Here is a list of successful HECtime allocations on ARCHER. Note this is a list of historical projects and is not used to notify applicants on the status of their application:
17th HECBioSim ARCHER Resource Allocation Panel Successful Applications - November 2020
| Applicant | Institution | Project Title |
| Tanmay A.M. Bharat | University of Oxford | Molecular Simulations of Ribosome Function in Nitrosopumilus maritimus cells: combining in situ structural biology with molecular simulations |
| Philip Biggin | University of Oxford | Understanding oligomerization requirements in different KDEL Receptors |
| Ian Collinson | University of Bristol | Mechanism of ATP-driven protein transport through the bacterial secretory machinery |
| Sarath Dantu | Brunel University London | Molecular dynamics simulations of Skp1-FBXO31to guide the solution state NMR experimental studies the complex |
| Jonathon Essex | University of Southampton | Investigating the differences in local dynamics between MHC-I alleles on peptide selector function |
| Douglas Houston | University of Edinburgh | Gaussian Accelerated Molecular Dynamics with Replica-Exchange Umbrella Sampling of Stapled Peptidomimetic Inhibitors |
| Antreas Kalli | University of Leeds | Molecular dynamics simulations of T-cell receptor clustering |
| Syma Khalid | University of Southampton | in-silico microbiology of the E. coli cell envelope: studying the behaviour of antibiotics |
| Gerhard Koenig | University of Portsmouth |
Computational predictions of protein stability |
| Valeria Lossasso | Science and Technology Facilities Council | Understanding the mutual interactions between water and biological membranes via the inspection of the topology of water's hydrogen bond network |
| Edina Rosta | University College London | Investigating Ligand-Receptor Binding Kinetics Through Unbinding Studies |
| Sarah Rouse | Imperial College London | Integrating molecular simulations and experiment to capture cardiolipin signalling in mitochondria |
| Michelle Sahai | University of Roehampton | Elucidating the molecular mechanism of action of stimulant novel psychoactive substances (NPS) that target the high-affinity transporter for dopamine |
| Mark Sansom | University of Oxford | Membrane Proteins and Lipids: Comparing Simulations with Experiments |
| Philip Stansfeld | University of Warwick | Oligosaccharide transport and synthesis across biological membranes |
| Irina Tikhonova | Queens University Belfast | Identification of Ligand Binding Sites and Allosteric Networks in Microbial Bile Salt Hydrolases (BSHs) |
| Adrian Mulholland | University of Bristol | Equilibrium and Nonequilibrium Simulation of SARS-CoV-2 Spike Protein Conformation, Dynamics and Ligand Binding |
16th HECBioSim ARCHER Resource Allocation Panel Successful Applications - April 2020
| Applicant | Institution | Project Title |
| Philip Biggin | University of Oxford | Mapping the influence of lipid composition to the free energy of chaperone transitions |
| Jonathon Essex | University of Southampton | Modelling the structure and dynamics of miRNA |
| Francesco Gervasio | University College London | Absolute fragment binding free energies with CV-based methods |
| D. Flemming Hansen | University College London | Drug Discovery for Viral Disordered Proteins |
| Jonathan Hirst | University of Nottingham | Binding energy calculations for bromodomain-inhibitor complexes through molecular dynamics simulation and free energy perturbation theory |
| Douglas Houston | University of Edinburgh | Computer Aided Design via Gaussian Accelerated Molecular Dynamics Simulation of Stabilised Peptidomimetic Inhibitors |
| Antreas Kalli | University of Leeds | Computational studies of the Piezo1 mechanosensitive channel |
| Syma Khalid | University of Southampton | Combining biology and chemistry: towards a realistic model of the E. coli periplasm |
| Mark Sansom | University of Oxford | Membrane Proteins and Disease: Molecular Calculations and Simulations at Multiple Scales |
| Philip Stansfield | University of Warwick | Molecular Mechanisms of Ion Transport |
| Irina Tikhonova | Queens University Belfast | Exploring binding cavities in the chemokine receptors (CCR4, CXCR4, CCR5 and CCR7) from computer simulations |
| Michele Vendruscolo | University of Cambridge | Identification of toxic conformations of the amyloid-β peptide |
15th HECBioSim ARCHER Resource Allocation Panel Successful Applications - November 2019
| Applicant | Institution | Project Title |
