Simulating GTP:Mg and GDP:Mg with a simple force field: A structural and thermodynamic analysis

PDB_REDO: constructive validation, more than just looking for errors

(2012) Robbie P. Joosten et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Conformational Selection by the aIF2 GTPase: A Molecular Dynamics Study of Functional Pathways

(2011) Priyadarshi Satpati et al.   BIOCHEMISTRY

Free Energy Simulations of a GTPase: GTP and GDP Binding to Archaeal Initiation Factor 2

(2011) Priyadarshi Satpati et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

(2011) Jejoong Yoo et al.   Journal of Physical Chemistry Letters

Conformational selection through electrostatics: Free energy simulations of gtp and gdp binding to archaeal initiation factor 2

(2011) Priyadarshi Satpati et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Conformational Selection in G-Proteins: Lessons from Ras and Rho

(2010) Barry J. Grant et al.   BIOPHYSICAL JOURNAL

Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ

(2010) Jozef Hritz et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

(2010) Christopher M. Baker et al.   Journal of Chemical Theory and Computation

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

(2010) Haibo Yu et al.   Journal of Chemical Theory and Computation

Solvation of Magnesium Dication: Molecular Dynamics Simulation and Vibrational Spectroscopic Study of Magnesium Chloride in Aqueous Solutions

(2010) Karen M. Callahan et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Why an A-Loop Phospho-Mimetic Fails to Activate PAK1: Understanding an Inaccessible Kinase State by Molecular Dynamics Simulations

(2010) Yuen-Wai Ng et al.   STRUCTURE

The Distinct Conformational Dynamics of K-Ras and H-Ras A59G

(2010) Suryani Lukman et al.   PLoS Computational Biology

A Transition Path Ensemble Study Reveals a Linchpin Role for Mg2+during Rate-Limiting ADP Release from Protein Kinase A

(2009) Ilja V. Khavrutskii et al.   BIOCHEMISTRY

PROCAIN: protein profile comparison with assisting information

(2009) Yong Wang et al.   NUCLEIC ACIDS RESEARCH

Nucleotide-dependent conformational states of actin

(2009) J. Pfaendtner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics

(2009) Barry J. Grant et al.   PLoS Computational Biology

Computer Simulations Reveal a Novel Nucleotide-Type Binding Orientation for Ellipticine-Based Anticancer c-kit Kinase Inhibitors†

(2008) Damien Thompson et al.   BIOCHEMISTRY

Detection of Innersphere Interactions between Magnesium Hydrate and the Phosphate Backbone of the HDV Ribozyme Using Raman Crystallography

(2008) Bo Gong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How subunit coupling produces the  -subunit rotary motion in F1-ATPase

(2008) J. Pu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Calculation of protein-ligand binding free energy by using a polarizable potential

(2008) D. Jiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements

(2008) M. Cecchini et al.   PLoS Computational Biology

Release of ADP from the catalytic subunit of protein kinase A: A molecular dynamics simulation study

(2004) Benzhuo Lu et al.   PROTEIN SCIENCE