Efficacy of different protein descriptors in predicting protein functional families.
BACKGROUND
Sequence-derived structural and physicochemical descriptors have frequently been used in machine learning prediction of protein functional families, thus there is a need to comparatively evaluate the effectiveness of these descriptor-sets by using the same method and parameter optimization algorithm, and to examine whether the combined use of these descriptor-sets help to improve predictive performance. Six individual descriptor-sets and four combination-sets were evaluated in support vector machines (SVM) prediction of six protein functional families.


RESULTS
The performance of these descriptor-sets were ranked by Matthews correlation coefficient (MCC), and categorized into two groups based on their performance. While there is no overwhelmingly favourable choice of descriptor-sets, certain trends were found. The combination-sets tend to give slightly but consistently higher MCC values and thus overall best performance such that three out of four combination-sets show slightly better performance compared to one out of six individual descriptor-sets.


CONCLUSIONS
Our study suggests that currently used descriptor-sets are generally useful for classifying proteins and the prediction performance may be enhanced by exploring combinations of descriptors.
Ong
Serene A K
SA
Department of Pharmacy, National University of Singapore, Blk S16, Level 8, 08-14, 3 Science Drive 2, Singapore 117543, Singapore. renese7@gmail.com
Lin
Hong Huang
HH
Chen
Yu Zong
YZ
Li
Ze Rong
ZR
Cao
Zhiwei
Z
D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000145:classification* / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013329:Structure-Activity Relationship
D011506:Proteins
Bioinformatics. 2006 Jul 1;22(13):1658-9
16731699
J Mol Biol. 1976 Jul 25;105(1):1-12
994183
Mol Biotechnol. 2002 Feb;20(2):153-62
11876472
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W414-9
15215421
In Silico Biol. 2002;2(3):291-303
12542414
J Chem Inf Comput Sci. 2004 Sep-Oct;44(5):1630-8
15446820
J Proteome Res. 2006 Feb;5(2):316-22
16457597
Nat Biotechnol. 1996 Nov;14(11):1516-8
9634812
Nucleic Acids Res. 2002 Jan 1;30(1):276-80
11752314
Glycobiology. 1999 Oct;9(10):961-78
10521532
Proteins. 2006 Jan 1;62(1):218-31
16287089
Bioinformatics. 2000 Oct;16(10):906-14
11120680
Bioinformatics. 2005 Jan 1;21(1):10-9
15308540
Biopolymers. 1988 Mar;27(3):451-77
3359010
Biochem Biophys Res Commun. 2006 Aug 18;347(1):150-7
16808903
J Protein Chem. 2001 Apr;20(3):217-20
11565901
Proteomics. 2005 Mar;5(4):876-84
15717327
Biochem Biophys Res Commun. 2000 Nov 19;278(2):477-83
11097861
J Med Chem. 1996 Aug 2;39(16):3049-59
8759626
Protein Sci. 2004 Nov;13(11):2857-63
15498934
Am J Phys Anthropol. 2006 Jan;129(1):121-31
16261547
Bioinformatics. 2001 Mar;17(3):282-3
11294794
J Biol Chem. 2002 Nov 29;277(48):45765-9
12186861
J Am Chem Soc. 1988 Aug 1;110(18):5959-67
22148765
J Chem Inf Comput Sci. 2000 Sep-Oct;40(5):1227-34
11045818
Proteins. 1999 Jun 1;35(4):401-7
10382667
Proc Natl Acad Sci U S A. 1981 Jun;78(6):3824-8
6167991
