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MMM: a sequence-to-structure alignment protocol.

Brajesh K Rai1, Carlos J Madrid-Aliste, J Eduardo Fajardo

  • 1Department of Biochemistry and Seaver Center for Bioinformatics, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, NY 10461, USA.

Bioinformatics (Oxford, England)
|August 25, 2006
PubMed
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Accurate protein structure modeling is improved by the Multiple Mapping Method (MMM) server. MMM optimizes sequence alignment to template structures, enhancing the quality of comparative protein models.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein modeling

Background:

  • Accurate sequence-to-structure alignment is crucial for comparative protein modeling.
  • Existing methods face challenges in producing high-quality models.

Purpose of the Study:

  • To present the Multiple Mapping Method (MMM) server for improved comparative protein structure modeling.
  • To introduce a novel alignment optimization protocol within MMM.

Main Methods:

  • MMM integrates alignments from five profile-to-profile methods.
  • It optimizes alignment by combining alternatively aligned regions based on structural fit.
  • The optimized alignment is used for automated full-atom model generation.

Main Results:

Related Experiment Videos

  • The MMM server provides an optimized alignment protocol.
  • This protocol enhances the accuracy of sequence-to-structure mapping.
  • It facilitates the production of high-quality comparative protein models.

Conclusions:

  • The MMM server offers a robust solution for a key bottleneck in protein structure modeling.
  • Its novel alignment optimization improves model quality.
  • The server is freely accessible for research use.