A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

The ONIOM Method and Its Applications

(2015) Lung Wa Chung et al.   CHEMICAL REVIEWS

Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules

(2015) Krishnan Raghavachari et al.   CHEMICAL REVIEWS

Energy-Based Molecular Fragmentation Methods

(2015) Michael A. Collins et al.   CHEMICAL REVIEWS

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins

(2015) Jinfeng Liu et al.   Journal of Chemical Theory and Computation

The Use of Many-Body Expansions and Geometry Optimizations in Fragment-Based Methods

(2014) Dmitri G. Fedorov et al.   ACCOUNTS OF CHEMICAL RESEARCH

The Successful Merger of Theoretical Thermochemistry with Fragment-Based Methods in Quantum Chemistry

(2014) Raghunath O. Ramabhadran et al.   ACCOUNTS OF CHEMICAL RESEARCH

The Combined Fragmentation and Systematic Molecular Fragmentation Methods

(2014) Michael A. Collins et al.   ACCOUNTS OF CHEMICAL RESEARCH

Generalized Energy-Based Fragmentation Approach and Its Applications to Macromolecules and Molecular Aggregates

(2014) Shuhua Li et al.   ACCOUNTS OF CHEMICAL RESEARCH

Some Practical Approaches to Treating Electrostatic Polarization of Proteins

(2014) Changge Ji et al.   ACCOUNTS OF CHEMICAL RESEARCH

Explicit Polarization: A Quantum Mechanical Framework for Developing Next Generation Force Fields

(2014) Jiali Gao et al.   ACCOUNTS OF CHEMICAL RESEARCH

Efficient and Accurate Fragmentation Methods

(2014) Spencer R. Pruitt et al.   ACCOUNTS OF CHEMICAL RESEARCH

Fragment Quantum Mechanical Calculation of Proteins and Its Applications

(2014) Xiao He et al.   ACCOUNTS OF CHEMICAL RESEARCH

Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method for Full Quantum Mechanical Calculation of Protein Energy

(2013) Xianwei Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY A

The Charge Transfer Problem in Density Functional Theory Calculations of Aqueously Solvated Molecules

(2013) Christine M. Isborn et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automation of AMOEBA polarizable force field parameterization for small molecules

(2012) Johnny C. Wu et al.   THEORETICAL CHEMISTRY ACCOUNTS

Fragmentation Methods: A Route to Accurate Calculations on Large Systems

(2011) Mark S. Gordon et al.   CHEMICAL REVIEWS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

(2011) Pengyu Ren et al.   Journal of Chemical Theory and Computation

Polarization of Intraprotein Hydrogen Bond Is Critical to Thermal Stability of Short Helix

(2011) Ya Gao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics

(2011) Ivan S. Ufimtsev et al.   Journal of Physical Chemistry Letters

Current Status of the AMOEBA Polarizable Force Field

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

Electrostatic Polarization Makes a Substantial Contribution to the Free Energy of Avidin−Biotin Binding

(2010) Yan Tong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds

(2010) Li L. Duan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

(2009) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

Developing Polarized Protein-Specific Charges for Protein Dynamics: MD Free Energy Calculation of pKa Shifts for Asp26/Asp20 in Thioredoxin

(2008) Changge Ji et al.   BIOPHYSICAL JOURNAL

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL