Selectivity of parvalbumin B protein binding to Ca2+ and Mg2+ at an ab initio QM/MM level using the reference-potential method

Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4. Adaptive QM/MM

(2021) Jia-Ning Wang et al.   Journal of Chemical Theory and Computation

Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 3. Gaussian Smoothing on Density-of-States

(2020) Wenxin Hu et al.   Journal of Chemical Theory and Computation

Host–Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations

(2019) Meiting Wang et al.   Journal of Chemical Theory and Computation

Computational Insights into Endo/Exo Selectivity of Diels--Alder Reaction in Explicit Solvent at ab Initio Quantum Mechanical/Molecular Mechanical Level

(2019) Pengfei Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Scalable Indirect Free Energy Method Applied to Divalent Cation-Metalloprotein Binding

(2019) Jacob Litman et al.   Journal of Chemical Theory and Computation

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

(2019) Chuan Tian et al.   Journal of Chemical Theory and Computation

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

(2018) Louis Lagardère et al.   Chemical Science

Many-body effect determines the selectivity for Ca2+and Mg2+in proteins

(2018) Zhifeng Jing et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation

(2018) Pengfei Li et al.   Journal of Chemical Theory and Computation

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

(2017) Zoe Cournia et al.   Journal of Chemical Information and Modeling

MIB: Metal Ion-Binding Site Prediction and Docking Server

(2016) Yu-Feng Lin et al.   Journal of Chemical Information and Modeling

Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials

(2016) Eric C. Dybeck et al.   Journal of Chemical Theory and Computation

Practical Aspects of Free-Energy Calculations: A Review

(2014) Niels Hansen et al.   Journal of Chemical Theory and Computation

Competition among Metal Ions for Protein Binding Sites: Determinants of Metal Ion Selectivity in Proteins

(2013) Todor Dudev et al.   CHEMICAL REVIEWS

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Frontiers in free-energy calculations of biological systems

(2013) Christophe Chipot   Wiley Interdisciplinary Reviews-Computational Molecular Science

Aqueous solutions of divalent chlorides: Ions hydration shell and water structure

(2012) F. Bruni et al.   JOURNAL OF CHEMICAL PHYSICS

Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases

(2012) Aleksandr V. Marenich et al.   Journal of Chemical Theory and Computation

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Two mechanisms of ion selectivity in protein binding sites

(2010) H. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Metalloproteins and metal sensing

(2009) Kevin J. Waldron et al.   NATURE

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS