Literature DB >> 12069625

Molecular dynamics applied to X-ray structure refinement.

Axel T Brunger1, Paul D Adams.   

Abstract

Simulated annealing, in the form of temperature-controlled molecular dynamics, has been successfully applied to macromolecular X-ray structure optimization. The theory and practice of the method are reviewed, and some recent improvements are described.

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Year:  2002        PMID： 12069625     DOI： 10.1021/ar010034r

Source DB:  PubMed          Journal:  Acc Chem Res        ISSN： 0001-4842            Impact factor:   22.384


  28 in total

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2.  Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.

Authors:  N Powers; Jan H Jensen
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3.  Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement.

Authors:  Ning Yu; Xue Li; Guanglei Cui; Seth A Hayik; Kenneth M Merz
Journal:  Protein Sci       Date:  2006-12       Impact factor: 6.725

Review 4.  Biomolecular simulation and modelling: status, progress and prospects.

Authors:  Marc W van der Kamp; Katherine E Shaw; Christopher J Woods; Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

5.  Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure.

Authors:  Prasad V Burra; Ying Zhang; Adam Godzik; Boguslaw Stec
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6.  Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling.

Authors:  Jennifer L Knight; Zhiyong Zhou; Emilio Gallicchio; Daniel M Himmel; Richard A Friesner; Eddy Arnold; Ronald M Levy
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-03-19

7.  Assigning the protonation states of the key aspartates in β-Secretase using QM/MM X-ray structure refinement.

Authors:  Ning Yu; Seth A Hayik; Bing Wang; Ning Liao; Charles H Reynolds; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2006       Impact factor: 6.006

8.  Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign.

Authors:  Karen Tran; Christian Poulsen; Javier Guenaga; Natalia de Val; Natalia de Val Alda; Richard Wilson; Christopher Sundling; Yuxing Li; Robyn L Stanfield; Ian A Wilson; Andrew B Ward; Gunilla B Karlsson Hedestam; Richard T Wyatt
Journal:  Proc Natl Acad Sci U S A       Date:  2014-02-03       Impact factor: 11.205

9.  Structural rationale for the cross-resistance of tumor cells bearing the A399V variant of elongation factor eEF1A1 to the structurally unrelated didemnin B, ternatin, nannocystin A and ansatrienin B.

Authors:  Pedro A Sánchez-Murcia; Álvaro Cortés-Cabrera; Federico Gago
Journal:  J Comput Aided Mol Des       Date:  2017-09-12       Impact factor: 3.686

10.  Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.

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Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-05-15
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