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For: Ofran Y, Mysore V, Rost B. Prediction of DNA-binding residues from sequence. ACTA ACUST UNITED AC 2007;23:i347-53. [PMID: 17646316 DOI: 10.1093/bioinformatics/btm174] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Number Cited by Other Article(s)
51
Miao Z, Westhof E. A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs. PLoS Comput Biol 2015;11:e1004639. [PMID: 26681179 PMCID: PMC4683125 DOI: 10.1371/journal.pcbi.1004639] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/30/2015] [Indexed: 11/18/2022]  Open
52
Wong KC, Li Y, Peng C, Moses AM, Zhang Z. Computational learning on specificity-determining residue-nucleotide interactions. Nucleic Acids Res 2015;43:10180-9. [PMID: 26527718 PMCID: PMC4666365 DOI: 10.1093/nar/gkv1134] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 10/18/2015] [Indexed: 01/02/2023]  Open
53
DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation. Sci Rep 2015;5:15479. [PMID: 26482832 PMCID: PMC4611492 DOI: 10.1038/srep15479] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/28/2015] [Indexed: 02/01/2023]  Open
54
Suvorova IA, Korostelev YD, Gelfand MS. GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution. PLoS One 2015;10:e0132618. [PMID: 26151451 PMCID: PMC4494728 DOI: 10.1371/journal.pone.0132618] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/16/2015] [Indexed: 12/03/2022]  Open
55
Yan J, Friedrich S, Kurgan L. A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues. Brief Bioinform 2015;17:88-105. [DOI: 10.1093/bib/bbv023] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 01/07/2023]  Open
56
An overview of the prediction of protein DNA-binding sites. Int J Mol Sci 2015;16:5194-215. [PMID: 25756377 PMCID: PMC4394471 DOI: 10.3390/ijms16035194] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/21/2015] [Accepted: 02/27/2015] [Indexed: 02/06/2023]  Open
57
Wong MH, Sze-To HYA, Lo LYP, Chan TMC, Leung KS. Discovering Binding Cores in Protein-DNA Binding Using Association Rule Mining with Statistical Measures. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015;12:142-154. [PMID: 26357085 DOI: 10.1109/tcbb.2014.2343952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
58
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: 1.9] [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]
59
Samant M, Jethva M, Hasija Y. INTERACT-O-FINDER: A Tool for Prediction of DNA-Binding Proteins Using Sequence Features. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
60
Yan C, Wang Y. A graph kernel method for DNA-binding site prediction. BMC SYSTEMS BIOLOGY 2014;8 Suppl 4:S10. [PMID: 25521807 PMCID: PMC4290685 DOI: 10.1186/1752-0509-8-s4-s10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
61
Fang C, Noguchi T, Yamana H. Simplified sequence-based method for ATP-binding prediction using contextual local evolutionary conservation. Algorithms Mol Biol 2014;9:7. [PMID: 24618258 PMCID: PMC3995811 DOI: 10.1186/1748-7188-9-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 03/05/2014] [Indexed: 12/23/2022]  Open
62
Li BQ, Feng KY, Ding J, Cai YD. Predicting DNA-binding sites of proteins based on sequential and 3D structural information. Mol Genet Genomics 2014;289:489-99. [PMID: 24448651 DOI: 10.1007/s00438-014-0812-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 01/04/2014] [Indexed: 11/26/2022]
63
Liu R, Hu J. DNABind: A hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches. Proteins 2013;81:1885-99. [DOI: 10.1002/prot.24330] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 05/02/2013] [Accepted: 05/12/2013] [Indexed: 01/10/2023]
64
Zhu X, Ericksen SS, Mitchell JC. DBSI: DNA-binding site identifier. Nucleic Acids Res 2013;41:e160. [PMID: 23873960 PMCID: PMC3763564 DOI: 10.1093/nar/gkt617] [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] [Indexed: 11/14/2022]  Open
65
Zhu Y, Zhou W, Dai DQ, Yan H. Identification of DNA-binding and protein-binding proteins using enhanced graph wavelet features. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013;10:1017-1031. [PMID: 24334394 DOI: 10.1109/tcbb.2013.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
66
Wong KC, Chan TM, Peng C, Li Y, Zhang Z. DNA motif elucidation using belief propagation. Nucleic Acids Res 2013;41:e153. [PMID: 23814189 PMCID: PMC3763557 DOI: 10.1093/nar/gkt574] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
67
Nagarajan R, Ahmad S, Gromiha MM. Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins. Nucleic Acids Res 2013;41:7606-14. [PMID: 23788679 PMCID: PMC3763535 DOI: 10.1093/nar/gkt544] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
68
