SAMPL6 host–guest binding affinities and binding poses from spherical-coordinates-biased simulations

BAR‐based optimum adaptive steered MD for configurational sampling

(2019) Xiaohui Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation

(2019) Zhaoxi Sun et al.   CHEMICAL PHYSICS LETTERS

Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics

(2019) Riccardo Capelli et al.   Journal of Physical Chemistry Letters

Understanding Aldose Reductase-Inhibitors interactions with free energy simulation

(2019) Zhaoxi Sun et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification

(2018) Xiaohui Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

SAMPL6 host–guest challenge: binding free energies via a multistep approach

(2018) Yiğitcan Eken et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

SAMPL6 host–guest blind predictions using a non equilibrium alchemical approach

(2018) Piero Procacci et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Detailed potential of mean force studies on host–guest systems from the SAMPL6 challenge

(2018) Lin Frank Song et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods

(2018) Octav Caldararu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host–guest challenges

(2018) Naohiro Nishikawa et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Overview of the SAMPL6 host–guest binding affinity prediction challenge

(2018) Andrea Rizzi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Thermodynamics of helix formation in small peptides of varying length in vacuo, in implicit solvent, and in explicit solvent

(2018) Xiaohui Wang et al.   JOURNAL OF MOLECULAR MODELING

Cucurbit[8]uril•guest complexes: blinded dataset for the SAMPL6 challenge

(2018) Steven Murkli et al.   SUPRAMOLECULAR CHEMISTRY

Extensive Assessment of Various Computational Methods for Aspartate’s pKa Shift

(2017) Zhaoxi Sun et al.   Journal of Chemical Information and Modeling

Interaction entropy for protein-protein binding

(2017) Zhaoxi Sun et al.   JOURNAL OF CHEMICAL PHYSICS

Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories

(2017) Piero Procacci et al.   Journal of Chemical Theory and Computation

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged–Hydrophobic/Polar and Polar–Hydrophobic/Polar Side Chains

(2017) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation

(2017) Zhao X. Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations

(2017) Federica Moraca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interaction entropy for computational alanine scanning in protein-protein binding

(2017) Linqiong Qiu et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

DOCK 6: Impact of new features and current docking performance

(2015) William J. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations

(2015) Gül H. Zerze et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Diffusion of Hydration Water around Intrinsically Disordered Proteins

(2015) Pooja Rani et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems

(2015) Phillip S. Hudson et al.   Journal of Physical Chemistry Letters

Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps

(2015) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Converging free energies of binding in cucurbit[7]uril and octa-acid host–guest systems from SAMPL4 using expanded ensemble simulations

(2014) Jacob I. Monroe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind prediction of solvation free energies from the SAMPL4 challenge

(2014) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A Time-Independent Free Energy Estimator for Metadynamics

(2014) Pratyush Tiwary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

(2013) John D. Chodera et al.   Annual Review of Biophysics

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Optimization of Umbrella Sampling Replica Exchange Molecular Dynamics by Replica Positioning

(2013) Danial Sabri Dashti et al.   Journal of Chemical Theory and Computation

Residue-Specific α-Helix Propensities from Molecular Simulation

(2012) Robert B. Best et al.   BIOPHYSICAL JOURNAL

Transmembrane Helix Assembly by Window Exchange Umbrella Sampling

(2012) Soohyung Park et al.   PHYSICAL REVIEW LETTERS

Advances and applications of binding affinity prediction methods in drug discovery

(2011) Marco Daniele Parenti et al.   BIOTECHNOLOGY ADVANCES

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Advances in all atom sampling methods for modeling protein–ligand binding affinities

(2011) Emilio Gallicchio et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Identifying low variance pathways for free energy calculations of molecular transformations in solution phase

(2011) Tri T. Pham et al.   JOURNAL OF CHEMICAL PHYSICS

Nonmonotonic Assembly of a Deep-Cavity Cavitand

(2011) Haiying Gan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Thermodynamics of Ligand Binding and Efficiency

(2011) Charles H. Reynolds et al.   ACS Medicinal Chemistry Letters

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

CHARMM: The biomolecular simulation program

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

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

(2009) Sarah E. Boyce et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

(2009) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Are Current Molecular Dynamics Force Fields too Helical?

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

Target Flexibility: An Emerging Consideration in Drug Discovery and Design†

(2008) Pietro Cozzini et al.   JOURNAL OF MEDICINAL CHEMISTRY

Variance Minimization of Free Energy Estimates from Optimized Expanded Ensembles

(2008) Francisco J. Martínez-Veracoechea et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

SFCscore: Scoring functions for affinity prediction of protein-ligand complexes

(2008) Christoph A. Sotriffer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computer-aided drug discovery and development (CADDD): In silico-chemico-biological approach

(2006) I.M. Kapetanovic   CHEMICO-BIOLOGICAL INTERACTIONS