Jonathan W. Essex

Publication Activity (10 Years)

Years Active: 1995-2023
Publications (10 Years): 13

Top Topics

Computational Methods

Protein Structure

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

J. Comput. Chem.

J. Cheminformatics

Publications

João Morado, Paul N. Mortenson, J. Willem M. Nissink, Jonathan W. Essex, Chris-Kriton Skylaris
Does a Machine-Learned Potential Perform Better Than an Optimally Tuned Traditional Force Field? A Case Study on Fluorohydrins. J. Chem. Inf. Model. 63 (9) (2023)
Marley L. Samways, Hannah E. Bruce Macdonald, Richard D. Taylor, Jonathan W. Essex
Water Networks in Complexes between Proteins and FDA-Approved Drugs. J. Chem. Inf. Model. 63 (1) (2023)
Yunhui Ge, Oliver J. Melling, Weiming Dong, Jonathan W. Essex, David L. Mobley
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo. J. Comput. Aided Mol. Des. 36 (10) (2022)
Pietro G. A. Aronica, Lauren M. Reid, Nirali Desai, Jianguo Li, Stephen J. Fox, Shilpa Yadahalli, Jonathan W. Essex, Chandra S. Verma
Computational Methods and Tools in Antimicrobial Peptide Research. J. Chem. Inf. Model. 61 (7) (2021)
João Morado, Paul N. Mortenson, Marcel L. Verdonk, Richard A. Ward, Jonathan W. Essex, Chris-Kriton Skylaris
ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields. J. Chem. Inf. Model. 61 (4) (2021)
Marley L. Samways, Hannah E. Bruce Macdonald, Jonathan W. Essex
grand: A Python Module for Grand Canonical Water Sampling in OpenMM. J. Chem. Inf. Model. 60 (10) (2020)
Richard Bradshaw, Jacek Dziedzic, Chris-Kriton Skylaris, Jonathan W. Essex
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields? J. Chem. Inf. Model. 60 (6) (2020)
Miroslav Suruzhon, Tharindu Senapathi, Michael S. Bodnarchuk, Russell C. Viner, Ian D. Wall, Christopher B. Barnett, Kevin J. Naidoo, Jonathan W. Essex
ProtoCaller: Robust Automation of Binding Free Energy Calculations. J. Chem. Inf. Model. 60 (4) (2020)
Tharindu Senapathi, Miroslav Suruzhon, Christopher B. Barnett, Jonathan W. Essex, Kevin J. Naidoo
BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations. J. Chem. Inf. Model. 60 (11) (2020)
James A. Graham, Jonathan W. Essex, Syma Khalid
PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories. J. Chem. Inf. Model. 57 (4) (2017)
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
Conformation and Dynamics of Human Urotensin II and Urotensin Related Peptide in Aqueous Solution. J. Chem. Inf. Model. 57 (2) (2017)
Samuel Genheden, Jonathan W. Essex
All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5. J. Comput. Aided Mol. Des. 30 (11) (2016)
Noor Asidah Mohamed, Richard Bradshaw, Jonathan W. Essex
Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field. J. Comput. Chem. 37 (32) (2016)
Michael S. Bodnarchuk, Russell C. Viner, Julien Michel, Jonathan W. Essex
Strategies to Calculate Water Binding Free Energies in Protein-Ligand Complexes. J. Chem. Inf. Model. 54 (6) (2014)
Samuel Genheden, Ana I. Cabedo Martinez, Michael P. Criddle, Jonathan W. Essex
Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge. J. Comput. Aided Mol. Des. 28 (3) (2014)
Barbara Sander, Oliver Korb, Jason C. Cole, Jonathan W. Essex
How to pick a winning team: approaches towards the selection of computationally derived protein structures for ensemble-based virtual screening. J. Cheminformatics 5 (S-1) (2013)
Andrea Bortolato, Benjamin G. Tehan, Michael S. Bodnarchuk, Jonathan W. Essex, Jonathan S. Mason
Antagonists as a Case Study. J. Chem. Inf. Model. 53 (7) (2013)
Barbara Sander, Oliver Korb, Jason C. Cole, Jonathan W. Essex
The assessment of computationally derived protein ensembles in protein-ligand docking. J. Cheminformatics 4 (S-1) (2012)
Ian R. Craig, Christopher Pfleger, Holger Gohlke, Jonathan W. Essex, Katrin Spiegel
Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins. J. Chem. Inf. Model. 51 (10) (2011)
Ian R. Craig, Jonathan W. Essex, Katrin Spiegel
Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments. J. Chem. Inf. Model. 50 (4) (2010)
Julien Michel, Jonathan W. Essex
Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations. J. Comput. Aided Mol. Des. 24 (8) (2010)
Nava Whiteford, Niall J. Haslam, Gerald Weber, Adam Prügel-Bennett, Jonathan W. Essex, Cameron Neylon
Visualizing the Repeat Structure of Genomic Sequences. Complex Syst. 17 (4) (2008)
Robert Geldhill, Sarah Kent, Andrew J. Milsted, Richard Chapman, Jonathan W. Essex, Jeremy G. Frey
e-Malaria: the schools Malaria project. Concurr. Comput. Pract. Exp. 20 (3) (2008)
Kieron R. Taylor, Jonathan W. Essex, Jeremy G. Frey, Hugo R. Mills, Gareth V. Hughes, Ed Zaluska
Chem. J. Web Semant. 4 (2) (2006)
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
BioSimGrid: Grid-enabled biomolecular simulation data storage and analysis. Future Gener. Comput. Syst. 22 (6) (2006)
Jeremy G. Frey, David De Roure, Kieron R. Taylor, Jonathan W. Essex, Hugo R. Mills, Ed Zaluska
CombeChem: A Case Study in Provenance and Annotation Using the Semantic Web. IPAW (2006)
Kieron R. Taylor, Robert J. Gledhill, Jonathan W. Essex, Jeremy G. Frey, Stephen W. Harris, David De Roure
Bringing Chemical Data onto the Semantic Web. J. Chem. Inf. Model. 46 (3) (2006)
Robert J. Gledhill, Sarah Kent, Brian Hudson, W. Graham Richards, Jonathan W. Essex, Jeremy G. Frey
A Computer-Aided Drug Discovery System for Chemistry Teaching. J. Chem. Inf. Model. 46 (3) (2006)
Ralph A. Mansson, Jeremy G. Frey, Jonathan W. Essex, Alan H. Welsh
Prediction of Properties from Simulations: A Re-examination with Modern Statistical Methods. J. Chem. Inf. Model. 45 (6) (2005)
Kieron R. Taylor, Robert J. Gledhill, Jonathan W. Essex, Jeremy G. Frey, Stephen W. Harris, David De Roure
A semantic datagrid for combinatorial chemistry. GRID (2005)
Julien Michel, Richard D. Taylor, Jonathan W. Essex
The parameterization and validation of generalized born models using the pairwise descreening approximation. J. Comput. Chem. 25 (14) (2004)
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
A Web / Grid Portal Implementation of BioSimGrid: A Biomolecular Simulation Database. ITCC (2) (2004)
Richard D. Taylor, Philip J. Jewsbury, Jonathan W. Essex
FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function. J. Comput. Chem. 24 (13) (2003)
Richard D. Taylor, Philip J. Jewsbury, Jonathan W. Essex
A review of protein-small molecule docking methods. J. Comput. Aided Mol. Des. 16 (3) (2002)
Lewis Whitehead, Colin M. Edge, Jonathan W. Essex
Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation model. J. Comput. Chem. 22 (14) (2001)
Christopher J. Woods, Michael A. King, Jonathan W. Essex
The configurational dependence of binding free energies: A Poisson-Boltzmann study of Neuraminidase inhibitors. J. Comput. Aided Mol. Des. 15 (2) (2001)
Richard H. Henchman, Jonathan W. Essex
Generation of OPLS-like charges from molecular electrostatic potential using restraints. J. Comput. Chem. 20 (5) (1999)
Richard H. Henchman, Jonathan W. Essex
Free energies of hydration using restrained electrostatic potential derived charges via free energy perturbations and linear response. J. Comput. Chem. 20 (5) (1999)
Jonathan W. Essex, William L. Jorgensen
An Empirical Boundary Potential for Water Droplet Simulations. J. Comput. Chem. 16 (8) (1995)
Daniel L. Severance, Jonathan W. Essex, William L. Jorgensen
Generalized Alteration of Structure and Parameters: A New Method for Free- Energy Perturbations in Systems Containing Flexible Degrees of Freedom. J. Comput. Chem. 16 (3) (1995)