Chan TM, Lo LY, Sze-To HY, Leung KS, Xiao X, Wong MH. Modeling associated protein-DNA pattern discovery with unified scores. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013;10:696-707. [PMID: 24091402 DOI: 10.1109/tcbb.2013.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
69
Li T, Li QZ, Liu S, Fan GL, Zuo YC, Peng Y. PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information. ACTA ACUST UNITED AC 2013;29:678-85. [PMID: 23335013 DOI: 10.1093/bioinformatics/btt029] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
70
Gromiha MM, Nagarajan R. Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013;91:65-99. [PMID: 23790211 DOI: 10.1016/b978-0-12-411637-5.00003-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
71
PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites. PLoS One 2012;7:e50300. [PMID: 23209700 PMCID: PMC3510211 DOI: 10.1371/journal.pone.0050300] [Citation(s) in RCA: 228] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 10/18/2012] [Indexed: 12/04/2022]  Open
72
Ma X, Guo J, Liu HD, Xie JM, Sun X. Sequence-based prediction of DNA-binding residues in proteins with conservation and correlation information. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012;9:1766-1775. [PMID: 22868682 DOI: 10.1109/tcbb.2012.106] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
73
Wang DD, Li TH, Sun JM, Li DP, Xiong WW, Wang WY, Tang SN. Shape string: a new feature for prediction of DNA-binding residues. Biochimie 2012;95:354-8. [PMID: 23116714 DOI: 10.1016/j.biochi.2012.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
74
Chan TM, Leung KS, Lee KH, Wong MH, Lau TCK, Tsui SKW. Subtypes of associated protein-DNA (Transcription Factor-Transcription Factor Binding Site) patterns. Nucleic Acids Res 2012;40:9392-403. [PMID: 22904079 PMCID: PMC3479201 DOI: 10.1093/nar/gks749] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]  Open
75
Schaefer C, Bromberg Y, Achten D, Rost B. Disease-related mutations predicted to impact protein function. BMC Genomics 2012;13 Suppl 4:S11. [PMID: 22759649 PMCID: PMC3394413 DOI: 10.1186/1471-2164-13-s4-s11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
76
Schaefer C, Rost B. Predict impact of single amino acid change upon protein structure. BMC Genomics 2012;13 Suppl 4:S4. [PMID: 22759652 PMCID: PMC3395892 DOI: 10.1186/1471-2164-13-s4-s4] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
77
Chen YC, Wright JD, Lim C. DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res 2012;40:W249-56. [PMID: 22661576 PMCID: PMC3394278 DOI: 10.1093/nar/gks481] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
78
Dey S, Pal A, Guharoy M, Sonavane S, Chakrabarti P. Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters. Nucleic Acids Res 2012;40:7150-61. [PMID: 22641851 PMCID: PMC3424558 DOI: 10.1093/nar/gks405] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
79
Qin S, Zhou HX. Structural models of protein-DNA complexes based on interface prediction and docking. Curr Protein Pept Sci 2012;12:531-9. [PMID: 21787304 DOI: 10.2174/138920311796957694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 04/01/2011] [Accepted: 05/04/2011] [Indexed: 11/22/2022]
80
Walia RR, Caragea C, Lewis BA, Towfic F, Terribilini M, El-Manzalawy Y, Dobbs D, Honavar V. Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. BMC Bioinformatics 2012;13:89. [PMID: 22574904 PMCID: PMC3490755 DOI: 10.1186/1471-2105-13-89] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 05/10/2012] [Indexed: 11/15/2022]  Open
81
Qi Y, Oja M, Weston J, Noble WS. A unified multitask architecture for predicting local protein properties. PLoS One 2012;7:e32235. [PMID: 22461885 PMCID: PMC3312883 DOI: 10.1371/journal.pone.0032235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 01/25/2012] [Indexed: 01/27/2023]  Open
82
Song J, Tan H, Wang M, Webb GI, Akutsu T. TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences. PLoS One 2012;7:e30361. [PMID: 22319565 PMCID: PMC3271071 DOI: 10.1371/journal.pone.0030361] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 12/14/2011] [Indexed: 12/29/2022]  Open
83
Xiong Y, Xia J, Zhang W, Liu J. Exploiting a reduced set of weighted average features to improve prediction of DNA-binding residues from 3D structures. PLoS One 2011;6:e28440. [PMID: 22174808 PMCID: PMC3234263 DOI: 10.1371/journal.pone.0028440] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 11/08/2011] [Indexed: 01/29/2023]  Open
84
Sarfstein R, Pasmanik-Chor M, Yeheskel A, Edry L, Shomron N, Warman N, Wertheimer E, Maor S, Shochat L, Werner H. Insulin-like growth factor-I receptor (IGF-IR) translocates to nucleus and autoregulates IGF-IR gene expression in breast cancer cells. J Biol Chem 2011;287:2766-76. [PMID: 22128190 DOI: 10.1074/jbc.m111.281782] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
85
