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Ido Y. Ben-Shalom et al.
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Rajat K. Pal et al.
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Samuel C. Gill et al.
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Matteo Aldeghi et al.
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BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation
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M. Amaral et al.
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Sensitivity in Binding Free Energies Due to Protein Reorganization
Nathan M. Lim et al.
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Bradley Sherborne et al.
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Guidelines for the analysis of free energy calculations
Pavel V. Klimovich et al.
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Christoph Dellago et al.
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Marco D'Abramo et al.
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Perspective: Alchemical free energy calculations for drug discovery
David L. Mobley et al.
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Daniel Seeliger et al.
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Thomas Steinbrecher et al.
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Jennifer L. Knight et al.
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Michael R. Shirts et al.
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Predicting absolute ligand binding free energies to a simple model site
David L. Mobley et al.
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Jeffrey R. Huth et al.
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Todd J. Dolinsky et al.
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Comparison of free energy methods for molecular systems
F. Marty Ytreberg et al.
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Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant
Yuqing Deng et al.
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On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
David L. Mobley et al.
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Rare events and the convergence of exponentially averaged work values
C Jarzynski
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Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation
D Wu et al.
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Calculation of absolute protein-ligand binding free energy from computer simulations
HJ Woo et al.
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MR Shirts et al.
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JM Wang et al.
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PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
TJ Dolinsky et al.
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The development of replica-exchange-based free-energy methods
CJ Woods et al.
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Enhanced configurational sampling in binding free-energy calculations
CJ Woods et al.
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Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods
MR Shirts et al.
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S Boresch et al.
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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
A Jakalian et al.
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Multidimensional replica-exchange method for free-energy calculations
Y Sugita et al.
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