Paircoil2: improved prediction of coiled coils from sequence

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.

[1]  U. Hobohm,et al.  Enlarged representative set of protein structures , 1994, Protein science : a publication of the Protein Society.

[2]  Philip E. Bourne,et al.  The Protein Data Bank (PDB) | NIST , 2002 .

[3]  F Arisaka,et al.  Identification of kinesin neck region as a stable alpha-helical coiled coil and its thermodynamic characterization. , 1997, Biochemistry.

[4]  J Walshaw,et al.  Socket: a program for identifying and analysing coiled-coil motifs within protein structures. , 2001, Journal of molecular biology.

[5]  E. Mandelkow,et al.  The coiled-coil helix in the neck of kinesin. , 1998, Journal of structural biology.

[6]  M. Delorenzi,et al.  An HMM model for coiled-coil domains and a comparison with PSSM-based predictions , 2002, Bioinform..

[7]  David Landsman,et al.  B-ZIP proteins encoded by the Drosophila genome: evaluation of potential dimerization partners. , 2002, Genome research.

[8]  Ueli Aebi,et al.  Molecular architecture of intermediate filaments , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[9]  Jessica H. Fong,et al.  Predicting specificity in bZIP coiled-coil protein interactions , 2004, Genome Biology.

[10]  M. Vincentz,et al.  Phylogenetic relationships between Arabidopsis and sugarcane bZIP transcriptional regulatory factors , 2001 .

[11]  A. Lupas,et al.  Predicting coiled coils from protein sequences , 1991, Science.

[12]  Adam Godzik,et al.  Tolerating some redundancy significantly speeds up clustering of large protein databases , 2002, Bioinform..

[13]  A. Keating,et al.  Comprehensive Identification of Human bZIP Interactions with Coiled-Coil Arrays , 2003, Science.

[14]  J. Thornton,et al.  PQS: a protein quaternary structure file server. , 1998, Trends in biochemical sciences.

[15]  M Singh,et al.  LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins , 1999, Journal of Molecular Biology.

[16]  B. Berger,et al.  Predicting coiled coils by use of pairwise residue correlations. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[17]  B. Berger,et al.  MultiCoil: A program for predicting two‐and three‐stranded coiled coils , 1997, Protein science : a publication of the Protein Society.

[18]  Richard B. Vallee,et al.  An extended microtubule-binding structure within the dynein motor domain , 1997, Nature.

[19]  K. Namba,et al.  Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy , 2003, Nature.

[20]  Deborah Fass,et al.  Core Structure of gp41 from the HIV Envelope Glycoprotein , 1997, Cell.