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ORCIDJonathan W. Essex
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2020 – today
- 2023
[j37]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): 387-396 (2023)- [j36]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): 2810-2827 (2023) - 2022
- [j35]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): 767-779 (2022) - 2021
- [j34]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): 2026-2047 (2021) - [j33]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): 3172-3196 (2021) - 2020
- [j32]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): 1917-1921 (2020) - [j31]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): 3131-3144 (2020) - [j30]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): 4436-4441 (2020) - [j29]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): 5290-5295 (2020)
2010 – 2019
- 2017
- [j28]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): 298-310 (2017) - [j27]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): 650-656 (2017) - 2016
- [j26]Samuel Genheden, Jonathan W. Essex:
All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5. J. Comput. Aided Mol. Des. 30(11): 969-976 (2016) - [j25]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): 2749-2758 (2016) - 2014
- [j24]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): 187-200 (2014) - [j23]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): 1623-1633 (2014) - 2013
- [j22]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): 7 (2013) - [j21]Andrea Bortolato, Benjamin G. Tehan, Michael S. Bodnarchuk, Jonathan W. Essex, Jonathan S. Mason:
Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study. J. Chem. Inf. Model. 53(7): 1700-1713 (2013) - 2012
- [j20]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): 34 (2012) - 2011
- [j19]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): 2666-2679 (2011) - 2010
- [j18]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): 639-658 (2010) - [j17]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): 511-524 (2010)
2000 – 2009
- 2008
- [j16]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) - [j15]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): 225-238 (2008) - 2006
- [j14]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): 657-664 (2006) - [j13]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): 939-952 (2006) - [j12]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): 960-970 (2006) - [j11]Kieron R. Taylor, Jonathan W. Essex, Jeremy G. Frey, Hugo R. Mills, Gareth V. Hughes, Ed Zaluska:
The Semantic Grid and chemistry: Experiences with CombeChem. J. Web Semant. 4(2): 84-101 (2006) - [c3]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: 270-277 - 2005
- [j10]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): 1791-1803 (2005) - [c2]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: 148-155 - 2004
- [j9]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): 1760-1770 (2004) - [c1]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: 50- - 2003
- [j8]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): 1637-1656 (2003) - 2002
- [j7]Richard D. Taylor, Philip J. Jewsbury, Jonathan W. Essex:
A review of protein-small molecule docking methods. J. Comput. Aided Mol. Des. 16(3): 151-166 (2002) - 2001
- [j6]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): 129-144 (2001) - [j5]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): 1622-1633 (2001)
1990 – 1999
- 1999
- [j4]Richard H. Henchman, Jonathan W. Essex:
Generation of OPLS-like charges from molecular electrostatic potential using restraints. J. Comput. Chem. 20(5): 483-498 (1999) - [j3]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): 499-510 (1999) - 1995
- [j2]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): 311-327 (1995) - [j1]Jonathan W. Essex, William L. Jorgensen:
An Empirical Boundary Potential for Water Droplet Simulations. J. Comput. Chem. 16(8): 951-972 (1995)
Coauthor Index
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