Computational scheme for pH-dependent binding free energy calculation with explicit solvent

Enhancing Constant-pH Simulation in Explicit Solvent with a Two-Dimensional Replica Exchange Method

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

An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald

(2014) Andrew C. Simmonett et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

(2014) Gerhard König et al.   Journal of Chemical Theory and Computation

An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

(2014) Yen-Lin Lin et al.   Journal of Chemical Theory and Computation

Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril–Guest Binding Enthalpies

(2014) Andrew T. Fenley et al.   Journal of Chemical Theory and Computation

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

(2014) Juyong Lee et al.   Journal of Chemical Theory and Computation

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4

(2014) Gerhard König et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protocols Utilizing Constant pH Molecular Dynamics to Compute pH-Dependent Binding Free Energies

(2014) M. Olivia Kim et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cucurbit[7]uril: A High-Affinity Host for Encapsulation of Amino Saccharides and Supramolecular Stabilization of Their α-Anomers in Water

(2013) Yoonjung Jang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical Calculations

(2013) Pedro Ojeda-May et al.   Journal of Chemical Theory and Computation

The therapeutic journey of benzimidazoles: A review

(2012) Yogita Bansal et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett’s Acceptance Ratio and Enveloping Distribution Sampling Methods

(2012) Gerhard König et al.   Journal of Chemical Theory and Computation

Blind prediction of host–guest binding affinities: a new SAMPL3 challenge

(2012) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Supramolecular encapsulation of benzimidazole-derived drugs by cucurbit[7]uril

(2011) Apurba L. Koner et al.   CANADIAN JOURNAL OF CHEMISTRY

Engineered epidermal growth factor mutants with faster binding on-rates correlate with enhanced receptor activation

(2011) Jennifer L. Lahti et al.   FEBS LETTERS

Cutoff radius effect of the isotropic periodic sum and Wolf method in liquid–vapor interfaces of water

(2011) Kazuaki Z. Takahashi et al.   JOURNAL OF CHEMICAL PHYSICS

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

(2011) Serena Donnini et al.   Journal of Chemical Theory and Computation

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

(2011) Garrett B. Goh et al.   Journal of Chemical Theory and Computation

MSCALE: A General Utility for Multiscale Modeling

(2011) H. Lee Woodcock et al.   Journal of Chemical Theory and Computation

Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations

(2011) Gerhard König et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Progress in the prediction of pKa values in proteins

(2011) Emil Alexov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

pH replica-exchange method based on discrete protonation states

(2011) Satoru G. Itoh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Is the prediction of pKa values by constant-pH molecular dynamics being hindered by inherited problems?

(2011) Miguel Machuqueiro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Cucurbituril chemistry: a tale of supramolecular success

(2011) Eric Masson et al.   RSC Advances

Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding

(2010) Boris Aguilar et al.   BIOPHYSICAL JOURNAL

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

Non-Boltzmann sampling and Bennett's acceptance ratio method: How to profit from bending the rules

(2010) Gerhard König et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Isotropic periodic sum of electrostatic interactions for polar systems

(2009) Xiongwu Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Unorthodox uses of Bennett's acceptance ratio method

(2009) Gerhard König et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMMing: A New, Flexible Web Portal for CHARMM

(2008) Benjamin T. Miller et al.   Journal of Chemical Information and Modeling

Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems

(2008) Xiongwu Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Multiple free energies from a single simulation: Extending enveloping distribution sampling to nonoverlapping phase-space distributions

(2008) Clara D. Christ et al.   JOURNAL OF CHEMICAL PHYSICS

Protein-protein binding is often associated with changes in protonation state

(2007) Aaron C. Mason et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS