Literature DB >> 14696384

Promise of advances in simulation methods for protein crystallography: implicit solvent models, time-averaging refinement, and quantum mechanical modeling.

Celia Schiffer1, Jan Hermans.   

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Year:  2003        PMID： 14696384     DOI： 10.1016/S0076-6879(03)74019-1

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN： 0076-6879            Impact factor:   1.600


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  7 in total

1.  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

2.  Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations.

Authors:  Poramaet Laowanapiban; Maryna Kapustina; Clemens Vonrhein; Marc Delarue; Patrice Koehl; Charles W Carter
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-27       Impact factor: 11.205

3.  Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling.

Authors:  Anthony K Felts; Emilio Gallicchio; Dmitriy Chekmarev; Kristina A Paris; Richard A Friesner; Ronald M Levy
Journal:  J Chem Theory Comput       Date:  2008       Impact factor: 6.006

4.  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

5.  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

6.  Interdependence of Inhibitor Recognition in HIV-1 Protease.

Authors:  Janet L Paulsen; Florian Leidner; Debra A Ragland; Nese Kurt Yilmaz; Celia A Schiffer
Journal:  J Chem Theory Comput       Date:  2017-04-11       Impact factor: 6.006

7.  An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings.

Authors:  Irene Maffucci; Xiao Hu; Valentina Fumagalli; Alessandro Contini
Journal:  Front Chem       Date:  2018-03-05       Impact factor: 5.221
  7 in total

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