Jonathan W. Essex

40 papers Journal 37Unranked 3
YearRankTypeTitle / Venue / Authors
2023 J jnl
Does a Machine-Learned Potential Perform Better Than an Optimally Tuned Traditional Force Field? A Case Study on Fluorohydrins.
J. Chem. Inf. Model.
João Morado, Paul N. Mortenson, J. Willem M. Nissink, Jonathan W. Essex, Chris-Kriton Skylaris
2023 J jnl
Water Networks in Complexes between Proteins and FDA-Approved Drugs.
J. Chem. Inf. Model.
Marley L. Samways, Hannah E. Bruce Macdonald, Richard D. Taylor, Jonathan W. Essex
2022 J jnl
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo.
J. Comput. Aided Mol. Des.
Yunhui Ge, Oliver J. Melling, Weiming Dong, Jonathan W. Essex, David L. Mobley
2021 J jnl
Computational Methods and Tools in Antimicrobial Peptide Research.
J. Chem. Inf. Model.
Pietro G. A. Aronica, Lauren M. Reid, Nirali Desai, Jianguo Li, Stephen J. Fox, Shilpa Yadahalli, Jonathan W. Essex, Chandra S. Verma
2021 J jnl
ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields.
J. Chem. Inf. Model.
João Morado, Paul N. Mortenson, Marcel L. Verdonk, Richard A. Ward, Jonathan W. Essex, Chris-Kriton Skylaris
2020 J jnl
BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations.
J. Chem. Inf. Model.
Tharindu Senapathi, Miroslav Suruzhon, Christopher B. Barnett, Jonathan W. Essex, Kevin J. Naidoo
2020 J jnl
ProtoCaller: Robust Automation of Binding Free Energy Calculations.
J. Chem. Inf. Model.
Miroslav Suruzhon, Tharindu Senapathi, Michael S. Bodnarchuk, Russell C. Viner, Ian D. Wall, Christopher B. Barnett, Kevin J. Naidoo, Jonathan W. Essex
2020 J jnl
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
J. Chem. Inf. Model.
Richard Bradshaw, Jacek Dziedzic, Chris-Kriton Skylaris, Jonathan W. Essex
2020 J jnl
grand: A Python Module for Grand Canonical Water Sampling in OpenMM.
J. Chem. Inf. Model.
Marley L. Samways, Hannah E. Bruce Macdonald, Jonathan W. Essex
2017 J jnl
Conformation and Dynamics of Human Urotensin II and Urotensin Related Peptide in Aqueous Solution.
J. Chem. Inf. Model.
Elke Haensele, Nawel Mele, Marija Miljak, Christopher M. Read, David C. Whitley, Lee Banting, Carla Delépée, Jana Sopkova-de Oliveira Santos, Alban Lepailleur, Ronan Bureau, Jonathan W. Essex, Timothy Clark
2017 J jnl
PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories.
J. Chem. Inf. Model.
James A. Graham, Jonathan W. Essex, Syma Khalid
2016 J jnl
All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.
J. Comput. Aided Mol. Des.
Samuel Genheden, Jonathan W. Essex
2016 J jnl
Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field.
J. Comput. Chem.
Noor Asidah Mohamed, Richard Bradshaw, Jonathan W. Essex
2014 J jnl
Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.
J. Comput. Aided Mol. Des.
Samuel Genheden, Ana I. Cabedo Martinez, Michael P. Criddle, Jonathan W. Essex
2014 J jnl
Strategies to Calculate Water Binding Free Energies in Protein-Ligand Complexes.
J. Chem. Inf. Model.
Michael S. Bodnarchuk, Russell C. Viner, Julien Michel, Jonathan W. Essex
2013 J jnl
How to pick a winning team: approaches towards the selection of computationally derived protein structures for ensemble-based virtual screening.
J. Cheminformatics
Barbara Sander, Oliver Korb, Jason C. Cole, Jonathan W. Essex
2013 J jnl
Water Network Perturbation in Ligand Binding: Adenosine A
J. Chem. Inf. Model.
Andrea Bortolato, Benjamin G. Tehan, Michael S. Bodnarchuk, Jonathan W. Essex, Jonathan S. Mason
2012 J jnl
The assessment of computationally derived protein ensembles in protein-ligand docking.
J. Cheminformatics
Barbara Sander, Oliver Korb, Jason C. Cole, Jonathan W. Essex
2011 J jnl
Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins.
J. Chem. Inf. Model.
Ian R. Craig, Christopher Pfleger, Holger Gohlke, Jonathan W. Essex, Katrin Spiegel
2010 J jnl
Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments.
J. Chem. Inf. Model.
Ian R. Craig, Jonathan W. Essex, Katrin Spiegel
2010 J jnl
Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations.
J. Comput. Aided Mol. Des.
Julien Michel, Jonathan W. Essex
2008 J jnl
Visualizing the Repeat Structure of Genomic Sequences.
Complex Syst.
Nava Whiteford, Niall J. Haslam, Gerald Weber, Adam Prügel-Bennett, Jonathan W. Essex, Cameron Neylon
2008 J jnl
e-Malaria: the schools Malaria project.
Concurr. Comput. Pract. Exp.
Robert Geldhill, Sarah Kent, Andrew J. Milsted, Richard Chapman, Jonathan W. Essex, Jeremy G. Frey
2006 J jnl
A Computer-Aided Drug Discovery System for Chemistry Teaching.
J. Chem. Inf. Model.
Robert J. Gledhill, Sarah Kent, Brian Hudson, W. Graham Richards, Jonathan W. Essex, Jeremy G. Frey
2006 J jnl
BioSimGrid: Grid-enabled biomolecular simulation data storage and analysis.
Future Gener. Comput. Syst.
Muan Hong Ng, Steven J. Johnston, Bing Wu, Stuart E. Murdock, Kaihsu Tai, Hans Fangohr, Simon J. Cox, Jonathan W. Essex, Mark S. P. Sansom, Paul Jeffreys
2006 J jnl
Bringing Chemical Data onto the Semantic Web.
J. Chem. Inf. Model.
Kieron R. Taylor, Robert J. Gledhill, Jonathan W. Essex, Jeremy G. Frey, Stephen W. Harris, David De Roure
2006 — conf
CombeChem: A Case Study in Provenance and Annotation Using the Semantic Web.
IPAW
Jeremy G. Frey, David De Roure, Kieron R. Taylor, Jonathan W. Essex, Hugo R. Mills, Ed Zaluska
2006 J jnl
The Semantic Grid and chemistry: Experiences with Comb
J. Web Semant.
Kieron R. Taylor, Jonathan W. Essex, Jeremy G. Frey, Hugo R. Mills, Gareth V. Hughes, Ed Zaluska
2005 — conf
A semantic datagrid for combinatorial chemistry.
GRID
Kieron R. Taylor, Robert J. Gledhill, Jonathan W. Essex, Jeremy G. Frey, Stephen W. Harris, David De Roure
2005 J jnl
Prediction of Properties from Simulations: A Re-examination with Modern Statistical Methods.
J. Chem. Inf. Model.
Ralph A. Mansson, Jeremy G. Frey, Jonathan W. Essex, Alan H. Welsh
2004 — conf
A Web / Grid Portal Implementation of BioSimGrid: A Biomolecular Simulation Database.
ITCC (2)
Bing Wu, Matthew J. Dovey, Muan Hong Ng, Kaihsu Tai, Stuart E. Murdock, Paul Jeffreys, Simon J. Cox, Jonathan W. Essex, Mark S. P. Sansom
2004 J jnl
The parameterization and validation of generalized born models using the pairwise descreening approximation.
J. Comput. Chem.
Julien Michel, Richard D. Taylor, Jonathan W. Essex
2003 J jnl
FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function.
J. Comput. Chem.
Richard D. Taylor, Philip J. Jewsbury, Jonathan W. Essex
2002 J jnl
A review of protein-small molecule docking methods.
J. Comput. Aided Mol. Des.
Richard D. Taylor, Philip J. Jewsbury, Jonathan W. Essex
2001 J jnl
Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation model.
J. Comput. Chem.
Lewis Whitehead, Colin M. Edge, Jonathan W. Essex
2001 J jnl
The configurational dependence of binding free energies: A Poisson-Boltzmann study of Neuraminidase inhibitors.
J. Comput. Aided Mol. Des.
Christopher J. Woods, Michael A. King, Jonathan W. Essex
1999 J jnl
Free energies of hydration using restrained electrostatic potential derived charges via free energy perturbations and linear response.
J. Comput. Chem.
Richard H. Henchman, Jonathan W. Essex
1999 J jnl
Generation of OPLS-like charges from molecular electrostatic potential using restraints.
J. Comput. Chem.
Richard H. Henchman, Jonathan W. Essex
1995 J jnl
An Empirical Boundary Potential for Water Droplet Simulations.
J. Comput. Chem.
Jonathan W. Essex, William L. Jorgensen
1995 J jnl
Generalized Alteration of Structure and Parameters: A New Method for Free- Energy Perturbations in Systems Containing Flexible Degrees of Freedom.
J. Comput. Chem.
Daniel L. Severance, Jonathan W. Essex, William L. Jorgensen