Microscopic mechanisms that govern the titration response and pK a values of buried residues in staphylococcal nuclease mutants

Getting the Right Answers for the Right Reasons: Toward Predictive Molecular Simulations of Water with Many-Body Potential Energy Functions

(2016) Francesco Paesani   ACCOUNTS OF CHEMICAL RESEARCH

Water Determines the Structure and Dynamics of Proteins

(2016) Marie-Claire Bellissent-Funel et al.   CHEMICAL REVIEWS

Concepts and protocols for electrostatic free energies

(2016) Thomas Simonson et al.   MOLECULAR SIMULATION

Conformational Reorganization Coupled to the Ionization of Internal Lys Residues in Proteins

(2015) Daniel E. Richman et al.   BIOCHEMISTRY

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

How amide hydrogens exchange in native proteins

(2015) Filip Persson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water

(2015) Xiongwu Wu et al.   PLoS Computational Biology

Predicting Protein Backbone Chemical Shifts From Cα Coordinates: Extracting High Resolution Experimental Observables from Low Resolution Models

(2014) Aaron T. Frank et al.   Journal of Chemical Theory and Computation

Underlying Thermodynamics of pH-Dependent Allostery

(2014) Natali V. Di Russo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Uncovering pH-Dependent Transient States of Proteins with Buried Ionizable Residues

(2014) Garrett B. Goh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Considering Protonation as a Posttranslational Modification Regulating Protein Structure and Function

(2013) André Schönichen et al.   Annual Review of Biophysics

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

(2013) Pedro E. M. Lopes et al.   Journal of Chemical Theory and Computation

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Charge regulation in biomolecular solution

(2013) Mikael Lund et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Thermodynamic Coupling of Protonation and Conformational Equilibria in Proteins: Theory and Simulation

(2012) Chuanyin Shi et al.   BIOPHYSICAL JOURNAL

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Structural Reorganization Triggered by Charging of Lys Residues in the Hydrophobic Interior of a Protein

(2012) Michael S. Chimenti et al.   STRUCTURE

pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

(2012) Natali V. Di Russo et al.   PLoS Computational Biology

SHIFTX2: significantly improved protein chemical shift prediction

(2011) Beomsoo Han et al.   JOURNAL OF BIOMOLECULAR NMR

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

(2011) Jason A. Wallace et al.   Journal of Chemical Theory and Computation

Conformational Relaxation and Water Penetration Coupled to Ionization of Internal Groups in Proteins

(2011) Ana Damjanović et al.   JOURNAL OF PHYSICAL CHEMISTRY A

The High Dielectric Constant of Staphylococcal Nuclease Is Encoded in Its Structural Architecture

(2011) Garrett B. Goh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Large shifts in pKa values of lysine residues buried inside a protein

(2011) D. G. Isom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics

(2011) Evan J. Arthur et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Developing hybrid approaches to predict pKa values of ionizable groups

(2011) Shawn Witham et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy

(2011) Jason A. Wallace et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Toward molecular models of proton pumping: Challenges, methods and relevant applications

(2011) Demian Riccardi et al.   Science China-Chemistry

NMR-Based Protein Potentials

(2010) Da-Wei Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Conformational Consequences of Ionization of Lys, Asp, and Glu Buried at Position 66 in Staphylococcal Nuclease

(2010) Daniel A. Karp et al.   BIOCHEMISTRY

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

(2010) Yang Shen et al.   JOURNAL OF BIOMOLECULAR NMR

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

Structural Origins of High Apparent Dielectric Constants Experienced by Ionizable Groups in the Hydrophobic Core of a Protein

(2010) Michael S. Chimenti et al.   JOURNAL OF MOLECULAR BIOLOGY

High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD

(2010) Wei Jiang et al.   Journal of Physical Chemistry Letters

Evidence for the adaptation of protein pH-dependence to subcellular pH

(2009) Pedro Chan et al.   BMC BIOLOGY

CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software

(2009) Michael F. Crowley et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

The pKa Values of Acidic and Basic Residues Buried at the Same Internal Location in a Protein Are Governed by Different Factors

(2009) Michael J. Harms et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular determinants of the pKavalues of Asp and Glu residues in staphylococcal nuclease

(2009) Carlos A. Castañeda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Backbone Relaxation Coupled to the Ionization of Internal Groups in Proteins: A Self-Guided Langevin Dynamics Study

(2008) Ana Damjanović et al.   BIOPHYSICAL JOURNAL

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Electrostatic Effects in a Network of Polar and Ionizable Groups in Staphylococcal Nuclease

(2008) Kelli L. Baran et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Direct Evidence for Deprotonation of a Lysine Side Chain Buried in the Hydrophobic Core of a Protein

(2008) Yuki Takayama et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

(2008) L. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High tolerance for ionizable residues in the hydrophobic interior of proteins

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

A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein-water interface as a determinant of pKavalues

(2008) Michael J. Harms et al.   PROTEIN SCIENCE