Publications
Below a list is displayed including some of the publications that present results involving the use of ProtoMS.
Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo, Matteo Aldeghi, Gregory A. Ross, Michael J. Bodkin, Jonathan W. Essex, Stefan Knapp, and Philip C. Biggin, Communications Chemistry 2018, 1, Article 19 DOI: https://doi.org/10.1038/s42004-018-0019-x
Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo, Gregory A. Ross, Hannah E. Bruce Macdonald, Christopher Cave-Ayland, Ana I. Cabedo Martinez, and Jonathan W. Essex, J. Chem. Theory Comput. 2017, 13 (12), pp 6373-6381 DOI: 10.1021/acs.jctc.7b00738
Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo, Gregory A. Ross, Michael S. Bodnarchuk, and Jonathan W. Essex, JACS 2015, 137 (47), pp 14930-14943 DOI: 10.1021/jacs.5b07940
Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge, Samuel Genheden, Ana I. Cabedo Martinez, Michael P. Criddle, Jonathan W. Essex, J. Comput. Aided Mol. Des. 2014, 28 (3), pp 187-200 DOI: 10.1007/s10822-014-9717-3
An efficient method for the calculation of quantum mechanics/molecular mechanics free energies, Christopher J. Woods, Frederick R. Manby, and Adrian J. Mulholland, J. Chem. Phys. 128, 014109 (2008) DOI: 10.1063/1.2805379
Protein-Ligand Binding Affinity by Nonequilibrium Free Energy Methods, Benjamin P. Cossins, Sebastien Foucher, Colin M. Edge and Jonathan W. Essex, J. Phys. Chem. B, 2008, 112 (47), pp 14985-14992 DOI: 10.1021/jp803533w
Classification of Water Molecules in Protein Binding Sites, Caterina Barillari, Justine Taylor, Russell Viner, and Jonathan W. Essex, J. Am. Chem. Soc., 2007, 129 (9), pp 2577-2587 DOI: 10.1021/ja066980q
The parameterization and validation of generalized born models using the pairwise descreening approximation, Julien Michel, Richard D. Taylor, Jonathan W. Essex, Volume 25, Issue 14, pp 1760-1770 DOI: 10.1002/jcc.20105
Protein-Ligand Binding Affinity Predictions by Implicit Solvent Simulat Protein-Ligand Complexes: Computation of the Relative Free Energy of Different Scaffolds and Binding Modes, Julien Michel, Marcel L. Verdonk, and Jonathan W. Essex, J. Chem. Theory Comput., 2007, 3 (5), pp 1645-1655 DOI: 10.1021/ct700081t Efficient Generalized Born Models for Monte Carlo Simulations, Julien Michel, Richard D. Taylor, and Jonathan W. Essex, J. Chem. Theory Comput., 2006, 2 (3), pp 732-739 DOI: 10.1021/ct600069r