Solving coiled-coil protein structures

Dauter, Zbigniew

doi:10.1107/S2052252515003486

Title: Solving coiled-coil protein structures

Journal Article · Thu Feb 26 00:00:00 EST 2015 · IUCrJ

DOI:https://doi.org/10.1107/S2052252515003486· OSTI ID:1209115

Dauter, Zbigniew ^[1]

Argonne National Lab. (ANL), Argonne, IL (United States)

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.

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Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1209115

Journal Information:: IUCrJ, Vol. 2, Issue 2; ISSN 2052-2525

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 6 works

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References (13)

AMPLE : a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models Bibby, Jaclyn; Keegan, Ronan M.; Mayans, Olga Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 12 https://doi.org/10.1107/S0907444912039194	journal	November 2012
The Buccaneer software for automated model building. 1. Tracing protein chains Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 9 https://doi.org/10.1107/S0907444906022116	journal	August 2006
Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von Heijne Jones, David T. Journal of Molecular Biology, Vol. 292, Issue 2 https://doi.org/10.1006/jmbi.1999.3091	journal	September 1999
MrBUMP : an automated pipeline for molecular replacement Keegan, Ronan M.; Winn, Martyn D. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S0907444907037195	journal	December 2007
Development and benchmarking of TASSERiter for the iterative improvement of protein structure predictions Lee, Seung Yup; Skolnick, Jeffrey Proteins: Structure, Function, and Bioinformatics, Vol. 68, Issue 1 https://doi.org/10.1002/prot.21440	journal	April 2007
ARP / wARP and molecular replacement Perrakis, Anastassis; Harkiolaki, Maria; Wilson, Keith S. Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 10 https://doi.org/10.1107/S0907444901014007	journal	September 2001
Automated de novo phasing and model building of coiled-coil proteins Rämisch, Sebastian; Lizatović, Robert; André, Ingemar Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 3 https://doi.org/10.1107/S1399004714028247	journal	February 2015
A short history of SHELX Sheldrick, George M. Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122 https://doi.org/10.1107/S0108767307043930	journal	December 2007
Clustering of low-energy conformations near the native structures of small proteins Shortle, D.; Simons, K. T.; Baker, D. Proceedings of the National Academy of Sciences, Vol. 95, Issue 19 https://doi.org/10.1073/pnas.95.19.11158	journal	September 1998
Likelihood-enhanced fast rotation functions Storoni, Laurent C.; McCoy, Airlie J.; Read, Randy J. Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 3 https://doi.org/10.1107/S0907444903028956	journal	February 2004
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S090744490705024X	journal	December 2007
Routine phasing of coiled-coil protein crystal structures with AMPLE Thomas, Jens M. H.; Keegan, Ronan M.; Bibby, Jaclyn IUCrJ, Vol. 2, Issue 2 https://doi.org/10.1107/S2052252515002080	journal	February 2015
Computational identification of self-inhibitory peptides from envelope proteins Xu, Yongtao; Rahman, Noorsaadah A. B. D.; Othman, Rozana Proteins: Structure, Function, and Bioinformatics, Vol. 80, Issue 9 https://doi.org/10.1002/prot.24105	journal	June 2012

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75 CONDENSED MATTER PHYSICS
SUPERCONDUCTIVITY AND SUPERFLUIDITY
molecular replacement
ab initio
modeling
coiled-coil proteins

Title: Solving coiled-coil protein structures

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