DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Solving coiled-coil protein structures

Abstract

With the availability of more than 100,000 entries stored in the Protein Data Bank (PDB) that can be used as search models, molecular replacement (MR) is currently the most popular method of solving crystal structures of macromolecules. Significant methodological efforts have been directed in recent years towards making this approach more powerful and practical. This resulted in the creation of several computer programs, highly automated and user friendly, that are able to successfully solve many structures even by researchers who, although interested in structures of biomolecules, are not very experienced in crystallography.

Authors:
 [1]
  1. Argonne National Lab. (ANL), Argonne, IL (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1209115
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
IUCrJ
Additional Journal Information:
Journal Volume: 2; Journal Issue: 2; Journal ID: ISSN 2052-2525
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; molecular replacement; ab initio; modeling; coiled-coil proteins

Citation Formats

Dauter, Zbigniew. Solving coiled-coil protein structures. United States: N. p., 2015. Web. doi:10.1107/S2052252515003486.
Dauter, Zbigniew. Solving coiled-coil protein structures. United States. https://doi.org/10.1107/S2052252515003486
Dauter, Zbigniew. Thu . "Solving coiled-coil protein structures". United States. https://doi.org/10.1107/S2052252515003486. https://www.osti.gov/servlets/purl/1209115.
@article{osti_1209115,
title = {Solving coiled-coil protein structures},
author = {Dauter, Zbigniew},
abstractNote = {With the availability of more than 100,000 entries stored in the Protein Data Bank (PDB) that can be used as search models, molecular replacement (MR) is currently the most popular method of solving crystal structures of macromolecules. Significant methodological efforts have been directed in recent years towards making this approach more powerful and practical. This resulted in the creation of several computer programs, highly automated and user friendly, that are able to successfully solve many structures even by researchers who, although interested in structures of biomolecules, are not very experienced in crystallography.},
doi = {10.1107/S2052252515003486},
journal = {IUCrJ},
number = 2,
volume = 2,
place = {United States},
year = {Thu Feb 26 00:00:00 EST 2015},
month = {Thu Feb 26 00:00:00 EST 2015}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 6 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

AMPLE : a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models
journal, November 2012

  • Bibby, Jaclyn; Keegan, Ronan M.; Mayans, Olga
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 12
  • DOI: 10.1107/S0907444912039194

The Buccaneer software for automated model building. 1. Tracing protein chains
journal, August 2006


Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von Heijne
journal, September 1999


MrBUMP : an automated pipeline for molecular replacement
journal, December 2007

  • Keegan, Ronan M.; Winn, Martyn D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1
  • DOI: 10.1107/S0907444907037195

Development and benchmarking of TASSERiter for the iterative improvement of protein structure predictions
journal, April 2007

  • Lee, Seung Yup; Skolnick, Jeffrey
  • Proteins: Structure, Function, and Bioinformatics, Vol. 68, Issue 1
  • DOI: 10.1002/prot.21440

ARP / wARP and molecular replacement
journal, September 2001

  • Perrakis, Anastassis; Harkiolaki, Maria; Wilson, Keith S.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 10
  • DOI: 10.1107/S0907444901014007

Automated de novo phasing and model building of coiled-coil proteins
journal, February 2015

  • Rämisch, Sebastian; Lizatović, Robert; André, Ingemar
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 3
  • DOI: 10.1107/S1399004714028247

A short history of SHELX
journal, December 2007

  • Sheldrick, George M.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122
  • DOI: 10.1107/S0108767307043930

Clustering of low-energy conformations near the native structures of small proteins
journal, September 1998

  • Shortle, D.; Simons, K. T.; Baker, D.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 19
  • DOI: 10.1073/pnas.95.19.11158

Likelihood-enhanced fast rotation functions
journal, February 2004

  • Storoni, Laurent C.; McCoy, Airlie J.; Read, Randy J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 3
  • DOI: 10.1107/S0907444903028956

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
journal, December 2007

  • Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1
  • DOI: 10.1107/S090744490705024X

Routine phasing of coiled-coil protein crystal structures with AMPLE
journal, February 2015


Computational identification of self-inhibitory peptides from envelope proteins
journal, June 2012

  • Xu, Yongtao; Rahman, Noorsaadah A. B. D.; Othman, Rozana
  • Proteins: Structure, Function, and Bioinformatics, Vol. 80, Issue 9
  • DOI: 10.1002/prot.24105