Jonathan W. Essex

According to our database1, Jonathan W. Essex authored at least 34 papers between 1995 and 2020.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 




ProtoCaller: Robust Automation of Binding Free Energy Calculations.
J. Chem. Inf. Model., 2020

BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations.
J. Chem. Inf. Model., 2020

grand: A Python Module for Grand Canonical Water Sampling in OpenMM.
J. Chem. Inf. Model., 2020

The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
J. Chem. Inf. Model., 2020

Conformation and Dynamics of Human Urotensin II and Urotensin Related Peptide in Aqueous Solution.
J. Chem. Inf. Model., 2017

PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories.
J. Chem. Inf. Model., 2017

Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field.
J. Comput. Chem., 2016

All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.
J. Comput. Aided Mol. Des., 2016

Strategies to Calculate Water Binding Free Energies in Protein-Ligand Complexes.
J. Chem. Inf. Model., 2014

Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.
J. Comput. Aided Mol. Des., 2014

Water Network Perturbation in Ligand Binding: Adenosine A<sub>2A</sub> Antagonists as a Case Study.
J. Chem. Inf. Model., 2013

How to pick a winning team: approaches towards the selection of computationally derived protein structures for ensemble-based virtual screening.
J. Cheminformatics, 2013

The assessment of computationally derived protein ensembles in protein-ligand docking.
J. Cheminformatics, 2012

Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins.
J. Chem. Inf. Model., 2011

Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments.
J. Chem. Inf. Model., 2010

Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations.
J. Comput. Aided Mol. Des., 2010

e-Malaria: the schools Malaria project.
Concurr. Comput. Pract. Exp., 2008

Visualizing the Repeat Structure of Genomic Sequences.
Complex Syst., 2008

The Semantic Grid and chemistry: Experiences with Comb<i>e</i>Chem.
J. Web Semant., 2006

Bringing Chemical Data onto the Semantic Web.
J. Chem. Inf. Model., 2006

A Computer-Aided Drug Discovery System for Chemistry Teaching.
J. Chem. Inf. Model., 2006

BioSimGrid: Grid-enabled biomolecular simulation data storage and analysis.
Future Gener. Comput. Syst., 2006

CombeChem: A Case Study in Provenance and Annotation Using the Semantic Web.
Proceedings of the Provenance and Annotation of Data, 2006

Prediction of Properties from Simulations: A Re-examination with Modern Statistical Methods.
J. Chem. Inf. Model., 2005

A semantic datagrid for combinatorial chemistry.
Proceedings of the 6th IEEE/ACM International Conference on Grid Computing (GRID 2005), 2005

A Web / Grid Portal Implementation of BioSimGrid: A Biomolecular Simulation Database.
Proceedings of the International Conference on Information Technology: Coding and Computing (ITCC'04), 2004

FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function.
J. Comput. Chem., 2003

A review of protein-small molecule docking methods.
J. Comput. Aided Mol. Des., 2002

Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation model.
J. Comput. Chem., 2001

The configurational dependence of binding free energies: A Poisson-Boltzmann study of Neuraminidase inhibitors.
J. Comput. Aided Mol. Des., 2001

Free energies of hydration using restrained electrostatic potential derived charges via free energy perturbations and linear response.
J. Comput. Chem., 1999

Generation of OPLS-like charges from molecular electrostatic potential using restraints.
J. Comput. Chem., 1999

Generalized Alteration of Structure and Parameters: A New Method for Free- Energy Perturbations in Systems Containing Flexible Degrees of Freedom.
J. Comput. Chem., 1995

An Empirical Boundary Potential for Water Droplet Simulations.
J. Comput. Chem., 1995