Jonathan W. Essex

发表

Towards a grid-enabled biomolecular simulation database

Jonathan W. Essex, Stuart Murdock, Kaihsu Tai, 2005 .

11th German Conference on Chemoinformatics (GCC 2015)

Timothy Clark, Jonathan W. Essex, Peter Kolb, 2016, Journal of Cheminformatics.

The Semantic Grid and chemistry: Experiences with CombeChem

Jonathan W. Essex, Ed Zaluska, Jeremy G. Frey, 2006, J. Web Semant..

Strategies to Calculate Water Binding Free Energies in Protein-Ligand Complexes

Jonathan W. Essex, Julien Michel, Michael S. Bodnarchuk, 2014, J. Chem. Inf. Model..

Implementation of Dual Resolution Simulation Methodology in LAMMPS

Jonathan W. Essex, Iain Bethune, Sophia Wheeler, 2016 .

The assessment of computationally derived protein ensembles in protein-ligand docking

Jonathan W. Essex, Oliver Korb, Jason C. Cole, 2012, Journal of Cheminformatics.

Generalized alteration of structure and parameters: A new method for free‐energy perturbations in systems containing flexible degrees of freedom

Jonathan W. Essex, William L. Jorgensen, Daniel L. Severance, 1995, J. Comput. Chem..

FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function

Jonathan W. Essex, Richard D. Taylor, Philip J. Jewsbury, 2003, J. Comput. Chem..

Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study

Jonathan W. Essex, Michael S. Bodnarchuk, Jonathan S. Mason, 2013, J. Chem. Inf. Model..

Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments

Jonathan W. Essex, Ian R. Craig, Katrin Spiegel, 2010, J. Chem. Inf. Model..

CombeChem: A Case Study in Provenance and Annotation Using the Semantic Web

Jonathan W. Essex, David De Roure, Ed Zaluska, 2006, IPAW.

The Application of Distributed Computing to the Investigation of Protein Conformational Change

Jonathan W. Essex, Christopher J. Woods, Jeremy G. Frey, 2004 .

Combinatorial chemistry and the Grid

Jonathan W. Essex, Michael Luck, Luc Moreau, 2003 .

An empirical boundary potential for water droplet simulations

Jonathan W. Essex, William L. Jorgensen, W. L. Jorgensen, 1995, J. Comput. Chem..

e-Malaria: the schools Malaria project

Jonathan W. Essex, Jeremy G. Frey, Richard Chapman, 2008, Concurr. Comput. Pract. Exp..

A semantic datagrid for combinatorial chemistry

Jonathan W. Essex, Robert J. Gledhill, David De Roure, 2005, The 6th IEEE/ACM International Workshop on Grid Computing, 2005..

BioSimGrid: a distributed database for biomolecular simulations

Jonathan W. Essex, Stuart Murdock, Muan Hong Ng, 2003 .

Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

Jonathan W. Essex, Julien Michel, J. Essex, 2010, J. Comput. Aided Mol. Des..

How to pick a winning team: approaches towards the selection of computationally derived protein structures for ensemble-based virtual screening

Jonathan W. Essex, Oliver Korb, Jason C. Cole, 2013, Journal of Cheminformatics.

Digital signal processing methods to analyze and enhance conformational change

Jonathan W. Essex, Robert J. Gledhill, Stephen Phillips, 2002 .

Generation of OPLS-like charges from molecular electrostatic potential using restraints

Jonathan W. Essex, Richard H. Henchman, 1999, J. Comput. Chem..

Bringing Chemical Data onto the Semantic Web

Jonathan W. Essex, Robert J. Gledhill, David De Roure, 2006, J. Chem. Inf. Model..

Free energies of hydration using restrained electrostatic potential derived charges via free energy perturbations and linear response

Jonathan W. Essex, Richard H. Henchman, J. Essex, 1999, J. Comput. Chem..

Prediction of Properties from Simulations: A Re-examination with Modern Statistical Methods

Jonathan W. Essex, Jeremy G. Frey, Ralph A. Mansson, 2005, J. Chem. Inf. Model..

Application of distributed computing to computer simulations

Jonathan W. Essex, Andrew R. Leach, Christopher J. Woods, 2004 .

A Computer-Aided Drug Discovery System for Chemistry Teaching

Jonathan W. Essex, Robert J. Gledhill, Brian Hudson, 2006, J. Chem. Inf. Model..

BioSimGrid: A distributed environment for archiving and the analysis of biomolecular simulations

Jonathan W. Essex, Stuart Murdock, Kaihsu Tai, 2005 .

Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation model

Jonathan W. Essex, Colin M. Edge, Lewis Whitehead, 2001, J. Comput. Chem..

The configurational dependence of binding free energies: A Poisson–Boltzmann study of Neuraminidase inhibitors

Michael A. King, Jonathan W. Essex, Christopher J. Woods, 2001, J. Comput. Aided Mol. Des..

Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

Jonathan W. Essex, Richard Bradshaw, Richard T. Bradshaw, 2016, J. Comput. Chem..

Application of digital filters to enhance conformational change in protein systems

Jonathan W. Essex, Adrian P. Wiley, 2005 .

Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins

Jonathan W. Essex, Holger Gohlke, Christopher Pfleger, 2011, J. Chem. Inf. Model..

A review of protein-small molecule docking methods

Jonathan W. Essex, Richard D. Taylor, Philip J. Jewsbury, 2002, J. Comput. Aided Mol. Des..

Security and BioSimGrid: A Biomolecular Simulation Database

Jonathan W. Essex, Stuart Murdock, Kaihsu Tai, 2004 .

grand: A Python Module for Grand Canonical Water Sampling in OpenMM

Jonathan W. Essex, Marley L. Samways, Hannah E. Bruce Macdonald, 2020, J. Chem. Inf. Model..

Triple Store Databases and their role in high throughput, automated, extensible, data analysis

Jonathan W. Essex, Robert J. Gledhill, Jeremy G. Frey, 2005 .

All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5

Jonathan W. Essex, Samuel Genheden, 2016, Journal of Computer-Aided Molecular Design.

BioSimGrid: Grid-enabled biomolecular simulation data storage and analysis

Jonathan W. Essex, Kaihsu Tai, Muan Hong Ng, 2006, Future Gener. Comput. Syst..

Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge

Jonathan W. Essex, Samuel Genheden, Ana I. Cabedo Martinez, 2014, Journal of Computer-Aided Molecular Design.

PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories

Jonathan W. Essex, Syma Khalid, James A. Graham, 2017, J. Chem. Inf. Model..

APPROACHES TO PROTEIN-LIGAND BINDING FROM COMPUTER SIMULATIONS

Jonathan W. Essex, William L. Jorgensen, Julian Tirado-Rives, 1997 .

Visualizing the Repeat Structure of Genomic Sequences

Jonathan W. Essex, Gerald Weber, Adam Prügel-Bennett, 2008, Complex Syst..

Efficient data storage and analysis for generic biomolecular simulation data

Jonathan W. Essex, Stuart Murdock, Kaihsu Tai, 2004 .

Conformation and Dynamics of Human Urotensin II and Urotensin Related Peptide in Aqueous Solution

Timothy Clark, Jonathan W. Essex, Jana Sopkova-de Oliveira Santos, 2017, J. Chem. Inf. Model..

ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields

Jonathan W. Essex, Marcel L. Verdonk, Chris-Kriton Skylaris, 2021, J. Chem. Inf. Model..

Computational Methods and Tools in Antimicrobial Peptide Research

Jonathan W. Essex, Stephen J. Fox, Pietro G. A. Aronica, 2021, J. Chem. Inf. Model..

The development of replica-exchange-based free-energy methods

Jonathan W. Essex, Christopher J. Woods, Michael A. King, 2003 .

Relative partition coefficients from partition functions: a theoretical approach to drug transport

Jonathan W. Essex, Christopher A. Reynolds, W. Graham Richards, 1989 .

Theoretical Calculation of a Solution Phase Torsional Free Energy Profile. π-Ethylimidazole in Water

Jonathan W. Essex, David R. Lowis, W. Graham Richards, 1993 .

Computational Studies of Molecular Recognition from Alkane Dimers to Protein-Ligand Complexes

Jonathan W. Essex, William L. Jorgensen, Julian Tirado-Rives, 1999 .

Permeation of small molecules through a lipid bilayer: a computer simulation study

Jonathan W. Essex, Claude Luttmann, J. Essex, 2004 .

The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes

Jonathan W. Essex, Mario Orsi, J. Essex, 2011, PloS one.

Chapter 4:Passive Permeation Across Lipid Bilayers: a Literature Review

Jonathan W. Essex, Mario Orsi, J. Essex, 2010 .

Digitally filtered molecular dynamics: The frequency specific control of molecular dynamics simulations

Jonathan W. Essex, Colin M. Edge, Stephen Phillips, 2000 .

Atomic charges for variable molecular conformations

Jonathan W. Essex, Christopher A. Reynolds, W. Graham Richards, 1992 .

Underlying data for "Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field"

Jonathan W. Essex, Richard T. Bradshaw, 2015 .

Application of the Hilbert-Huang transform to the analysis of molecular dynamics simulations

Jonathan W. Essex, Robert J. Gledhill, Colin M. Edge, 2003 .

Theoretical determination of partition coefficients

Jonathan W. Essex, Christopher A. Reynolds, W. Graham Richards, 1992 .

Permeability of drugs and hormones through a lipid bilayer: insights from dual-resolution molecular dynamics†

Jonathan W. Essex, Mario Orsi, J. Essex, 2010 .

Monte Carlo Simulations for Proteins: Binding Affinities for Trypsin−Benzamidine Complexes via Free-Energy Perturbations

Jonathan W. Essex, William L. Jorgensen, Julian Tirado-Rives, 1997 .

Errors in free-energy perturbation calculations due to neglecting the conformational variation of atomic charges

Jonathan W. Essex, Christopher A. Reynolds, W. Graham Richards, 1992 .

Generation of OPLS‐like charges from molecular electrostatic potential using restraints

Jonathan W. Essex, Richard H. Henchman, 1999 .