Simulating electrostatic energies in proteins: Perspectives and some recent studies of pKas, redox, and other crucial functional properties

Membrane-Induced Conformational Changes of Kyotorphin Revealed by Molecular Dynamics Simulations

(2010) Miguel Machuqueiro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Renormalizing SMD: The Renormalization Approach and Its Use in Long Time Simulations and Accelerated PMF Calculations of Macromolecules

(2010) Anatoly Dryga et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Constant-pH Molecular Dynamics Simulations Reveal a β-Rich Form of the Human Prion Protein

(2010) Sara R. R. Campos et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization

(2010) S. C. L. Kamerlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes

(2010) Anna Rychkova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability

(2010) Ken C. Usher et al.   PROTEIN SCIENCE

Do salt bridges stabilize proteins? A continuum electrostatic analysis

(2010) Zachary S. Hendsch et al.   PROTEIN SCIENCE

The Electrostatics of VDAC: Implications for Selectivity and Gating

(2009) Om P. Choudhary et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Dynamics at Constant pH and Reduction Potential: Application to Cytochromec3

(2009) Miguel Machuqueiro et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase

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

Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models

(2009) Benjamin M. Messer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Effective approach for calculations of absolute stability of proteins using focused dielectric constants

(2009) Spyridon Vicatos et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Associative Versus Dissociative Mechanisms of Phosphate Monoester Hydrolysis: On the Interpretation of Activation Entropies

(2008) Shina C. L. Kamerlin et al.   CHEMPHYSCHEM

pKaof Residue 66 inStaphylococal nuclease. I. Insights from QM/MM Simulations with Conventional Sampling

(2008) Nilanjan Ghosh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Progress inAb InitioQM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies†

(2008) Shina C. L. Kamerlin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

(2008) Paul A. Sigala et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase

(2008) A. V. Pisliakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Acidic range titration of HEWL using a constant-pH molecular dynamics method

(2008) Miguel Machuqueiro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS