Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site
- 11 December 2009
- journal article
- Published by Elsevier in Journal of Molecular Biology
- Vol. 394 (4) , 747-763
- https://doi.org/10.1016/j.jmb.2009.09.049
Abstract
No abstract availableKeywords
This publication has 45 references indexed in Scilit:
- Predictions of Hydration Free Energies from All-Atom Molecular Dynamics SimulationsThe Journal of Physical Chemistry B, 2009
- Host−Guest Complexes with Protein−Ligand-like Affinities: Computational Analysis and DesignJournal of the American Chemical Society, 2009
- Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic SimulationsJournal of Chemical Theory and Computation, 2009
- Accelerating QM/MM Free Energy Calculations: Representing the Surroundings by an Updated Mean Charge DistributionThe Journal of Physical Chemistry B, 2008
- A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy–entropy compensationProceedings of the National Academy of Sciences, 2007
- Predicting Absolute Ligand Binding Free Energies to a Simple Model SiteJournal of Molecular Biology, 2007
- Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational ChangeJournal of Chemical Theory and Computation, 2007
- On the use of orientational restraints and symmetry corrections in alchemical free energy calculationsThe Journal of Chemical Physics, 2006
- GROMACS: Fast, flexible, and freeJournal of Computational Chemistry, 2005
- [20] Processing of X-ray diffraction data collected in oscillation modePublished by Elsevier ,1997