2+ ligand binding sites by deep neural network algorithm. BMC Bioinformatics 2022;22:324. [PMID: 35045825 PMCID: PMC8772041 DOI: 10.1186/s12859-021-04250-0] [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: 05/30/2021] [Accepted: 06/09/2021] [Indexed: 11/25/2022]  Open
5
Zhou J, Bo S, Wang H, Zheng L, Liang P, Zuo Y. Identification of Disease-Related 2-Oxoglutarate/Fe (II)-Dependent Oxygenase Based on Reduced Amino Acid Cluster Strategy. Front Cell Dev Biol 2021;9:707938. [PMID: 34336861 PMCID: PMC8323781 DOI: 10.3389/fcell.2021.707938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]  Open
6
Stanton JE, Malijauskaite S, McGourty K, Grabrucker AM. The Metallome as a Link Between the "Omes" in Autism Spectrum Disorders. Front Mol Neurosci 2021;14:695873. [PMID: 34290588 PMCID: PMC8289253 DOI: 10.3389/fnmol.2021.695873] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/14/2021] [Indexed: 12/26/2022]  Open
7
Ireland SM, Martin ACR. Zincbindpredict-Prediction of Zinc Binding Sites in Proteins. Molecules 2021;26:molecules26040966. [PMID: 33673040 PMCID: PMC7918553 DOI: 10.3390/molecules26040966] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/26/2021] [Accepted: 02/09/2021] [Indexed: 11/21/2022]  Open
8
Grosjean N, Blaby-Haas CE. Leveraging computational genomics to understand the molecular basis of metal homeostasis. THE NEW PHYTOLOGIST 2020;228:1472-1489. [PMID: 32696981 DOI: 10.1111/nph.16820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
9
Liu L, Hu X, Feng Z, Wang S, Sun K, Xu S. Recognizing Ion Ligand-Binding Residues by Random Forest Algorithm Based on Optimized Dihedral Angle. Front Bioeng Biotechnol 2020;8:493. [PMID: 32596216 PMCID: PMC7303464 DOI: 10.3389/fbioe.2020.00493] [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: 12/20/2019] [Accepted: 04/28/2020] [Indexed: 11/26/2022]  Open
10
Xi B, Tao J, Liu X, Xu X, He P, Dai Q. RaaMLab: A MATLAB toolbox that generates amino acid groups and reduced amino acid modes. Biosystems 2019;180:38-45. [PMID: 30904554 DOI: 10.1016/j.biosystems.2019.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/25/2018] [Accepted: 03/06/2019] [Indexed: 01/31/2023]
11
Haberal İ, Oğul H. Prediction of Protein Metal Binding Sites Using Deep Neural Networks. Mol Inform 2019;38:e1800169. [PMID: 30977960 DOI: 10.1002/minf.201800169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/29/2019] [Indexed: 11/06/2022]
12
Greener JG, Moffat L, Jones DT. Design of metalloproteins and novel protein folds using variational autoencoders. Sci Rep 2018;8:16189. [PMID: 30385875 PMCID: PMC6212568 DOI: 10.1038/s41598-018-34533-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/19/2018] [Indexed: 12/26/2022]  Open
13
Shaik NA, Awan ZA, Verma PK, Elango R, Banaganapalli B. Protein phenotype diagnosis of autosomal dominant calmodulin mutations causing irregular heart rhythms. J Cell Biochem 2018;119:8233-8248. [PMID: 29932249 DOI: 10.1002/jcb.26834] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 03/09/2018] [Indexed: 12/21/2022]
14
Cao X, Hu X, Zhang X, Gao S, Ding C, Feng Y, Bao W. Identification of metal ion binding sites based on amino acid sequences. PLoS One 2017;12:e0183756. [PMID: 28854211 PMCID: PMC5576659 DOI: 10.1371/journal.pone.0183756] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/10/2017] [Indexed: 11/26/2022]  Open
15
Computational approaches for de novo design and redesign of metal-binding sites on proteins. Biosci Rep 2017;37:BSR20160179. [PMID: 28167677 PMCID: PMC5482196 DOI: 10.1042/bsr20160179] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 02/06/2017] [Accepted: 02/06/2017] [Indexed: 12/25/2022]  Open
