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|
journal
|
March 2007 |
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|
journal
|
September 1978 |
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|
journal
|
May 1997 |
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|
journal
|
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|
journal
|
November 1963 |
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|
journal
|
March 2006 |
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|
journal
|
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|
journal
|
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|
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|
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|
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|
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|
journal
|
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|
journal
|
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|
journal
|
March 2012 |
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|
journal
|
July 1987 |
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|
journal
|
April 2008 |
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|
journal
|
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Comparison of simple potential functions for simulating liquid water
|
journal
|
July 1983 |
Refinement of large structures by simultaneous minimization of energy and R factor
|
journal
|
November 1978 |
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|
journal
|
December 1991 |
Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters
|
journal
|
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Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum
|
journal
|
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|
journal
|
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|
journal
|
January 1999 |
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|
journal
|
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Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS
- Grindon, Christina; Harris, Sarah; Evans, Tom
-
Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences, Vol. 362, Issue 1820
https://doi.org/10.1098/rsta.2004.1381
|
journal
|
July 2004 |
Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms 1 1Edited by J. Thornton
|
journal
|
January 1999 |
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|
journal
|
March 2008 |
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|
journal
|
July 1991 |
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|
journal
|
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|
journal
|
January 1989 |
A short history of SHELX
|
journal
|
December 2007 |
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
|
journal
|
June 1993 |
All-atom crystal simulations of DNA and RNA duplexes
|
journal
|
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|
journal
|
June 2014 |
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|
journal
|
January 1987 |
Application and Limitations of X-ray Crystallographic Data in Structure-Based Ligand and Drug Design
|
journal
|
June 2003 |
Simulations of a Protein Crystal: Explicit Treatment of Crystallization Conditions Links Theory and Experiment in the Streptavidin−Biotin Complex †
|
journal
|
November 2008 |
REFMAC 5 for the refinement of macromolecular crystal structures
|
journal
|
March 2011 |
Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the α → β Anomerization of Glucose
|
journal
|
June 1998 |
Peptide Crystal Simulations Reveal Hidden Dynamics
|
journal
|
May 2013 |
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|
journal
|
January 2003 |
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|
journal
|
November 2018 |
R free and the R free ratio. II. Calculation of the expected values and variances of cross-validation statistics in macromolecular least-squares refinement
|
journal
|
April 2000 |
PHENIX: a comprehensive Python-based system for macromolecular structure solution
|
journal
|
January 2010 |
KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program
|
journal
|
November 2009 |
The Protein Data Bank
|
journal
|
January 2000 |
Molecular dynamics simulations with experimental restraints
|
journal
|
February 1991 |
Protein Data Bank: the single global archive for 3D macromolecular structure data
|
journal
|
October 2018 |
On the complexity of Engh and Huber refinement restraints: the angle τ as example
|
journal
|
November 2010 |
Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus a 1Edited by R. Huber
|
journal
|
November 1998 |
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|
journal
|
January 2003 |
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
|
journal
|
June 2013 |
Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement
|
journal
|
May 1997 |
The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
|
journal
|
November 1993 |
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
|
journal
|
July 2015 |
Application and Limitations of X-Ray Crystallographic Data in Structure-Based Ligand and Drug Design.
|
journal
|
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|
journal
|
June 2015 |
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|
journal
|
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The Backrub Motion: How Protein Backbone Shrugs When a Sidechain Dances
|
journal
|
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Diffuse X-Ray Scattering to Model Protein Motions
|
journal
|
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Dynamics of the Streptavidin−Biotin Complex in Solution and in Its Crystal Lattice: Distinct Behavior Revealed by Molecular Simulations
|
journal
|
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|
journal
|
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|
journal
|
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|
journal
|
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|
journal
|
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Crystal structure refinement with SHELXL
|
journal
|
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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
|
text
|
January 2019 |
Structure and dynamics of two β-peptides in solution from molecular dynamics simulations validated against experiment
|
text
|
January 2008 |
PHENIX: a comprehensive Python-based system for macromolecular structure solution.
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text
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January 2010 |