JADE2

Here is a list of successful HECtime allocations on JADE2. Note this is a list of historical projects and is not used to notify applicants on the status of their application:

3rd HECBioSim JADE2 Resource Allocation Panel Successful Applications - May 2022

Applicant	Institution	Project Title
Doryen Bubeck	Imperial College London	Molecular Mechanism of Pore Formation by the Membrane Attack Complex
Jonathon Essex	University of Southampton	Enhanced Sampling of Relative Binding Free Energy Pathways using Fully Adaptive Simulated Tempering (FAST) Methods
Arianna Fornili	Queen Mary University of London	Allosterism in the Proton Sensing G-protein Coupled Receptor GPR68
Jonathan Hirst	University of Nottingham	Free Energy Simulations for Drug Discovery: Inhibitors of Bromodomain-containing protein 4 (BRD4)
Julien Michel	University of Edinburgh	A High-Throughput FEP Pipeline for Systematic Comparison of RBFE Calculations Between Different MD Engines
Agnes Noy	University of York	Sequence-Dependence of DNA Supercoiling
Alessandro Pandini	Brunel University London	Subsampling Molecular Dynamics Trajectories to Extract Ensembles of Structures for Machine Learning Analysis.
Edina Rosta	University College London	Investigating the Kinetic Selectivity Between Muscarinic M2 and M3 receptor’s for Tiotropium
Phillip Stansfeld	University of Warwick	Assembly of the Twin-Arginine Translocase Pore

2nd HECBioSim JADE2 Resource Allocation Panel Successful Applications - November 2021

Applicant	Institution	Project Title
Philip Biggin	University of Oxford	Quantifying Dimerization Energetics in KDEL Receptors
Sarath Dantu	Brunel University London	Role of Individual Proteins in the Conformational Dynamics of Skp1-Cullin-Fbox Protein Complex
Carmen Domene	University of Bath	Computational Studies of Oxygenases
Fernanda Duarte	University of Oxford	Exploring peptide ligand binding to TRIM PHD-bromodomains using Gaussian Accelerated Molecular Dynamics
Jonathon Essex	University of Southampton	Optimising Fragment Based Drug Design by Molecular Simulation
Arianna Fornili	Queen Mary University of London	Optimisation of Myosin Modulators
Syma Khalid	University of Oxford	Developing Computational Assays to Study the Action of the Antibiotic Polymyxin B1 on E. coli membranes
Charlie Laughton	University of Nottingham	Evaluation of Self-Avoiding Walk MD (SAW-MD) as a method for predicting ligand unbinding pathways and kinetics.
Chris Lorenz	Kings College London	Synergistic Effect of Winter Flounder Anitmicrobial Peptides
Agnes Noy	University of York	Towards the Complete DNA Interaction Landscape of HU Nucleoid-Associated Protein
Alessandro Pandini	Brunel University London	Subsampling Molecular Dynamics Trajectories to Extract Ensembles of Structures Compatible with Mutation Profiles of Functional Regions in Proteins.
Phillip Stansfeld	University of Warwick	Assembly & Substrate Interactions with the Twin-Arginine Translocase
Marc Van der Kamp	University of Bristol	Evaluating the specificity and kinetics of therapeutic TCRs using molecular dynamics

1st HECBioSim JADE2 Resource Allocation Panel Successful Applications - April 2021

Applicant	Institution	Project Title
Philip Biggin	University of Oxford	Quantifying Dimerization Energetics in KDEL Receptors
Doryen Bubeck	Imperial College London	How bacterial cytolysins initiate membrane rupture
Timothy Craggs	University of Sheffield	Probing the conformational dynamics of supercoiled DNA minicircles in explicit solvent
Sarath Dantu	Brunel University London	Conformational dynamics of Skp1-Cullin-Fbox protein complex
Carmen Domene	University of Bath	Computational Studies of Oxygenases
Fernanda Duarte	University of Oxford	Computational investigation of histone H3 peptide binding to TRIM proteins
Jonathon Essex	University of Southampton	Methods for Accurate and Efficient Simulation of the Conformational Landscape of Ligands
Arianna Fornili	Queen Mary University of London	Designing myosin modulators
Syma Khalid	University of Oxford	Lipopolysaccharide interactions with outer membrane proteins: finding the patterns
Julien Michel	University of Edinburgh	Building Markov State Models for Prioritising Allosteric Fragment Binders for Hit-to- Lead Optimisation Validation of a novel FEP approach to increase reliability for large molecular transformations
Agnes Noy	University of York	Modelling supercoiling on linear DNA
Alessandro Pandini	Brunel University London	Developing a machine learning model to predict ‘dynamically-compatible’ changes in the sequence of a bacterial protein.
Claire-Louise Peyton	University of Bradford	Investigation of the Sp protein family and interactions with DNA
Edina Rosta	University College London	Molecular modelling, synthesis and development of SARS-CoV-2 inhibitors
Phillip Stansfeld	University of Warwick	Conformational Dynamics of the Mycobacterium LpqY-SugABC Transport System
Marc Van der Kamp	University of Bristol	Evaluating molecular dynamics simulations for TCR therapeutic design
Tobias Warnecke	Imperial College London	Targeting lung cancer’s ‘safe-space’ with novel p21 mimics