16
Valasatava Y, Rosato A, Banci L, Andreini C. MetalPredator: a web server to predict iron-sulfur cluster binding proteomes. Bioinformatics 2016;32:2850-2. [PMID: 27273670 DOI: 10.1093/bioinformatics/btw238] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
17
Tiwari AK, Srivastava R. A survey of computational intelligence techniques in protein function prediction. INTERNATIONAL JOURNAL OF PROTEOMICS 2014;2014:845479. [PMID: 25574395 PMCID: PMC4276698 DOI: 10.1155/2014/845479] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/31/2014] [Accepted: 11/07/2014] [Indexed: 02/08/2023]
18
Mazumder M, Padhan N, Bhattacharya A, Gourinath S. Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity. PLoS One 2014;9:e96202. [PMID: 24760183 PMCID: PMC3997525 DOI: 10.1371/journal.pone.0096202] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/04/2014] [Indexed: 12/31/2022]  Open
19
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]
20
Zhou Y, Xue S, Yang JJ. Calciomics: integrative studies of Ca2+-binding proteins and their interactomes in biological systems. Metallomics 2013;5:29-42. [PMID: 23235533 DOI: 10.1039/c2mt20009k] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
21
Liu Z, Wang Y, Zhou C, Xue Y, Zhao W, Liu H. Computationally characterizing and comprehensive analysis of zinc-binding sites in proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013;1844:171-80. [PMID: 23499845 DOI: 10.1016/j.bbapap.2013.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/02/2013] [Accepted: 03/04/2013] [Indexed: 10/27/2022]
22
An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins. PLoS One 2012;7:e49716. [PMID: 23166753 PMCID: PMC3499040 DOI: 10.1371/journal.pone.0049716] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 10/12/2012] [Indexed: 11/30/2022]  Open
23
Lim CK, Hassan KA, Penesyan A, Loper JE, Paulsen IT. The effect of zinc limitation on the transcriptome ofPseudomonas protegens Pf-5. Environ Microbiol 2012;15:702-15. [DOI: 10.1111/j.1462-2920.2012.02849.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 07/09/2012] [Accepted: 07/21/2012] [Indexed: 02/03/2023]
24
Lu CH, Lin YF, Lin JJ, Yu CS. Prediction of metal ion-binding sites in proteins using the fragment transformation method. PLoS One 2012;7:e39252. [PMID: 22723976 PMCID: PMC3377655 DOI: 10.1371/journal.pone.0039252] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 05/21/2012] [Indexed: 11/19/2022]  Open
25
MOHAN ABHILASH, ANISHETTY SHARMILA, GAUTAM PENNATHUR. GLOBAL METAL-ION BINDING PROTEIN FINGERPRINT: A METHOD TO IDENTIFY MOTIF-LESS METAL-ION BINDING PROTEINS. J Bioinform Comput Biol 2011. [DOI: 10.1142/s0219720010004884] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
26
Zhao W, Xu M, Liang Z, Ding B, Niu L, Liu H, Teng M. Structure-based de novo prediction of zinc-binding sites in proteins of unknown function. ACTA ACUST UNITED AC 2011;27:1262-8. [PMID: 21414989 DOI: 10.1093/bioinformatics/btr133] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
27
Dutta A, Bahar I. Metal-binding sites are designed to achieve optimal mechanical and signaling properties. Structure 2011;18:1140-8. [PMID: 20826340 DOI: 10.1016/j.str.2010.06.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 05/21/2010] [Accepted: 06/17/2010] [Indexed: 11/29/2022]
28
Brylinski M, Skolnick J. FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins 2010;79:735-51. [PMID: 21287609 DOI: 10.1002/prot.22913] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 09/27/2010] [Accepted: 10/07/2010] [Indexed: 12/13/2022]
