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September 2018 |
Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages
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October 2018 |
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
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August 2006 |
Absolute Binding Free Energies: A Quantitative Approach for Their Calculation
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September 2003 |
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations: GENESIS
- Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa
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Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 5, Issue 4
https://doi.org/10.1002/wcms.1220
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May 2015 |
CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates
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February 2019 |
Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy
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February 2015 |
On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities
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January 2012 |
CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems : CHARMM-GUI
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January 2019 |
Scalable molecular dynamics with NAMD
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January 2005 |
Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges
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October 2018 |
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
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February 2008 |
Efficient estimation of free energy differences from Monte Carlo data
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October 1976 |
Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations
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March 2001 |
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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March 1977 |
Isothermal-isobaric molecular dynamics using stochastic velocity rescaling
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February 2009 |
Alchemical free energy methods for drug discovery: progress and challenges
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April 2011 |
Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
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February 2009 |
Rigorous Free Energy Simulations in Virtual Screening
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June 2020 |
Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant
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July 2006 |
The Many Roles of Computation in Drug Discovery
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March 2004 |
CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application
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December 2012 |
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations
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August 2014 |
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD
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March 2014 |
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
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January 2009 |
MATCH: An atom-typing toolset for molecular mechanics force fields
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November 2011 |
FESetup: Automating Setup for Alchemical Free Energy Simulations
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November 2015 |
Constant pressure molecular dynamics simulation: The Langevin piston method
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September 1995 |
The statistical-thermodynamic basis for computation of binding affinities: a critical review
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March 1997 |
CHARMM: The biomolecular simulation program
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July 2009 |
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
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July 2017 |
Development and testing of a general amber force field
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January 2004 |
Massively parallel computation of absolute binding free energy with well-equilibrated states
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February 2009 |
Sensitivity in Binding Free Energies Due to Protein Reorganization
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August 2016 |
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
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June 2010 |
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins
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December 2015 |
The Role of Bonded Terms in Free Energy Simulations: 1. Theoretical Analysis
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December 1998 |
Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
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June 1994 |
Free energy calculations for DNA base stacking by replica-exchange umbrella sampling
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February 2004 |
Hierarchical Grouping to Optimize an Objective Function
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March 1963 |
Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD
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August 2019 |
Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods
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January 2003 |
CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes
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July 2009 |
Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets
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November 2017 |
Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation
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August 2016 |
CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules: CHARMM-GUI Ligand Reader and Modeler for CHARMM Force Field Generation of Small Molecules
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May 2017 |
Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: Linkage of dynamics and structural plasticity
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July 1995 |
Hydration of Amino Acid Side Chains: Nonpolar and Electrostatic Contributions Calculated from Staged Molecular Dynamics Free Energy Simulations with Explicit Water Molecules
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October 2004 |
CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems
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July 2013 |
Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials
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October 2006 |
CHARMM-GUI: A web-based graphical user interface for CHARMM
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March 2008 |
Canonical sampling through velocity rescaling
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January 2007 |
Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change
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May 2007 |
Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
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July 2010 |
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
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June 1993 |
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
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April 2009 |
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features
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September 2018 |
CHARMM-GUI supports the Amber force fields
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July 2020 |
Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package
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August 2013 |
Free Energy Simulations: Thermodynamic Reversibility and Variability
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May 2000 |
Solvation thermodynamics of nonionic solutes
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August 1984 |
Structure of the Adenosine A2A Receptor in Complex with ZM241385 and the Xanthines XAC and Caffeine
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September 2011 |
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
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August 2012 |
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
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October 1992 |
Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability
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October 2019 |
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
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December 2015 |
Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations
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September 2007 |
Prediction of Protein–Ligand Binding Pose and Affinity Using the gREST+FEP Method
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July 2020 |
Separation‐shifted scaling, a new scaling method for Lennard‐Jones interactions in thermodynamic integration
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June 1994 |
Efficient Drug Lead Discovery and Optimization
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June 2009 |
FMCS: a novel algorithm for the multiple MCS problem
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March 2013 |
CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans
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November 2018 |
Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank
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June 2017 |
Calculation of Protein-Ligand Binding Affinities
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June 2007 |
Statistically optimal analysis of samples from multiple equilibrium states
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September 2008 |
Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions
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October 2016 |
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
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October 1992 |
2- n -Butyl-9-methyl-8-[1,2,3]triazol-2-yl-9 H -purin-6-ylamine and Analogues as A 2A Adenosine Receptor Antagonists. Design, Synthesis, and Pharmacological Characterization
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November 2005 |
A smooth particle mesh Ewald method
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November 1995 |
Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape
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August 2019 |
Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery
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December 2016 |
Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
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August 2007 |
Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data
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July 2013 |
Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration
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April 2005 |
CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues
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August 2014 |