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

Abstract

An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.

Authors:
ORCiD logo [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
810424
Report Number(s):
LA-UR-02-3903
Journal ID: ISSN 0907-4449; ABCRE6
Grant/Contract Number:  
W-7405-ENG-36
Resource Type:
Accepted Manuscript
Journal Name:
Acta Crystallographica. Section D: Biological Crystallography
Additional Journal Information:
Journal Volume: 59; Journal Issue: 1; Journal ID: ISSN 0907-4449
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Terwilliger, Thomas C. Automated side-chain model building and sequence assignment by template matching. United States: N. p., 2002. Web. doi:10.1107/S0907444902018048.
Terwilliger, Thomas C. Automated side-chain model building and sequence assignment by template matching. United States. doi:10.1107/S0907444902018048.
Terwilliger, Thomas C. Fri . "Automated side-chain model building and sequence assignment by template matching". United States. doi:10.1107/S0907444902018048. https://www.osti.gov/servlets/purl/810424.
@article{osti_810424,
title = {Automated side-chain model building and sequence assignment by template matching},
author = {Terwilliger, Thomas C.},
abstractNote = {An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.},
doi = {10.1107/S0907444902018048},
journal = {Acta Crystallographica. Section D: Biological Crystallography},
number = 1,
volume = 59,
place = {United States},
year = {2002},
month = {12}
}

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