29
Wang X, Zhao K, Kirberger M, Wong H, Chen G, Yang JJ. Analysis and prediction of calcium-binding pockets from apo-protein structures exhibiting calcium-induced localized conformational changes. Protein Sci 2010;19:1180-90. [PMID: 20512971 DOI: 10.1002/pro.394] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
30
Kirberger M, Wang X, Zhao K, Tang S, Chen G, Yang JJ. Integration of Diverse Research Methods to Analyze and Engineer Ca-Binding Proteins: From Prediction to Production. Curr Bioinform 2010;5:68-80. [PMID: 20802832 PMCID: PMC2927018 DOI: 10.2174/157489310790596358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
31
Tang ZQ, Lin HH, Zhang HL, Han LY, Chen X, Chen YZ. Prediction of functional class of proteins and peptides irrespective of sequence homology by support vector machines. Bioinform Biol Insights 2009;1:19-47. [PMID: 20066123 PMCID: PMC2789692 DOI: 10.4137/bbi.s315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
32
Bertini I, Cavallaro G. Bioinformatics in bioinorganic chemistry. Metallomics 2009;2:39-51. [PMID: 21072373 DOI: 10.1039/b912156k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
33
Wang X, Kirberger M, Qiu F, Chen G, Yang JJ. Towards predicting Ca2+-binding sites with different coordination numbers in proteins with atomic resolution. Proteins 2009;75:787-98. [PMID: 19003991 DOI: 10.1002/prot.22285] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
34
Faria D, Ferreira AEN, Falcão AO. Enzyme classification with peptide programs: a comparative study. BMC Bioinformatics 2009;10:231. [PMID: 19630945 PMCID: PMC2724424 DOI: 10.1186/1471-2105-10-231] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 07/24/2009] [Indexed: 11/29/2022]  Open
35
Muthukrishnan S, Garg A, Raghava GPS. Oxypred: prediction and classification of oxygen-binding proteins. GENOMICS PROTEOMICS & BIOINFORMATICS 2008;5:250-2. [PMID: 18267306 PMCID: PMC5054225 DOI: 10.1016/s1672-0229(08)60012-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
36
Vilasi S, Ragone R. Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle. FEBS J 2008;275:763-74. [DOI: 10.1111/j.1742-4658.2007.06242.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
37
Andreini C, Banci L, Bertini I, Rosato A. Occurrence of Copper Proteins through the Three Domains of Life: A Bioinformatic Approach. J Proteome Res 2008;7:209-16. [DOI: 10.1021/pr070480u] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
38
Ebert JC, Altman RB. Robust recognition of zinc binding sites in proteins. Protein Sci 2007;17:54-65. [PMID: 18042678 DOI: 10.1110/ps.073138508] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
39
Bertini I, Cavallaro G. Metals in the “omics” world: copper homeostasis and cytochrome c oxidase assembly in a new light. J Biol Inorg Chem 2007;13:3-14. [DOI: 10.1007/s00775-007-0316-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 10/25/2007] [Indexed: 01/20/2023]
40
Ong SAK, Lin HH, Chen YZ, Li ZR, Cao Z. Efficacy of different protein descriptors in predicting protein functional families. BMC Bioinformatics 2007;8:300. [PMID: 17705863 PMCID: PMC1997217 DOI: 10.1186/1471-2105-8-300] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 08/17/2007] [Indexed: 02/02/2023]  Open
41
Ranganathan S, Tammi M, Gribskov M, Tan TW. Establishing bioinformatics research in the Asia Pacific. BMC Bioinformatics 2006. [PMCID: PMC1764485 DOI: 10.1186/1471-2105-7-s5-s1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
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