Paircoil2: improved prediction of coiled coils from sequence

被引：337

作者：

McDonnell, AV

Jiang, T

Keating, AE

Berger, B

机构：

[1] MIT, Dept Biol, Cambridge, MA 02139 USA

[2] MIT, Dept Math, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA

来源：

BIOINFORMATICS | 2006年 / 22卷 / 03期

关键词：

D O I：

10.1093/bioinformatics/bti797

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We introduce Paircoil2, a new version of the Paircoil program, which uses pairwise residue probabilities to detect coiled-coil motifs in protein sequence data. Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. It also shows superior performance compared with published methods in tests on proteins of known structure. Availability: Paircoil2 is freely available as a web application and for download at http://paircoil2.csail.mit.edu Contact: keating@mit.edu; bab@mit.edu Supplementary information: Available at Bioinformatics online and at the Paircoil website.

引用

收藏

页码：356 / 358

页数：3

相关论文

共 21 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] PREDICTING COILED COILS BY USE SF PAIRWISE RESIDUE CORRELATIONS [J].

BERGER, B ;

WILSON, DB ;

WOLF, E ;

TONCHEV, T ;

MILLA, M ;

KIM, PS .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1995, 92 (18) :8259-8263

[3] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[4] Core structure of gp41 from the HIV envelope glycoprotein [J].

Chan, DC ;

Fass, D ;

Berger, JM ;

Kim, PS .

CELL, 1997, 89 (02) :263-273

[5] An HMM model for coiled-coil domains and a comparison with PSSM-based predictions [J].

Delorenzi, M ;

Speed, T .

BIOINFORMATICS, 2002, 18 (04) :617-625

[6] B-ZIP proteins encoded by the Drosophila genome:: Evaluation of potential dimerization partners [J].

Fassler, J ;

Landsman, D ;

Acharya, A ;

Moll, JR ;

Bonovich, M ;

Vinson, C .

GENOME RESEARCH, 2002, 12 (08) :1190-1200

[7] Predicting specificity in bZIP coiled-coil protein interactions [J].

Fong, JH ;

Keating, AE ;

Singh, M .

GENOME BIOLOGY, 2004, 5 (02)

[8] An extended microtubule-binding structure within the dynein motor domain [J].

Gee, MA ;

Heuser, JE ;

Vallee, RB .

NATURE, 1997, 390 (6660) :636-639

[9] PQS: a protein quaternary structure file server [J].

Henrick, K ;

Thornton, JM .

TRENDS IN BIOCHEMICAL SCIENCES, 1998, 23 (09) :358-361

[10]

HOBOHM U, 1994, PROTEIN SCI, V3, P522