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For: Gromiha MM. Motifs in outer membrane protein sequences: Applications for discrimination. Biophys Chem 2005;117:65-71. [PMID: 15905018 DOI: 10.1016/j.bpc.2005.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Revised: 04/01/2005] [Accepted: 04/01/2005] [Indexed: 12/31/2022]
Number Cited by Other Article(s)
1
Montezano D, Bernstein R, Copeland MM, Slusky JSG. General features of transmembrane beta barrels from a large database. Proc Natl Acad Sci U S A 2023;120:e2220762120. [PMID: 37432995 PMCID: PMC10629564 DOI: 10.1073/pnas.2220762120] [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: 12/10/2022] [Accepted: 06/03/2023] [Indexed: 07/13/2023]  Open
2
Yan R, Lin J, Chen Z, Wang X, Huang L, Cai W, Zhang Z. Prediction of outer membrane proteins by combining the position- and composition-based features of sequence profiles. MOLECULAR BIOSYSTEMS 2014;10:1004-13. [DOI: 10.1039/c3mb70435a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
3
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]
4
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: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 07/17/2012] [Indexed: 11/25/2022]
5
E-komon T, Burchmore R, Herzyk P, Davies R. Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation. BMC Bioinformatics 2012;13:63. [PMID: 22540951 PMCID: PMC3403877 DOI: 10.1186/1471-2105-13-63] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 04/27/2012] [Indexed: 01/26/2023]  Open
6
Outer membrane proteins can be simply identified using secondary structure element alignment. BMC Bioinformatics 2011;12:76. [PMID: 21414186 PMCID: PMC3072342 DOI: 10.1186/1471-2105-12-76] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 03/17/2011] [Indexed: 02/04/2023]  Open
7
iFC²: an integrated web-server for improved prediction of protein structural class, fold type, and secondary structure content. Amino Acids 2010;40:963-73. [PMID: 20730460 DOI: 10.1007/s00726-010-0721-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 08/06/2010] [Indexed: 10/19/2022]
8
Chen K, Kurgan LA, Ruan J. Prediction of protein structural class using novel evolutionary collocation-based sequence representation. J Comput Chem 2008;29:1596-604. [PMID: 18293306 DOI: 10.1002/jcc.20918] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
9
Ou YY, Gromiha M, Chen SA, Suwa M. TMBETADISC-RBF: Discrimination of -barrel membrane proteins using RBF networks and PSSM profiles. Comput Biol Chem 2008;32:227-31. [DOI: 10.1016/j.compbiolchem.2008.03.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 03/11/2008] [Accepted: 03/11/2008] [Indexed: 10/22/2022]
10
Kurgan LA, Zhang T, Zhang H, Shen S, Ruan J. Secondary structure-based assignment of the protein structural classes. Amino Acids 2008;35:551-64. [DOI: 10.1007/s00726-008-0080-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 02/27/2008] [Indexed: 11/24/2022]
11
Martin J, de Brevern AG, Camproux AC. In silico local structure approach: a case study on outer membrane proteins. Proteins 2008;71:92-109. [PMID: 17932925 DOI: 10.1002/prot.21659] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
12
Lin H. The modified Mahalanobis Discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition. J Theor Biol 2008;252:350-6. [PMID: 18355838 DOI: 10.1016/j.jtbi.2008.02.004] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 12/02/2007] [Accepted: 02/04/2008] [Indexed: 11/15/2022]
13
Gromiha MM, Yabuki Y, Suwa M. TMB finding pipeline: novel approach for detecting beta-barrel membrane proteins in genomic sequences. J Chem Inf Model 2007;47:2456-61. [PMID: 17958348 DOI: 10.1021/ci700222s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
14
Zhang G, Fang B. LogitBoost classifier for discriminating thermophilic and mesophilic proteins. J Biotechnol 2007;127:417-24. [PMID: 17045354 DOI: 10.1016/j.jbiotec.2006.07.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Revised: 07/04/2006] [Accepted: 07/19/2006] [Indexed: 11/17/2022]
15
Gromiha MM, Yabuki Y, Kundu S, Suharnan S, Suwa M. TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences. Nucleic Acids Res 2006;35:D314-6. [PMID: 17088282 PMCID: PMC1669718 DOI: 10.1093/nar/gkl805] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
16
Gromiha MM, Suwa M. Influence of amino acid properties for discriminating outer membrane proteins at better accuracy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006;1764:1493-7. [PMID: 16963325 DOI: 10.1016/j.bbapap.2006.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 07/13/2006] [Accepted: 07/28/2006] [Indexed: 10/24/2022]
17
Gromiha MM, Suwa M. Discrimination of outer membrane proteins using machine learning algorithms. Proteins 2006;63:1031-7. [PMID: 16493651 DOI: 10.1002/prot.20929] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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