| Philip Biggin | University of Oxford | Using Free Energy Calculations to Map out Binding Determinants in Receptor involved in Trafficking |
| Jonathan Essex | University of Southampton | Rationalising Alternative Epitopes in Antibody-Antigen Simulations |
| Philip Fowler | University of Oxford | Predicting the effect on fluoroquinolone susceptibility of three DNA gyrase mutations identified from clinical samples of tuberculosis. |
| Francesco Gervasio | University College London | Combining Machine Learning and Metadynamics for Absolute Free Energies of Binding to Epoxide Hydrolase |
| Daniel Kattnig | King's College London | Towards coarse-grained models of microbial filaments involved in motility and biofilm formation |
| Syma Khalid | University of Southampton | The path taken by polymyxin B1 through the congested periplasmic space of E. coli |
| Agnes Noy | University of York | The influence of protein-induced bent on DNA topology unveiled by atomic simulations in explicit solvent |
| Alessandro Pandini | Brunel University London | Identification of coevolutionary constraints for the design of protein dynamics |
| Maria Carmen Romano | University of Aberdeen | Effect of Macromolecular Crowding on the tRNA-Regulated Translational Control of Genetic Expression |
| Mark Sansom | University of Oxford | Lipid interactions with membrane proteins: from characterisation to prediction |
| Gabriele Sosso | Warwick University | Toward the Microscopic Understanding of Ice Formation in Biological Matter |
| Phillip Stansfeld | Warwick University | Complex proteins, Complex Membranes: Simulations Alongside Structural Biology |
14th HECBioSim ARCHER Resource Allocation Panel Successful Applications - April 2019
| Applicant | Institution | Project Title |
| Agnes Noy | University of York | The influence of supercoiling on DNA local structural landscape and ionic distribution |
| Alessandro Pandini | Brunel University London | Coarse-grained simulations of a large dataset of proteins to detect recurrent patterns of functional motions in unrelated proteins |
| Antreas Kalli | University of Leeds | Computational studies of the human red blood cell Band 3 anion exchanger |
| Arianna Fornili | Queen Mary University of London | Role of the Essential Light Chain domains in determining cardiac myosin dynamics |
| Edina Rosta | King's College London | Structural reasons for drug resistance of HIV integrase inhibitors |
| Franca Fraternali | King's College London | Improving the description of protein-membrane interactions in the GROMOS force field |
| John Christodoulou | University College London | Integrative structural biology approaches to study protein co-translational protein folding on the ribosome |
| Jonathan Essex | University of Southampton | Rationalising the Limitations in Computational Antibody Design |
| Maria Carmen Romano | University of Aberdeen | A multiscale modeling approach to understanding the effect of macromolecular crowding on protein translation |
| Mark Sansom | University of Oxford | Complex proteins, Complex Membranes: Simulations Alongside Structural Biology |
| Martin Ulmschneider | King's College London | Molecular dynamics simulations as a tool to understand the role histidines in the periplasmic loops of Helicobacter pylori inner membrane urea channel proteins play in urea regulaton |
| Michelle Sahai | University of Roehampton | Elucidating the molecular mechanism of action of stimulant novel psychoactive substances (NPS) that target the high-affinity transporter for dopamine |
| Philip Biggin | University of Oxford | Evaluating the use of absolute binding free energy alchemical free energy simulations in guiding fragment-based lead discovery |
| Philip Fowler | University of Oxford | Can alchemical free energy methods predict the effect of DNA gyrase mutations on fluoroquinolone susceptibility? |
| Philip Stansfeld | University of Oxford | Assembly and Dynamics of Bacterial Surface-layer Arrays |
| Steve Matthews | Imperial College | Characterising the role of nanodiscs on dynamic properties of the bacterial membrane protein CsgG |
| Syma Khalid | University of Southampton | Characterisation of the interaction of bacterial outer membrane vesicles with mammalian membranes |
13th HECBioSim ARCHER Resource Allocation Panel Successful Applications - September 2018
| Applicant | Institution | Project Title |
| Agnes Noy | University of York | The influence of supercoiling on DNA local structural landscape and ionic distribution |
