Publications

Below a list is displayed including some of the publications that present results involving the use of ProtoMS.

  • 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

  • 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

  • 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

  • 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, pages 1760-1770 DOI: 10.1002/jcc.20105

  • 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

  • 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

  • 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

  • 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

  • Current version of ProtoMS 3.3.0