J Proteome Res. 2003 Mar-Apr;2(2):183-90
12716132
Curr Opin Struct Biol. 2001 Feb;11(1):53-8
11179892
FASEB J. 1994 Oct;8(13):1019-25
7926366
Bioinformatics. 2002 Jan;18(1):77-82
11836214
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D181-6
16381841
Bioinformatics. 2006 Jul 15;22(14):1784-5
16787975
J Cell Biochem. 2007 Feb 15;100(3):665-78
16983686
Biometrika. 1950 Jun;37(1-2):17-23
15420245
Curr Med Chem. 2000 Sep;7(9):861-88
10911020
J Mol Med (Berl). 1995 Feb;73(2):51-63
7627630
J Theor Biol. 1981 Jul 7;91(1):115-23
7300379
RNA. 2004 Mar;10(3):355-68
14970381
BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S13
17254297
J Proteome Res. 2002 Sep-Oct;1(5):429-33
12645914
Proc Natl Acad Sci U S A. 1995 Sep 12;92(19):8700-4
7568000
J Theor Biol. 1982 Dec 21;99(4):629-44
7183857
Trends Biochem Sci. 2000 May;25(5):241-6
10782096
J Proteome Res. 2005 Jul-Aug;4(4):1413-8
16083294
J Mol Biol. 1999 Oct 22;293(2):255-70
10550207
FEBS Lett. 2005 Jun 20;579(16):3444-8
15949806
J Biol Chem. 2005 Apr 15;280(15):14427-32
15647269
Genome Res. 1999 Nov;9(11):1106-15
10568750
Comput Chem. 2001 Dec;26(1):5-14
11765851
Nucleic Acids Res. 2000 Jan 1;28(1):374
10592278
J Biol Chem. 2004 May 28;279(22):23262-6
15039428
Nucleic Acids Res. 2003 Jan 1;31(1):365-70
12520024
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W32-7
16845018
Mol Immunol. 2007 Feb;44(5):866-77
16806474
Protein Eng. 1992 Jul;5(5):373-5
1518784
Crit Rev Biochem Mol Biol. 2002;37(5):287-337
12449427
Science. 1994 Jul 29;265(5172):615-21
8036511
Proteins. 2004 Apr 1;55(1):66-76
14997540
Bioinformatics. 2005 May 15;21(10):2522-4
15699023
Bioinformatics. 2001 May;17(5):455-60
11331240
Science. 1974 Sep 6;185(4154):862-4
4843792
J Cell Biochem. 2002;84(2):343-8
11787063
J Theor Biol. 1975 Mar;50(1):167-83
1127956
Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):262-7
10618406
Biochem Biophys Res Commun. 2004 Aug 6;320(4):1236-9
15249222
Biophys J. 1994 Feb;66(2 Pt 1):335-44
8161687
J Chem Inf Model. 2005 Mar-Apr;45(2):407-13
15807506
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W383-9
15215416
J Theor Biol. 1967 Aug;16(2):187-211
6048539
Anal Biochem. 2006 Oct 1;357(1):116-21
16920060
Bioinformatics. 2000 May;16(5):412-24
10871264
Proteomics. 2006 Oct;6(19):5099-105
16955516
Crit Rev Biochem Mol Biol. 1995;30(4):275-349
7587280
J Med Chem. 1997 Apr 11;40(8):1219-29
9111296
Bioinformatics. 2002 Jan;18(1):147-59
11836223
Nucleic Acids Res. 2003 Jul 1;31(13):3692-7
12824396
Bioinformatics. 2003 Sep 1;19(13):1650-5
12967961
J Lipid Res. 2006 Apr;47(4):824-31
16443826
Annu Rev Genet. 1997;31:61-89
9442890
Int J Pept Protein Res. 1984 Aug;24(2):180-91
6480218
J Biol Chem. 1989 Oct 25;264(30):17615-8
2681181
Proteins. 2001 May 15;43(3):246-55
11288174
Bioinformatics. 2003 Jan;19(1):125-34
12499302
Mol Cell Biochem. 2002 Oct;239(1-2):3-7
12479562
Nucleic Acids Res. 2004 Dec 07;32(21):6437-44
15585667
Proc IEEE Comput Soc Bioinform Conf. 2003;2:220-8
16452796
J Protein Chem. 2000 May;19(4):269-75
11043931
Curr Biol. 2000 Dec 14-28;10(24):R916-8
11137029
Comb Chem High Throughput Screen. 2000 Oct;3(5):363-72
11032954