| Alessandro Pandini | Brunel University London | A molecular simulation study of the resilience of networks of coevolved residues upon mutation. |
| Arianna Fornili | Queen Mary University of London | in silico design of cardiac myosin modulators |
| Carmen Domene | University of Bath | ‘Chameleonic’ behaviour of small peptides: mechanistic studies of the micelle-induced structural transition between two ordered peptide structures |
| Daniel Kattnig | University of Exeter | On the magnetic field sensitivity of lipid peroxidation: Probing into the plausibility of three-radical effects |
| Edina Rosta | King's College London | Design of new inhibitors for D-Ala:D:Ala ligase |
| Francesco Gervasio | University College London | Understanding the mechanism of cryptic pocket formation at protein-protein interfaces |
| Jonathan Essex | University of Southampton | The Role of Antibody Flexibility in Antigen Binding |
| Julien Michel | University of Edinburgh | Characterising the loop closing mechanism in Protein Tyrosine Phosphatase 1B (PTP1B) |
| Marc Van der Kamp | University of Bristol | Development of a Generalised Protocol for Alanine Scanning TCR-pHLA interactions with MMPB/GBSA |
| Maria Carmen Romano | Maria Carmen Romano | The physics of translation in the cell |
| Philip Stansfeld | University of Oxford | MD simulations of the lipoprotein biogenesis pathway |
| Syma Khalid | University of Southampton | UNDERSTANDING UPTAKE OF MONOAROMATIC HYDROCARBONS BY BACTERIAL OUTER MEMBRANE PROTEINS |
| Clare Towse | University of Bradford | Conformational Propensities of Novel Non-Proteinogenic Amino Acids |
| Reynier Suardiaz Del Rio | University of Bristol | No Record |
12th HECBioSim ARCHER Resource Allocation Panel Successful Applications - April 2018
| Applicant | Institution | Project Title |
| Agnes Noy | University of York | The influence of supercoiling on DNA local structural landscape and ionic distribution |
| Alessandro Pandini | Brunel University London | A comparative molecular simulation study of the dynamics of coevolved residues in homologous proteins |
| Arianna Fornili | Queen Mary University of London | Rescuing dilated cardiomyopathy mutations in myosin |
| Carmen Domene | University of Bath | 'Chameleonic’ behaviour of small peptides: mechanistic studies of the micelle-induced structural transition between two ordered peptide structures |
| Clare-Louise Towse | University of Bradford | Conformational Propensities of Novel Non-Proteinogenic Amino Acids |
| Daniel Kattnig | University of Exeter | Are magnetic field effects on lipid peroxidation plausible? MD to estimate coherence times in lipid peroxyl radical pairs |
| Edina Rosta | King's College London | Developing enhanced sampling methods to elucidate active site metal ion coordination |
| Francesco Gervasio | University College London | Understanding the mechanism of cryptic pocket formation at protein-protein interfaces: the case of TNFa. |
| Irina Tikhonova | Queens University Belfast | Understanding allosteric regulation and allosteric ligand binding in the corticotropin releasing factor 1 receptor. |
| Jonathan Doye | University of Oxford | Chiral liquid-crystal phases of supercoiled DNA plasmids |
| Jonathan Essex | University of Southampton | The Role of Antibody Flexibility in Antigen Binding |
| Jozef R Lewandowski | University of Warwick | Molecular dynamics to elucidate allosteric regulation in condensation domains of PKS-NPRS mega enzymes |
| Julien Michel | University of Edinburgh | Exploring disorder to order transitions of MDM2 oncoprotein triggered by ligand binding |
| Maria Carmen Romano | University of Aberdeen | The physics of translation in the cell |
| Mario Orsi | University of West of England (UWE) | Action mechanism of antimicrobial peptide amphiphiles |
| Mark Sansom | University of Oxford | Molecular Simulations of Protein-Lipid Interactions |
| Martin Ulmschneider | King's College London | Substrate binding and atomic detail transport mechanisms within the P-gp drug transport cavity |
| Michele Vendruscolo | University of Cambridge | Metadynamic metainference simulations of alpha-synuclein |
| Philip Biggin | University of Oxford | Absolute binding free energy calculations to guide development of a TRIM33 bromodomain inhibitor |
| Philip Stansfeld | University of Oxford | Molecular Simulations of a bacterial S-layer |
| Stephen Euston | Heriot-Watt University | Modelling Crystallisation in Triglycerides |
| Syma Khalid | University of Southampton | Substrate Permeation Across the Outer Membrane Porin of the Human Pathogen Pseudomonas Aeruginosa |
