Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis

Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?

(2016) Xiaodong Pang et al.   Communications in Computational Physics

pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa

(2015) Lin Wang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Biological applications of classical electrostatics methods

(2014) Wesley M. Botello-Smith et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

Recent progress in adapting Poisson–Boltzmann methods to molecular simulations

(2014) Li Xiao et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

(2013) Wei Ye et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Exploring accurate Poisson–Boltzmann methods for biomolecular simulations

(2013) Changhao Wang et al.   Computational and Theoretical Chemistry

Reducing Grid Dependence in Finite-Difference Poisson–Boltzmann Calculations

(2012) Jun Wang et al.   Journal of Chemical Theory and Computation

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Development of Polarizable Models for Molecular Mechanical Calculations. 4. van der Waals Parametrization

(2012) Junmei Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Development of Polarizable Models for Molecular Mechanical Calculations. 3. Polarizable Water Models Conforming to Thole Polarization Screening Schemes

(2012) Jun Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On-the-Fly Numerical Surface Integration for Finite-Difference Poisson–Boltzmann Methods

(2011) Qin Cai et al.   Journal of Chemical Theory and Computation

Analyzing the robustness of the MM/PBSA free energy calculation method: Application to DNA conformational transitions

(2011) Allyn R. Brice et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Development of Polarizable Models for Molecular Mechanical Calculations I: Parameterization of Atomic Polarizability

(2011) Junmei Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Development of Polarizable Models for Molecular Mechanical Calculations II: Induced Dipole Models Significantly Improve Accuracy of Intermolecular Interaction Energies

(2011) Junmei Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Virtual screening using molecular simulations

(2011) Tianyi Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson–Boltzmann-Based Molecular Electrostatics

(2011) Chandrajit Bajaj et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Accounting for Ligand Conformational Restriction in Calculations of Protein-Ligand Binding Affinities

(2010) Cen Gao et al.   BIOPHYSICAL JOURNAL

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

A Revised Density Function for Molecular Surface Calculation in Continuum Solvent Models

(2010) Xiang Ye et al.   Journal of Chemical Theory and Computation

Poisson–Nernst–Planck equations for simulating biomolecular diffusion–reaction processes I: Finite element solutions

(2010) Benzhuo Lu et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Exploring a coarse-grained distributive strategy for finite-difference Poisson–Boltzmann calculations

(2010) Meng-Juei Hsieh et al.   JOURNAL OF MOLECULAR MODELING

Roles of Boundary Conditions in DNA Simulations: Analysis of Ion Distributions with the Finite-Difference Poisson-Boltzmann Method

(2009) Xiang Ye et al.   BIOPHYSICAL JOURNAL

On removal of charge singularity in Poisson–Boltzmann equation

(2009) Qin Cai et al.   JOURNAL OF CHEMICAL PHYSICS

An Adaptive Fast Multipole Boundary Element Method for Poisson−Boltzmann Electrostatics

(2009) Benzhuo Lu et al.   Journal of Chemical Theory and Computation

Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model

(2009) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Performance of Nonlinear Finite-Difference Poisson−Boltzmann Solvers

(2009) Qin Cai et al.   Journal of Chemical Theory and Computation

Quantitative analysis of Poisson–Boltzmann implicit solvent in molecular dynamics

(2009) Jun Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Achieving energy conservation in Poisson–Boltzmann molecular dynamics: Accuracy and precision with finite-difference algorithms

(2008) Jun Wang et al.   CHEMICAL PHYSICS LETTERS

Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements

(2008) Michael D. Altman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry

(2008) Anthony Nicholls et al.   JOURNAL OF MEDICINAL CHEMISTRY

Protein Stability Prediction:  A Poisson−Boltzmann Approach

(2008) Yu-Hong Tan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme

(2004) Jim Warwicker   PROTEIN SCIENCE