Prediction of lipid-binding sites based on support vector machine and position specific scoring matrix

Protein Journal

Volumn 29, Issue 6, 2010, Pages 427-431

  Xiong, Wenjia ^a   Guo, Yanzhi ^a   Li, Menglong ^a  

^a SICHUAN UNIVERSITY   (China)

Author keywords

Lipid binding sites; Lipid protein interactions; Position specific scoring matrix; Support vector machine

Indexed keywords

AMINO ACID; LIPID;

ACCURACY; AREA UNDER THE CURVE; ARTICLE; BINDING SITE; CORRELATION COEFFICIENT; INTERMETHOD COMPARISON; POSITION SPECIFIC SCORING MATRIX; PREDICTION; PROTEIN LIPID INTERACTION; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; SUPPORT VECTOR MACHINE;

EID: 77956263332     PISSN: 15723887     EISSN: 18758355     Source Type: Journal    
DOI: 10.1007/s10930-010-9269-x     Document Type: Article

References (31)

1. S Ahmad A Sarai 2005 BMC Bioinformatics 6 33 10.1186/1471-2105-6-33
2. SF Altschul TL Madden AA Schaffer JH Zhang Z Zhang W Miller DJ Lipman 1997 Nucleic Acids Res 25 17 3389 3402 10.1093/nar/25.17.3389 1:CAS:528:DyaK2sXlvFyhu7w%3D
3. T Balla 2005 J Cell Sci 118 10 2093 2104 10.1242/jcs.02387 1:CAS:528:DC%2BD2MXlsFCgurk%3D
4. DA Bernlohr MA Simpson AV Hertzel LJ Banaszak 1997 Annu Rev Nutr 17 277 303 10.1146/annurev.nutr.17.1.277 1:CAS:528:DyaK2sXkvFGmtL4%3D
5. YD Cai KY Feng YX Li KC Chou 2003 Peptides 24 4 629 630 10.1016/S0196-9781(03)00100-1
6. YD Cai XJ Liu XB Xu KC Chou 2002 J Comput Chem 23 2 267 274 10.1002/jcc.10017 1:CAS:528:DC%2BD38XksFShuw%3D%3D
7. CW Cheng ECY Su JK Hwang TY Sung WL Hsu 2008 BMC Bioinformatics 9 S6 10.1186/1471-2105-9-S12-S6
8. KC Chou YD Cai 2002 J Biol Chem 277 48 45765 45769 10.1074/jbc.M204161200 1:CAS:528:DC%2BD38XovFKjurg%3D
9. Christie WW (1989) High-performance liquid chromatography and lipids: a practical guide. The Oily Press Ltd, Ayrshire, 42 pp
10. HE Findlay PJ Booth 2006 J Phys Condens Matter 18 28 S1281 S1291 10.1088/0953-8984/18/28/S11 1:CAS:528:DC%2BD28Xot1ymsL4%3D
11. AN Fonteh RJ Harrington AF Huhmer RG Biringer JN Riggins MG Harrington 2006 Dis Markers 22 1-2 39 64 1:CAS:528:DC%2BD2MXhtlCnsrrP
12. JFC Glatz 2007 Mol Cell Biochem 299 1-2 1 3 10.1007/s11010-006-9372-7 1:CAS:528:DC%2BD2sXltFSrt7s%3D
13. RW Gross CM Jenkins JY Yang DJ Mancuso XL Han 2005 Prostaglandins Other Lipid Mediat 77 1-4 52 64 10.1016/j.prostaglandins.2004.09.005 1:CAS:528:DC%2BD2MXnslyksb4%3D
14. C Hunte S Richers 2008 Curr Opin Struct Biol 18 4 406 411 10.1016/j.sbi.2008.03.008 1:CAS:528:DC%2BD1cXhtValtrfK
15. DT Jones 1999 J Mol Biol 292 2 195 202 10.1006/jmbi.1999.3091 1:CAS:528:DyaK1MXlvFyksb0%3D
16. H Kaur GPS Raghava 2003 Protein Sci 12 3 627 634 10.1110/ps.0228903 1:CAS:528:DC%2BD3sXhsFKmtbY%3D
17. M Kumar AM Gromiha GPS Raghava 2008 Proteins 71 1 189 194 10.1002/prot.21677 1:CAS:528:DC%2BD1cXjt1Ckurs%3D
18. IB Kuznetsov ZK Gou R Li SW Hwang 2006 Proteins 64 1 19 27 10.1002/prot.20977 1:CAS:528:DC%2BD28XlsFahs70%3D
19. CJ Lelliott A Ljungberg A Ahnmark L William-Olsson K Ekroos A Elmgren G Arnerup CC Shoulders J Oscarsson D Linden 2007 Arterioscler Thromb Vasc Biol 27 12 2707 2713 10.1161/ATVBAHA.107.155739 1:CAS:528:DC%2BD2sXhtlahtLjM
20. HH Lin LY Han HL Zhang CJ Zheng B Xie YZ Chen 2006 J Lipid Res 47 4 824 831 10.1194/jlr.M500530-JLR200 1:CAS:528:DC%2BD28XjsFCgtbY%3D
21. BW Matthews 1975 Biochim Biophys Acta 405 2 442 451 1:CAS:528: DyaE2MXlslCksbk%3D
22. V Niggli 2001 Trends Biochem Sci 26 10 604 611 10.1016/S0968-0004(01) 01927-2 1:CAS:528:DC%2BD3MXnt1Wjtr4%3D
23. E Pebay-Peyroula JP Rosenbusch 2001 Curr Opin Struct Biol 11 4 427 432 10.1016/S0959-440X(00)00228-1 1:CAS:528:DC%2BD3MXlslGlsbk%3D
24. D Piomelli 2005 Prostaglandins Other Lipid Mediat 77 1-4 23 34 10.1016/j.prostaglandins.2004.09.006 1:CAS:528:DC%2BD2MXnslyks7g%3D
25. DL Scott G Diez WH Goldmann 2006 Theor Biol Med Model 3 17 10.1186/1742-4682-3-17
26. X Su XL Han DJ Mancuso DR Abendschein RW Gross 2005 Biochemistry 44 13 5234 5245 10.1021/bi047773a 1:CAS:528:DC%2BD2MXitVynsbg%3D
27. M Tempel WH Goldmann G Isenberg E Sackmann 1995 Biophys J 69 1 228 241 10.1016/S0006-3495(95)79894-0 1:CAS:528:DyaK2MXmsFWqs7k%3D
28. Y Tomiki S Suda M Tanaka A Okuzawa M Matsuda Y Ishibiki K Sakamoto T Kamano M Tsurumaru Y Watanabe 2004 J Exp Clin Cancer Res 23 2 233 240 1:CAS:528:DC%2BD2cXms1Kjtb8%3D
29. Vapnik V (1998) Statistical learning theory. Wiley, New York
30. L Wang SJ Irausquin JY Yang 2008 Int J Comput Biol Drug Des 1 1 14 25 10.1504/IJCBDD.2008.018707 1:CAS:528:DC%2BD1cXht1Kru7zO
31. C Zhu P Hu QL Liang YM Wang GA Luo 2009 Chin J Anal Chem 37 9 1390 1396 10.1016/S1872-2040(08)60132-2 1:CAS:528:DC%2BD1MXhsVWrtLbL