| Zak Hughes | University of Bradford | Elucidating the Effect of Salt Concentration on the Structure of a DNA Aptamer |
| Richard Sessions | University of Bristol | Simulations of single-chain SAGE patches |
11th HECBioSim ARCHER Resource Allocation Panel Successful Applications - October 2017
| Applicant | Institution | Project Title |
| Agnes Noy | University of York | The influence of supercoiling on DNA local structural landscape and ionic distribution |
| Alessandro Pandini | Brunel University London | Molecular dynamics investigation of rescue mutants in HIF-2?:ARNT heterodimer |
| Arianna Fornili | Queen Mary University of London | Modulation of myosin dynamics by Omecamtiv Mecarbil: transition to the pre-power stroke state |
| Chris Lorenz | King's College London | Metadynamics simulations of permeation of 6-MAM & flurbiporofen across blood-brain barrier |
| Daniel Kattnig | University of Exeter | Deciphering the magnetic sense: Spin relaxation in an animal cryptochrome |
| Danilo Roccatano | University of Lincoln | Molecular Dynamics Simulations Study of Absorption Mechanism of Peptides by Polyether Block Copolymers |
| Edina Rosta | King's College London | Catalytic reaction mechanism of HIV-1 RNase H using free energy calculations |
| Julien Michel | University of Edinburgh | Towards a computational platform for the rational design of stapled peptides |
| Martin Ulmchneider | King's College London | Exploring the mechanisms of pH-gating and solute selectivity the urea channel of Helicobacter pylori |
| Michele Vendruscolo | University of Cambridge | Metadynamic metainference simulations of alpha-synuclein |
| Mike Payne | University of Cambridge | Relation of disordered protein dynamics to modern water models |
| Philip Biggin | University of Oxford | Free Energy of Partial Agonists at Glycine Receptors |
10th HECBioSim ARCHER Resource Allocation Panel Successful Applications - April 2017
| Applicant | Institution | Project Title |
| Agnes Noy | University of York | Predictive modelling on DNA minicircles |
| Arianna Fornili | Queen Mary University of London | Effect of Omecamtiv Mecarbil on the dynamics of myosin mutants |
| Attila Csikasz-Nagy | King's College London | Understanding the catalytic binding site of Synaptojanin |
| Carmen Domene | Kings College London | Chameleonic’ behaviour of small peptides:mechanistic studies of the micelle induced structural transition between two ordered peptide structures |
| Chris Lorenz | King's College London | Investigating the beginnings of material-driven fibrillogenesis |
| Chris Lorenz | King's College London | Metadynamics simulations of permeation of cocaine across blood-brain barrier |
| Clare-Louise Towse | University of Bradford | Probing the Conformational Impact of Non-Proteinogenic Amino Acids in Peptides and Proteins |
| David Huggins | University of Cambridge | Activation and Functional Selectivity in the Apelin Receptor |
| Douglas Houston | University of Edinburgh | Computer Aided Design via Molecular Dynamics Simulation of Stabilised Peptidomimetic Inhibitors of the Oncoprotein Skp2 |
| Edina Rosta | King's College London | Mechanism of the electron transfer in the ferredoxin:ferredoxin-NADP+ oxidoreductase complex |
| Francesco Gervasio | University College London | Targeting membrane-protein interactions and cryptic pockets in receptor kinases |
| Irina Tikhonova | Queen's University Belfast | Allosteric regulation of M1 aminopeptidase from computer simulations Project duration |
| Mario Orsi | UWE Bristol | Self-assembling of Elastin-like-proteins (ELPs) and Peptide Amphiphiles (PAs) |
| Mark Sansom | University of Oxford | Investigating membrane protein interactions using large scale MD simulations |
| Michele Vendruscolo | University of Cambridge | Metadynamic metainference simulations of alpha-synuclein |
| Michelle Sahai | University of Roehampton | Computational Modeling and Simulation Studies of Dopamine Transporter function: de novo mutations |
| Philip Biggin | University of Oxford | Targeting a protein-protein interface in glutamate receptors for novel drugs |
| Philip Fowler | University of Oxford | How reproducible are predictions of antibiotic resistance made by alchemical free energy methods? |
| Phillip Stansfeld | University of Oxford | Molecular Simulations of the KATP Complex: Assessing the dynamic basis of Neonatal Diabetes |
| Ricahrd Sessions | University of Bristol | Exploring the dynamics of the ACTN1 dimer |
