MMM

A sequence-to-structure alignment protocol

Brajesh K. Rai, Carlos J. Madrid-Aliste, Jorge E. Fajardo, Andras Fiser

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

Motivation: Accurate alignment of a target sequence to a template structure continues to be a bottleneck in producing good quality comparative protein structure models. Results: Multiple Mapping Method (MMM) is a comparative protein structure modeling server with an emphasis on a novel alignment optimization protocol. MMM takes inputs from five profile-to-profile based alignment methods. The alternatively aligned regions from the input alignment set are combined according to their fit in the structural environment of the template structure. The resulting, optimally spliced MMM alignment is used as input to an automated comparative modeling module to produce a full atom model.

Original languageEnglish (US)
Pages (from-to)2691-2692
Number of pages2
JournalBioinformatics
Volume22
Issue number21
DOIs
StatePublished - Nov 1 2006

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Alignment
Network protocols
Protein Structure
Template
Proteins
Model structures
Modeling
Continue
Servers
Server
Module
Atoms
Target
Optimization
Model
Profile

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

MMM : A sequence-to-structure alignment protocol. / Rai, Brajesh K.; Madrid-Aliste, Carlos J.; Fajardo, Jorge E.; Fiser, Andras.

In: Bioinformatics, Vol. 22, No. 21, 01.11.2006, p. 2691-2692.

Research output: Contribution to journalArticle

Rai, Brajesh K. ; Madrid-Aliste, Carlos J. ; Fajardo, Jorge E. ; Fiser, Andras. / MMM : A sequence-to-structure alignment protocol. In: Bioinformatics. 2006 ; Vol. 22, No. 21. pp. 2691-2692.
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