A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream
Abstract
Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriartyet al.(2014),FEBS J.281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used byPhenixis described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or deposition in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries.
- Authors:
-
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences
- Oregon State Univ., Corvallis, OR (United States). Dept. of Biochemistry and Biophysics
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE; National Institutes of Health (NIH)
- OSTI Identifier:
- 1378757
- Grant/Contract Number:
- AC02-05CH11231; R01-GM083136; 1P01 GM063210
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Acta Crystallographica. Section D. Structural Biology
- Additional Journal Information:
- Journal Volume: 72; Journal Issue: 1; Journal ID: ISSN 2059-7983
- Publisher:
- IUCr
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; covalent geometry restraints; crystallographic refinement; protein structure; validation; Phenix
Citation Formats
Moriarty, Nigel W., Tronrud, Dale E., Adams, Paul D., and Karplus, P. Andrew. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream. United States: N. p., 2016.
Web. doi:10.1107/S2059798315022408.
Moriarty, Nigel W., Tronrud, Dale E., Adams, Paul D., & Karplus, P. Andrew. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream. United States. https://doi.org/10.1107/S2059798315022408
Moriarty, Nigel W., Tronrud, Dale E., Adams, Paul D., and Karplus, P. Andrew. Fri .
"A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream". United States. https://doi.org/10.1107/S2059798315022408. https://www.osti.gov/servlets/purl/1378757.
@article{osti_1378757,
title = {A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream},
author = {Moriarty, Nigel W. and Tronrud, Dale E. and Adams, Paul D. and Karplus, P. Andrew},
abstractNote = {Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriartyet al.(2014),FEBS J.281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used byPhenixis described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or deposition in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries.},
doi = {10.1107/S2059798315022408},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 1,
volume = 72,
place = {United States},
year = {Fri Jan 01 00:00:00 EST 2016},
month = {Fri Jan 01 00:00:00 EST 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 33 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Experimentally observed conformation-dependent geometry and hidden strain in proteins
journal, July 1996
- Karplus, P. Andrew
- Protein Science, Vol. 5, Issue 7
The Computational Crystallography Toolbox : crystallographic algorithms in a reusable software framework
journal, January 2002
- Grosse-Kunstleve, Ralf W.; Sauter, Nicholas K.; Moriarty, Nigel W.
- Journal of Applied Crystallography, Vol. 35, Issue 1
Ab initio studies of molecular geometries. 27. Optimized molecular structures and conformational analysis of N.alpha.-acetyl-N-methylalaninamide and comparison with peptide crystal data and empirical calculations
journal, June 1983
- Scarsdale, J. N.; Van Alsenoy, C.; Klimkowski, V. J.
- Journal of the American Chemical Society, Vol. 105, Issue 11
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
Conformation Dependence of Backbone Geometry in Proteins
journal, October 2009
- Berkholz, Donald S.; Shapovalov, Maxim V.; Dunbrack, Roland L.
- Structure, Vol. 17, Issue 10
Predictions of protein backbone structural parameters from first principles: Systematic comparisons of calculated N-C(.alpha.)-C' angles with high-resolution protein crystallographic results
journal, June 1995
- Jiang, Xiaoqin; Cao, Ming; Teppen, Brian
- The Journal of Physical Chemistry, Vol. 99, Issue 26
Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement
journal, June 2014
- Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.
- FEBS Journal, Vol. 281, Issue 18
MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009
- Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions
journal, February 2008
- Karplus, P. Andrew; Shapovalov, Maxim V.; Dunbrack, Roland L.
- Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 3
Conformational transitions and geometry differences between low-energy conformers of N -acetyl- N ′-methyl alanineamide: An ab initio study at the 4-21G level with gradient relaxed geometries : CONFORMATIONAL TRANSITIONS
journal, November 1984
- Schäfer, Lothar; Klimkowski, V. J.; Momany, Frank A.
- Biopolymers, Vol. 23, Issue 11
Proteins Do Not Have Strong Spines After All
journal, October 2009
- Dauter, Zbigniew; Wlodawer, Alexander
- Structure, Vol. 17, Issue 10
Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins
journal, June 2010
- Tronrud, Dale E.; Berkholz, Donald S.; Karplus, P. Andrew
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 7
Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012
- Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
An efficient general-purpose least-squares refinement program for macromolecular structures
journal, July 1987
- Tronrud, D. E.; Ten Eyck, L. F.; Matthews, B. W.
- Acta Crystallographica Section A Foundations of Crystallography, Vol. 43, Issue 4
PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010
- Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution
journal, July 2011
- Tronrud, Dale E.; Karplus, P. Andrew
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 8
Works referencing / citing this record:
Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations
journal, January 2018
- Jiang, Zhongming; Biczysko, Malgorzata; Moriarty, Nigel W.
- Proteins: Structure, Function, and Bioinformatics, Vol. 86, Issue 3
Systematic exploration of protein conformational space using a Distance Geometry approach
journal, August 2019
- Malliavin, Thérèse E.; Mucherino, Antonio; Lavor, Carlile
- Journal of Chemical Information and Modeling
An editor for the generation and customization of geometry restraints
journal, February 2017
- Moriarty, Nigel W.; Draizen, Eli J.; Adams, Paul D.
- Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 2
Strategies for carbohydrate model building, refinement and validation
journal, February 2017
- Agirre, Jon
- Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 2
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
text, January 2019
- Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L.
- Apollo - University of Cambridge Repository
Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach
journal, August 2019
- Malliavin, Thérèse E.; Mucherino, Antonio; Lavor, Carlile
- Journal of Chemical Information and Modeling, Vol. 59, Issue 10