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For: Faraggi E, Zhang T, Yang Y, Kurgan L, Zhou Y. SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. J Comput Chem 2012;33:259-67. [PMID: 22045506 PMCID: PMC3240697 DOI: 10.1002/jcc.21968] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 09/16/2011] [Accepted: 09/18/2011] [Indexed: 11/11/2022]
Number Cited by Other Article(s)
151
Dehzangi A, Paliwal K, Lyons J, Sharma A, Sattar A. A Segmentation-Based Method to Extract Structural and Evolutionary Features for Protein Fold Recognition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014;11:510-519. [PMID: 26356019 DOI: 10.1109/tcbb.2013.2296317] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
152
Zheng W, Zhang C, Hanlon M, Ruan J, Gao J. An ensemble method for prediction of conformational B-cell epitopes from antigen sequences. Comput Biol Chem 2014;49:51-8. [DOI: 10.1016/j.compbiolchem.2014.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/26/2014] [Accepted: 02/10/2014] [Indexed: 12/12/2022]
153
Feng Y, Lin H, Luo L. Prediction of protein secondary structure using feature selection and analysis approach. Acta Biotheor 2014;62:1-14. [PMID: 24052343 DOI: 10.1007/s10441-013-9203-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 08/24/2013] [Indexed: 01/09/2023]
154
Ahmed MH, Kellogg GE, Selley DE, Safo MK, Zhang Y. Predicting the molecular interactions of CRIP1a-cannabinoid 1 receptor with integrated molecular modeling approaches. Bioorg Med Chem Lett 2014;24:1158-65. [PMID: 24461351 PMCID: PMC4353595 DOI: 10.1016/j.bmcl.2013.12.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/26/2013] [Accepted: 12/29/2013] [Indexed: 12/14/2022]
155
Maurice KJ. SSThread: Template-free protein structure prediction by threading pairs of contacting secondary structures followed by assembly of overlapping pairs. J Comput Chem 2014;35:644-56. [PMID: 24523210 DOI: 10.1002/jcc.23543] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 11/15/2013] [Accepted: 01/05/2014] [Indexed: 11/12/2022]
156
Dehzangi A, Paliwal K, Lyons J, Sharma A, Sattar A. Proposing a highly accurate protein structural class predictor using segmentation-based features. BMC Genomics 2014;15 Suppl 1:S2. [PMID: 24564476 PMCID: PMC4046757 DOI: 10.1186/1471-2164-15-s1-s2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
157
Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes. PLoS One 2014;9:e86703. [PMID: 24475169 PMCID: PMC3901691 DOI: 10.1371/journal.pone.0086703] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 12/10/2013] [Indexed: 11/22/2022]  Open
158
Folkman L, Stantic B, Sattar A. Towards sequence-based prediction of mutation-induced stability changes in unseen non-homologous proteins. BMC Genomics 2014;15 Suppl 1:S4. [PMID: 24564514 PMCID: PMC4046685 DOI: 10.1186/1471-2164-15-s1-s4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]  Open
159
Yang Y, Zhao H, Wang J, Zhou Y. SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction. Methods Mol Biol 2014;1137:119-30. [PMID: 24573478 PMCID: PMC3937850 DOI: 10.1007/978-1-4939-0366-5_9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
160
Belushkin AA, Vinogradov DV, Gelfand MS, Osterman AL, Cieplak P, Kazanov MD. Sequence-derived structural features driving proteolytic processing. Proteomics 2013;14:42-50. [PMID: 24227478 DOI: 10.1002/pmic.201300416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 10/22/2013] [Accepted: 10/28/2013] [Indexed: 12/11/2022]
161
Minhas FUAA, Geiss BJ, Ben-Hur A. PAIRpred: partner-specific prediction of interacting residues from sequence and structure. Proteins 2013;82:1142-55. [PMID: 24243399 DOI: 10.1002/prot.24479] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 11/04/2013] [Accepted: 11/09/2013] [Indexed: 11/10/2022]
162
Mitra P, Shultis D, Brender JR, Czajka J, Marsh D, Gray F, Cierpicki T, Zhang Y. An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis. PLoS Comput Biol 2013;9:e1003298. [PMID: 24204234 PMCID: PMC3812052 DOI: 10.1371/journal.pcbi.1003298] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 09/09/2013] [Indexed: 01/31/2023]  Open
163
Zhao H, Yang Y, Zhou Y. Prediction of RNA binding proteins comes of age from low resolution to high resolution. MOLECULAR BIOSYSTEMS 2013;9:2417-25. [PMID: 23872922 PMCID: PMC3870025 DOI: 10.1039/c3mb70167k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
164
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: 3.5] [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]
165
Novel GUCA1A mutations suggesting possible mechanisms of pathogenesis in cone, cone-rod, and macular dystrophy patients. BIOMED RESEARCH INTERNATIONAL 2013;2013:517570. [PMID: 24024198 PMCID: PMC3759255 DOI: 10.1155/2013/517570] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/19/2013] [Indexed: 01/06/2023]
166
Saraswathi S, Fernández-Martínez JL, Koliński A, Jernigan RL, Kloczkowski A. Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structure. J Mol Model 2013;19:4337-48. [PMID: 23907551 DOI: 10.1007/s00894-013-1911-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/05/2013] [Indexed: 11/27/2022]
167
Kubrycht J, Sigler K, Souček P, Hudeček J. Structures composing protein domains. Biochimie 2013;95:1511-24. [DOI: 10.1016/j.biochi.2013.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 04/02/2013] [Indexed: 12/21/2022]
168
Maksimov MO, Link AJ. Discovery and Characterization of an Isopeptidase That Linearizes Lasso Peptides. J Am Chem Soc 2013;135:12038-47. [DOI: 10.1021/ja4054256] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
169
Zhao H, Yang Y, Lin H, Zhang X, Mort M, Cooper DN, Liu Y, Zhou Y. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Genome Biol 2013;14:R23. [PMID: 23497682 PMCID: PMC4053752 DOI: 10.1186/gb-2013-14-3-r23] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 03/13/2013] [Indexed: 02/07/2023]  Open
170
Li Z, Yang Y, Zhan J, Dai L, Zhou Y. Energy functions in de novo protein design: current challenges and future prospects. Annu Rev Biophys 2013;42:315-35. [PMID: 23451890 DOI: 10.1146/annurev-biophys-083012-130315] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
171
Dehzangi A, Paliwal K, Lyons J, Sharma A, Sattar A. Enhancing Protein Fold Prediction Accuracy Using Evolutionary and Structural Features. PATTERN RECOGNITION IN BIOINFORMATICS 2013. [DOI: 10.1007/978-3-642-39159-0_18] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
172
Saraswathi S, Fernández-Martínez JL, Kolinski A, Jernigan RL, Kloczkowski A. Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction. J Mol Model 2012;18:4275-89. [PMID: 22562230 PMCID: PMC3694724 DOI: 10.1007/s00894-012-1410-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 03/19/2012] [Indexed: 10/28/2022]
173
Zhang T, Faraggi E, Xue B, Dunker AK, Uversky VN, Zhou Y. SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method. J Biomol Struct Dyn 2012;29:799-813. [PMID: 22208280 PMCID: PMC3297974 DOI: 10.1080/073911012010525022] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
174
Yang Y, Faraggi E, Zhao H, Zhou Y. Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics 2011;27:2076-82. [PMID: 21666270 DOI: 10.1093/bioinformatics/btr350] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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