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DMAPS: a database of multiple alignments for protein structures.

Chittibabu Guda1, Lipika R Pal, Ilya N Shindyalov

  • 1Gen*NY*sis Center for Excellence in Cancer Genomics and Department of Epidemiology and Biostatistics, University at Albany, State University of New York, One Discovery drive, Rensselaer, NY 12144-3456, USA. cguda@albany.edu

Nucleic Acids Research
|December 31, 2005
PubMed
Summary
This summary is machine-generated.

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The database of multiple alignments for protein structures (DMAPS) offers access to pre-computed protein structure alignments for all Protein Data Bank families. This resource aids researchers in protein structure analysis and comparison.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Protein structure families are crucial for understanding protein function and evolution.
  • Accessing and comparing multiple protein structures is essential for detailed analysis.
  • Existing methods for structural alignment can be computationally intensive and time-consuming.

Purpose of the Study:

  • To create a comprehensive database of pre-computed multiple structure alignments for protein families.
  • To provide researchers with easy and rapid access to these alignments for analysis.
  • To facilitate the study of protein structure-function relationships and evolutionary conservation.

Main Methods:

  • Utilized four classification methods (SCOP, CATH, ENZYME, CE) to define protein structure families.

Related Experiment Videos

  • Employed CE-MC software to generate multiple structure alignments for families with at least three members.
  • Developed a web-based query system for retrieving alignments using Protein Data Bank (PDB) chain IDs.

    • Main Results:

    • The database, DMAPS, contains multiple structure alignments for 3050 SCOP, 3087 CATH, 664 ENZYME, and 1707 CE-based families.
    • Alignments are available for families with a minimum of three members.
    • A user-friendly web interface allows for efficient retrieval and viewing/downloading of alignments.

    Conclusions:

    • DMAPS provides a valuable, readily accessible resource for structural bioinformatics.
    • The database simplifies the process of comparing and analyzing protein structures within families.
    • Facilitates research in protein evolution, function, and drug discovery through structural insights.