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Automated side-chain model building and sequence assignment by template matching.

Thomas C Terwilliger1

  • 1Los Alamos National Laboratory, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

Acta Crystallographica. Section D, Biological Crystallography
|December 25, 2002
PubMed
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This study presents an automated algorithm for building protein side chains in electron-density maps, improving structural modeling accuracy. The method aligns protein sequences and builds side chains, aiding crystallographers in model refinement.

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Automated model building in X-ray crystallography is crucial for determining protein structures.
  • Accurate placement and identification of amino acid side chains are essential for high-resolution protein models.

Purpose of the Study:

  • To develop and implement an automated algorithm for building protein side chains within electron-density maps.
  • To align protein sequences with electron-density maps for improved structural determination.

Main Methods:

  • An algorithm was developed comparing electron density at expected side-chain positions with templates derived from 574 refined protein structures.
  • A Bayesian approach was used to estimate the probability of amino acid identities and sequence alignments.

Related Experiment Videos

  • The most probable rotamer for each side chain was built into the model.

    • Main Results:

    • The algorithm successfully automates the building of side chains in electron-density maps.
    • High-confidence sequence-to-map alignments were achieved.
    • The RESOLVE software incorporates this automated procedure.

    Conclusions:

    • The automated side-chain building algorithm, combined with automated main-chain building, generates preliminary protein models.
    • These models are suitable for further refinement and extension by experienced crystallographers.
    • This advancement streamlines the protein structure determination process.