Related references
Note: Only part of the references are listed.Improvements to the APBS biomolecular solvation software suite
Elizabeth Jurrus et al.
PROTEIN SCIENCE (2018)
Simple Models for Nonpolar Solvation: Parameterization and Testing
Eleni Michael et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)
Accurate, Robust, and Reliable Calculations of Poisson-Boltzmann Binding Energies
Duc D. Nguyen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)
Electrostatic Component of Binding Energy: Interpreting Predictions from Poisson-Boltzmann Equation and Modeling Protocols
Arghya Chakavorty et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2016)
Implicit solvent methods for free energy estimation
Sergio Decherchi et al.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY (2015)
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
Samuel Genheden et al.
EXPERT OPINION ON DRUG DISCOVERY (2015)
Introducing Charge Hydration Asymmetry into the Generalized Born Model
Abhishek Mukhopadhyay et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
A New Set of Atomic Radii for Accurate Estimation of Solvation Free Energy by Poisson-Boltzmann Solvent Model
Junya Yamagishi et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)
All- Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model
Alexey Savelyev et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)
FreeSolv: a database of experimental and calculated hydration free energies, with input files
David L. Mobley et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2014)
Effects of geometry and chemistry on hydrophobic solvation
Robert C. Harris et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
Pedro E. M. Lopes et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Optimizing Electrostatic Field Calculations with the Adaptive Poisson-Boltzmann Solver to Predict Electric Fields at Protein-Protein Interfaces. I. Sampling and Focusing
Andrew W. Ritchie et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes
Hege Beard et al.
PLOS ONE (2013)
Variational approach for nonpolar solvation analysis
Zhan Chen et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations
Jens Kleinjung et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Charge Hydration Asymmetry: The Basic Principle and How to Use It to Test and Improve Water Models
Abhishek Mukhopadhyay et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
The ORCA program system
Frank Neese
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2012)
Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii
Boris Aguilar et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Do salt bridges stabilize proteins? A continuum electrostatic analysis
Zachary S. Hendsch et al.
PROTEIN SCIENCE (2010)
CHARMM: The Biomolecular Simulation Program
B. R. Brooks et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
Yuqing Deng et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Improved prediction of protein side-chain conformations with SCWRL4
Georgii G. Krivov et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Continuum polarizable force field within the Poisson-Boltzmann framework
Yu-Hong Tan et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Optimized parameters for continuum solvation calculations with carbohydrates
David F. Green
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Analysis of integral expressions for effective Born radii
John Mongan et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Polarizable atomic multipole solutes in a generalized Kirkwood continuum
Michael J. Schnieders et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum
Michael J. Schnieders et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Continuum treatment of electronic polarization effect
Yu-Hong Tan et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Computational alanine scanning mutagenesis - An improved methodological approach
Irina S. Moreira et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)
Optimizing the Poisson dielectric boundary with explicit solvent forces and energies: Lessons learned with atom-centered dielectric functions
Jessica M. J. Swanson et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis
Chunhu Tan et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms
Jason A. Wagoner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Electrostatics calculations: latest methodological advances
P Koehl
CURRENT OPINION IN STRUCTURAL BIOLOGY (2006)
A polarizable model of water for molecular dynamics simulations of biomolecules
G Lamoureux et al.
CHEMICAL PHYSICS LETTERS (2006)
Scalable molecular dynamics with NAMD
JC Phillips et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Very fast empirical prediction and rationalization of protein pKa values
H Li et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Limitations of atom-centered dielectric functions in implicit solvent models
JMJ Swanson et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
A polarizable force field and continuum solvation methodology for modeling of protein-ligand interactions
JR Maple et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
Optimized radii for Poisson-Boltzmann calculations with the AMBER force field
JMJ Swanson et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)
Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy
F Weigend et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2005)
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
E Gallicchio et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
H Gohlke et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
TJ Dolinsky et al.
NUCLEIC ACIDS RESEARCH (2004)
Hydration of amino acid side chains: Nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules
YQ Deng et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation
T Grycuk
JOURNAL OF CHEMICAL PHYSICS (2003)
On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy
RM Levy et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Modeling the structure of Agitoxin in complex with the Shaker K+ channel:: A computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles
MAL Eriksson et al.
BIOPHYSICAL JOURNAL (2002)
Accurate transferable model for water, n-octanol, and n-hexadecane solvation free energies
AJ Bordner et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2002)
Free energy simulations come of age: Protein-ligand recognition
T Simonson et al.
ACCOUNTS OF CHEMICAL RESEARCH (2002)
Electrostatics of nanosystems: Application to microtubules and the ribosome
NA Baker et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
PA Kollman et al.
ACCOUNTS OF CHEMICAL RESEARCH (2000)
The bacterial cell-division protein ZipA and its interaction with an FtsZ fragment revealed by X-ray crystallography
L Mosyak et al.
EMBO JOURNAL (2000)
Share Paper
