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:
5th HECBioSim JADE2 Resource Allocation Panel Successful Applications - July 2023
| Applicant | Institution | Project Title |
| Graeme Barker | Heriot-Watt University | Markov State Modelling of Non-Cyclic Nucleotide Isoform-Selective EPAC Activators |
| Richard Bryce | University of Manchester | Simulation of Ligand Conformation in Solution Using Machine Learning Potentials |
| Robin Corey | University of Bristol | Interactions of the μ-Opioid Receptor with Fentanyl and Carfentanil |
| Craggs Tim | The University of Sheffield | Understanding the Relative Effects of Mismatches on Plectoneme Pinning |
| Carmen Domene | University of Bath | Basis for Sensory Transduction and Nociception in the TRPM8 Ion Channel |
| Jonathan Essex | University of Southampton | Alchemical Free Energy Calculations for Drug Discovery using Fully Adaptive SimulatedTempering (FAST) |
| Arianna Fornili | Queen Mary University of London | Targeting Skeletal Myosin Mutants |
| Arianna Fornili | Queen Mary University of London | In-Silico Investigation of Myosin Rod Dynamics |
| Chris Lorenz | King's College London | Investigate the Interactions of Legionella Collagen-like Protein with Legionella Pneumphila Membranes |
| Julien Michel | University of Edinburgh | Validating a Multi-Engine/Multi-Methodology Alchemical Free Energy Platform |
| Alessandro Pandini | Brunel University London | Detecting the Residues Inducing Fold-Switching in Metamorphic Proteins |
| Clare-Louise Peyton | University of Bradford | Investigating the Role of Post-Translational Modifications within the Sp Protein Family and the Interaction with DNA |
| Edina Rosta | University College London | In-Silico Probing of Cysteine Residues for Covalent Drug Design |
| Sarah Rouse | Imperial College London | Lipid Binding Site Library of GPCRs in Active and Inactive Conformations |
| Phillip Stansfeld | University of Warwick | Structural Dynamics of Arabinose-4-amino modification of LPS |
4th HECBioSim JADE2 Resource Allocation Panel Successful Applications - Jan 2023
| Applicant | Institution | Project Title |
| Sarath Dantu | Brunel University London | Using SARS-CoV2 Nsp10 Protein to Develop a Model of Protein Stability Using Molecular Dynamics Simulations |
| Arianna Fornili | Queen Mary University of London | Myosin Dynamics in Skeletal Muscle |
| Brendan Howlin | University of Surrey | Continuing Quantum and Classical Investigations into Three Different Biological Systems |
| Julien Michel | University of Edinburgh | Benchmarking a Pipeline for Absolute Binding Free Energy Calculations with Adaptive Sampling |
| Alessandro Pandini | Brunel University London | Small Molecular Inhibition of Protein Conformational Changes: The Case of Ametamorphic Bacterial Protein |
| Phillip Stansfeld | University of Warwick | Elucidating the recycling pathway for bacterial undecaprenyl phosphate (C55P) |
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- Validation of a novel FEP approach to increase reliability for large molecular |
| 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 |