CSS-Palm 2.0: An updated software for palmitoylation sites prediction

Protein Engineering, Design and Selection

Volumn 21, Issue 11, 2008, Pages 639-644

  Ren, Jian ^a   Wen, Longping ^a   Gao, Xinjiao ^a   Jin, Changjiang ^a   Xue, Yu ^a   Yao, Xuebiao ^a  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Clustering and scoring strategy; CSS Palm; Palmitoylated proteins; Palmitoylation

Indexed keywords

CLUSTERING ALGORITHMS; FLOW OF SOLIDS; FORECASTING; INTERNET; KETONES; STATISTICAL TESTS;

BUDDING YEASTS; CELLULAR PROCESSES; CLUSTERING; CLUSTERING AND SCORING STRATEGY; CSS-PALM; DATA SETS; EXPERIMENTAL APPROACHES; IN SILICO PREDICTIONS; LEAVE-ONE-OUT; LIPID MODIFICATIONS; MOLECULAR MECHANISMS; ONLINE SERVICES; PALMITOYLATED PROTEINS; PALMITOYLATION; PREDICTION PERFORMANCES; REGULATORY;

PROTEINS;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; MOLECULAR MECHANICS; PALMITOYLATION; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN MODIFICATION; VALIDATION PROCESS; YEAST;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; CLUSTER ANALYSIS; COMPUTER SIMULATION; LIPOYLATION; MODELS, MOLECULAR; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; SACCHAROMYCETALES; SOFTWARE;

SACCHAROMYCETALES;

EID: 54249148026     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzn039     Document Type: Article

References (30)

1. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang, Z. and Miller,W. (1997) Nucleic Acids Res., 25, 3389-3402.
2. Bijlmakers,M.J. and Marsh,M. (2003) Trends Cell Biol., 13, 32-42.
3. Bologna, G., Yvon, C., Duvaud, S. and Veuthey, A.L. (2004) Proteomics, 4, 1626-1632.
4. Casey, P.J. (1995) Science, 268, 221-225.
5. Chakrabandhu,K., Herincs,Z., Huault,S., Dost,B., Peng,L., Conchonaud,F., Marguet,D., He,H.T. and Hueber,A.O. (2007) EMBO J., 26, 209-220.
6. Dietrich,L.E. and Ungermann,C. (2004) EMBO Rep., 5, 1053-1057.
7. Draper,J.M., Xia,Z. and Smith,C.D. (2007) J. Lipid Res., 48, 1873-1884.
8. Eisenhaber,B., Bork,P. and Eisenhaber,F. (1999) J. Mol. Biol., 292, 741-758.
9. Eisenhaber,F., Eisenhaber,B., Kubina,W., Maurer-Stroh,S., Neuberger,G., Schneider,G. and Wildpaner,M. (2003) Nucleic Acids Res., 31, 3631-3634.
10. Eisenhaber,B., Schneider,G., Wildpaner,M. and Eisenhaber,F. (2004) J. Mol. Biol., 337, 243-253.
11. el-Husseini Ael,D. and Bredt,D.S. (2002) Nat. Rev. Neurosci., 3, 791-802.
12. Fankhauser,N. and Maser,P. (2005) Bioinformatics, 21, 1846-1852.
13. Greaves,J. and Chamberlain,L.H. (2007) J. Cell Biol., 176, 249-254.
14. Hancock,J.F., Magee,A.I., Childs,J.E. and Marshall,C.J. (1989) Cell, 57, 1167-1177.
15. Li,W. and Godzik,A. (2006) Bioinformatics, 22, 1658-1659.
16. Linder,M.E. and Deschenes,R.J. (2007) Nat. Rev., 8, 74-84.
17. Maurer-Stroh,S., Eisenhaber,B. and Eisenhaber,F. (2002) J. Mol.Biol., 317, 541-557.
18. Maurer-Stroh,S., Eisenhaber,B. and Eisenhaber,F. (2002) J. Mol. Biol., 317, 523-540.
19. Maurer-Stroh,S. and Eisenhaber,F. (2005) Genome Biol., 6, R55.
20. Nadolski,M.J. and Linder,M.E. (2007) FEBS J., 274, 5202-5210.
21. Podell,S. and Gribskov,M. (2004) BMC Genomics, 5, 37.
22. Resh,M.D. (2006) Sci STKE, 2006, re14.
23. Resh,M.D. (2006) Nat. Chem. Biol., 2, 584-590.
24. Roth,A.F., Feng,Y., Chen,L. and Davis,N.G. (2002) J. Cell Biol., 159, 23-28.
25. Roth,A.F., Wan,J., Bailey,A.O., Sun,B., Kuchar,J.A., Green,W.N., Phinney,B.S., Yates,J.R., III and Davis,N.G. (2006) Cell, 125, 1003-1013.
26. Smotrys,J.E. and Linder,M.E. (2004) Annu. Rev. Biochem., 73, 559-587.
27. Wan,J., Roth,A.F., Bailey,A.O. and Davis,N.G. (2007) Nat. Protoc., 2, 1573-1584.
28. Xue,Y., Chen,H., Jin,C., Sun,Z. and Yao,X. (2006) BMC Bioinformatics, 7, 458.
29. Zhou,B., Liu,L., Reddivari,M. and Zhang,X.A. (2004) Cancer Res., 64, 7455-7463.
30. Zhou,F., Xue,Y., Yao,X. and Xu,Y. (2006) Bioinformatics, 22, 894-896.