Milanowska K, Rother K, Bujnicki JM. Databases and bioinformatics tools for the study of DNA repair. Mol Biol Int 2011;2011:475718. [PMID: 22091405 PMCID: PMC3200286 DOI: 10.4061/2011/475718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/28/2011] [Accepted: 05/22/2011] [Indexed: 12/12/2022]  Open
86
Wang CC, Chen CY. Predicting DNA-binding locations and orientation on proteins using knowledge-based learning of geometric properties. Proteome Sci 2011;9 Suppl 1:S11. [PMID: 22166082 PMCID: PMC3289072 DOI: 10.1186/1477-5956-9-s1-s11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
87
Fedonin GG, Rakhmaninova AB, Korostelev YD, Laikova ON, Gelfand MS. Machine learning study of DNA binding by transcription factors from the LacI family. Mol Biol 2011. [DOI: 10.1134/s0026893311040054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
88
Conformational studies and solvent-accessible surface area analysis of known selective DNA G-Quadruplex binders. Biochimie 2011;93:1267-74. [DOI: 10.1016/j.biochi.2011.06.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 06/14/2011] [Indexed: 12/18/2022]
89
Si J, Zhang Z, Lin B, Schroeder M, Huang B. MetaDBSite: a meta approach to improve protein DNA-binding sites prediction. BMC SYSTEMS BIOLOGY 2011;5 Suppl 1:S7. [PMID: 21689482 PMCID: PMC3121123 DOI: 10.1186/1752-0509-5-s1-s7] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
90
Xiong Y, Liu J, Wei DQ. An accurate feature-based method for identifying DNA-binding residues on protein surfaces. Proteins 2011;79:509-17. [PMID: 21069866 DOI: 10.1002/prot.22898] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
91
Gromiha MM, Fukui K. Scoring function based approach for locating binding sites and understanding recognition mechanism of protein-DNA complexes. J Chem Inf Model 2011;51:721-9. [PMID: 21361378 DOI: 10.1021/ci1003703] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
92
Wong KC, Peng C, Wong MH, Leung KS. Generalizing and learning protein-DNA binding sequence representations by an evolutionary algorithm. Soft comput 2011. [DOI: 10.1007/s00500-011-0692-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
93
van Ham TJ, Holmberg MA, van der Goot AT, Teuling E, Garcia-Arencibia M, Kim HE, Du D, Thijssen KL, Wiersma M, Burggraaff R, van Bergeijk P, van Rheenen J, Jerre van Veluw G, Hofstra RMW, Rubinsztein DC, Nollen EAA. Identification of MOAG-4/SERF as a regulator of age-related proteotoxicity. Cell 2010;142:601-12. [PMID: 20723760 DOI: 10.1016/j.cell.2010.07.020] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 03/31/2010] [Accepted: 06/17/2010] [Indexed: 01/03/2023]
94
Cai Y, He Z, Shi X, Kong X, Gu L, Xie L. A novel sequence-based method of predicting protein DNA-binding residues, using a machine learning approach. Mol Cells 2010;30:99-105. [PMID: 20706794 DOI: 10.1007/s10059-010-0093-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 04/06/2010] [Accepted: 04/22/2010] [Indexed: 11/29/2022]  Open
95
Leung KS, Wong KC, Chan TM, Wong MH, Lee KH, Lau CK, Tsui SKW. Discovering protein-DNA binding sequence patterns using association rule mining. Nucleic Acids Res 2010;38:6324-37. [PMID: 20529874 PMCID: PMC2965231 DOI: 10.1093/nar/gkq500] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
96
Ozbek P, Soner S, Erman B, Haliloglu T. DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues. Nucleic Acids Res 2010;38:W417-23. [PMID: 20478828 PMCID: PMC2896127 DOI: 10.1093/nar/gkq396] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
97
Carson MB, Langlois R, Lu H. NAPS: a residue-level nucleic acid-binding prediction server. Nucleic Acids Res 2010;38:W431-5. [PMID: 20478832 PMCID: PMC2896077 DOI: 10.1093/nar/gkq361] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]  Open
98
Aggarwal P, Das Gupta M, Joseph AP, Chatterjee N, Srinivasan N, Nath U. Identification of specific DNA binding residues in the TCP family of transcription factors in Arabidopsis. THE PLANT CELL 2010;22:1174-89. [PMID: 20363772 PMCID: PMC2879757 DOI: 10.1105/tpc.109.066647] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 03/02/2010] [Accepted: 03/22/2010] [Indexed: 05/18/2023]
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Mishra NK, Raghava GPS. Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information. BMC Bioinformatics 2010;11 Suppl 1:S48. [PMID: 20122222 PMCID: PMC3009520 DOI: 10.1186/1471-2105-11-s1-s48] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
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Rastogi S, Rost B. Bioinformatics predictions of localization and targeting. Methods Mol Biol 2010;619:285-305. [PMID: 20419417 DOI: 10.1007/978-1-60327-412-8_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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