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Related Experiment Videos

CE-MC: a multiple protein structure alignment server.

Chittibabu Guda1, Sifang Lu, Eric D Scheeff

  • 1San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. babu@sdsc.edu

Nucleic Acids Research
|June 25, 2004
PubMed
Summary
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The CE-MC server offers a web-based tool for aligning multiple protein structures using Combinatorial Extension (CE) and Monte Carlo (MC) methods. It facilitates structural comparisons for up to 25 protein chains, aiding in understanding protein function and evolution.

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Protein structure alignment is crucial for understanding biological function and evolutionary relationships.
  • Existing methods may have limitations in handling multiple protein structures simultaneously.
  • A need exists for accessible computational tools for large-scale structural comparisons.

Purpose of the Study:

  • To introduce the CE-MC server, a web-based facility for multiple protein structure alignment.
  • To provide a user-friendly platform for comparing user-selected or uploaded protein structures.
  • To enable efficient and accurate alignment of up to 25 protein structural chains.

Main Methods:

  • Utilizes Combinatorial Extension (CE) for all-to-all pairwise structural alignments.

Related Experiment Videos

  • Employs Monte Carlo (MC) optimization for iterative global alignment refinement.
  • Integrates the JOY program for formatting alignment results.

    • Main Results:

    • The CE-MC server successfully performs multiple protein structure alignments based on C-alpha coordinate distances.
    • It supports alignments of user-selected Protein Data Bank (PDB) chains, uploaded structures, or a combination.
    • The server allows for the alignment of up to 25 protein structural chains.

    Conclusions:

    • The CE-MC server provides a valuable resource for researchers needing to perform multiple protein structure alignments.
    • Its web-based interface and flexible input options enhance accessibility for structural biology studies.
    • The availability of source code and binaries supports large-scale applications and local installations.