Bioinformatics Advance Access originally published online on September 6, 2007
Bioinformatics 2007 23(19):2558-2565; doi:10.1093/bioinformatics/btm377
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
Department of Biochemistry and Seaver Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA, Institute of Enzymology and Alfred Renyi Institute of Mathematics, Hungarian Academy of Sciences, H-1113 Budapest, Karolina ut 29, Hungary
*To whom correspondence should be addressed.
 |
Abstract |
|---|
Motivation: Two major bottlenecks in advancing comparative protein structure modeling are the efficient combination of multiple template structures and the generation of a correct input target-template alignment.
Results: A novel method, Multiple Mapping Method with Multiple Templates (M4T) is introduced that implements an algorithm to automatically select and combine Multiple Template structures (MT) and an alignment optimization protocol (Multiple Mapping Method, MMM). The MT module of M4T selects and combines multiple template structures through an iterative clustering approach that takes into account the ‘unique’ contribution of each template, their sequence similarity among themselves and to the target sequence, and their experimental resolution. MMM is a sequence-to-structure alignment method that optimally combines alternatively aligned regions according to their fit in the structural environment of the template structure. The resulting M4T alignment is used as input to a comparative modeling module. The performance of M4T has been benchmarked on CASP6 comparative modeling target sequences and on a larger independent test set, and showed favorable performance to current state of the art methods.
Availability: A web server was established for the method at http://www.fiserlab.org/servers/M4T
Contact: afiser{at}aecom.yu.edu or andras{at}fiserlab.org
Associate Editor: Burkhard Rost
Present address: Wyeth Research, CN8000, Princeton, New Jersey, 08543-8000, USA.
Received on March 8, 2007; revised on June 20, 2007; accepted on July 14, 2007
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. A. Assi, T. Tanaka, T. H. Rabbitts, and N. Fernandez-Fuentes PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces Nucleic Acids Res., December 11, 2009; (2009) gkp1158v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. N. Grozdanov, N. Fernandez-Fuentes, A. Fiser, and U. T. Meier Pathogenic NAP57 mutations decrease ribonucleoprotein assembly in dyskeratosis congenita Hum. Mol. Genet., December 1, 2009; 18(23): 4546 - 4551. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. A. Welling and K. Ho A comprehensive guide to the ROMK potassium channel: form and function in health and disease Am J Physiol Renal Physiol, October 1, 2009; 297(4): F849 - F863. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M.S. Madhusudhan, B. M. Webb, M. A. Marti-Renom, N. Eswar, and A. Sali Alignment of multiple protein structures based on sequence and structure features Protein Eng. Des. Sel., September 1, 2009; 22(9): 569 - 574. [Abstract] [Full Text] [PDF]
|
|