MMM: A sequence-to-structure alignment protocol

Brajesh K. Rai, Carlos J. Madrid-Aliste, J. Eduardo Fajardo, András Fiser

Research output: Contribution to journalArticlepeer-review

31 Scopus citations


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
Issue number21
StatePublished - Nov 1 2006

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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