Related references
Note: Only part of the references are listed.Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software
Yuriy Khalak et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2021)
AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge
Yuanjun Shi et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2021)
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations
Andrea Rizzi et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2020)
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies
Conor D. Parks et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2020)
An open-source drug discovery platform enables ultra-large virtual screens
Christoph Gorgulla et al.
NATURE (2020)
Rigorous Free Energy Simulations in Virtual Screening
Zoe Cournia et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS)
Jan Walther Perthold et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials
Tai-Sung Lee et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects
Christina E. M. Schindler et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery
Tai-Sung Lee et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo
Gregory A. Ross et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease
Marina Macchiagodena et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Exploring Novel Directions in Free Energy Calculations
Kira A. Armacost et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Large scale relative protein ligand binding affinities using non-equilibrium alchemy
Vytautas Gapsys et al.
CHEMICAL SCIENCE (2020)
Simulating Water Exchange to Buried Binding Sites
Ido Y. Ben-Shalom et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo
Kalistyn H. Burley et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Perturbation potentials to overcome order/disorder transitions in alchemical binding free energy calculations
Rajat K. Pal et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules
Joel Wahl et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
Free Energy Methods in Drug Design: Prospects of Alchemical Perturbation in Medicinal Chemistry
Billy J. Williams-Noonan et al.
JOURNAL OF MEDICINAL CHEMISTRY (2018)
Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo
Samuel C. Gill et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis
Wei Jiang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations
Matteo Aldeghi et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)
BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation
Zhao X. Sun et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding
M. Amaral et al.
NATURE COMMUNICATIONS (2017)
Sensitivity in Binding Free Energies Due to Protein Reorganization
Nathan M. Lim et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Collaborating to improve the use of free-energy and other quantitative methods in drug discovery
Bradley Sherborne et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2016)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Guidelines for the analysis of free energy calculations
Pavel V. Klimovich et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2015)
pmx: Automated Protein Structure and Topology Generation for Alchemical Perturbations
Vytautas Gapsys et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)
Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics
Christoph Dellago et al.
ENTROPY (2014)
Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges
Marco D'Abramo et al.
FRONTIERS IN GENETICS (2014)
Perspective: Alchemical free energy calculations for drug discovery
David L. Mobley et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
Protein Thermostability Calculations Using Alchemical Free Energy Simulations
Daniel Seeliger et al.
BIOPHYSICAL JOURNAL (2010)
Towards Accurate Free Energy Calculations in Ligand Protein-Binding Studies
Thomas Steinbrecher et al.
CURRENT MEDICINAL CHEMISTRY (2010)
λ-Dynamics Free Energy Simulation Methods
Jennifer L. Knight et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
Statistically optimal analysis of samples from multiple equilibrium states
Michael R. Shirts et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Predicting absolute ligand binding free energies to a simple model site
David L. Mobley et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Confine-and-release method: Obtaining correct binding free energies in the presence of protein conformational change
David L. Mobley et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Discovery and design of novel HSP90 inhibitors using multiple fragment-based design strategies
Jeffrey R. Huth et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2007)
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
Todd J. Dolinsky et al.
NUCLEIC ACIDS RESEARCH (2007)
Comparison of free energy methods for molecular systems
F. Marty Ytreberg et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant
Yuqing Deng et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
David L. Mobley et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Rare events and the convergence of exponentially averaged work values
C Jarzynski
PHYSICAL REVIEW E (2006)
Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation
D Wu et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Calculation of absolute protein-ligand binding free energy from computer simulations
HJ Woo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration
MR Shirts et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Development and testing of a general amber force field
JM Wang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
TJ Dolinsky et al.
NUCLEIC ACIDS RESEARCH (2004)
The development of replica-exchange-based free-energy methods
CJ Woods et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2003)
Enhanced configurational sampling in binding free-energy calculations
CJ Woods et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2003)
Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods
MR Shirts et al.
PHYSICAL REVIEW LETTERS (2003)
Absolute binding free energies: A quantitative approach for their calculation
S Boresch et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2003)
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
A Jakalian et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
Multidimensional replica-exchange method for free-energy calculations
Y Sugita et al.
JOURNAL OF CHEMICAL PHYSICS (2000)