| Stephen Euston | Heriot-Watt University | Further Modelling of Structure Formation in Food Oleo-gels |
| Syma Khalid | University of Southampton | Building and Simulating the Virtual Bacterial Cell Envelope |
9th HECBioSim ARCHER Resource Allocation Panel Successful Applications - October 2016
| Applicant | Institution | Project Title |
| Agnes Noy | University of York | Predictive modelling on DNA minicircles for designing switchable gene-therapy vectors |
| Alessandro Pandini | Brunel University London | Unveiling the the role of coevolved residues in modulating the interface dynamics of PAS domain heterodimers |
| Arianna Fornili | Queen Mary University of London | Rescuing myosin dynamics |
| Cait MacPhee | University of Edinbrurgh | Effect of salt on conformational sampling of an intrinsically disordered peptide |
| Charlie Laughton | University of Nottingham | Advanced sampling methods for the detection of rare conformational states |
| Clare-Louise Towse | University of Bradford | Probing the Structural Impact of Epimerization in Amyloid and Crystallin Proteins |
| D Flemming Hansen | University College London | Developing methods to dynamic regulation in macromolecular systems: integrating NMR and MD |
| David Huggins | University of Cambridge | Relative binding affinity calculations to develop inhibitors of the BPTF bromodomain |
| Dmitry Nerukh | Aston University | Engineering bacteriophages for treating antimicrobial resistance using all-atom models of entire viruses |
| Edina Rosta | King's College London | Insights into the αC-helix dynamics in RAF Kinases |
| Francesco Gervasio | University College London | Targeting membrane-protein interactions in the allosteric regulation of a receptor kinase (FGFR) |
| Ian Collinson | University of Bristol | Protein translocation through the Sec translocon |
| Irina Tikhonova | Queen's University Belfast | Predictive modelling of GPCR allosteric sites |
| Jiayun Pang | University of Greenwich | Atomistic Understanding of Positive And Negative Cooperativity Within A Single Enzyme |
| Jonathan Doye | University of Oxford | The chirality of DNA: From microscopic to macroscopic |
| Julien Michel | University of Edinburgh | Rational control of microsecond-millisecond Cyclophilin dynamics |
| Mario Orsi | UWE Bristol | Effect of hydrostatic pressure on membrane physical properties |
| Michele Vendruscolo | University of Cambridge | Characterisation of the mechanism by which ClpB mediates protein disaggregation |
| Michele Vendruscolo | University of Cambridge | Replica-averaged metadynamics simulations of α-synuclein |
| Michelle Sahai | University of Roehampton | Computational Modeling and Simulation Studies of Dopamine Transporter function: de novo mutations. |
| Philip Biggin | University of Oxford | Cryo-EM refinement and dynamics investigation of Glycine Receptors |
| Richard Sessions | University of Bristol | Simulation and experiments on the archaeal thermosome |
| Stephen Euston | Heriot-Watt University | Modelling Structure Formation in Food Oleo-gels |
| Syma Khalid | University of Southampton | Large Scale Simulations of the Complex Cell Envelope of E. coli |
| Douglas Houston | University of Edinbrugh | A Molecular Dynamics Study of the Oligomerisation of the Oncoprotein Reptin Hexamer |
8th HECBioSim ARCHER Resource Allocation Panel Successful Applications - April 2016
| Applicant | Institution | Project Title |
| Irina Tikhonova | Queens University Belfast | Multiscale modelling of drug interactions and diffusion in hydrogels to improve drug delivery via microneedles. |
| Francesco Gervasio | University College London | Understanding the role of the membrane in the allosteric regulation of a receptor kinase (FGFR) |
| Michele Vendruscolo | University of Cambridge | Replica-averaged metadynamics simulations of alpha-synuclein |
| Philip Biggin | University of Oxford | Absolute Binding Free Energy Calculations for Epigenetic Mark Readers |
| Michelle Sahai | University of Roehampton | In silico approach to the assessment of stimulant properties of novel psychoactive substances |
| Edina Rosta | King's College London | Catalytic reaction mechanism of D-Ala:D:Ala ligase using free energy calculations |
| Dmitry Nerukh | Aston University | Engineering bacteriophages for treating antimicrobial resistance using all-atom models of entire viruses |
| Jonathan Essex | University of Southampton | Elastic Properties of Mixed Membranes |
| Charles Laughton | University of Nottingham | MODEST.0: Molecular Origins and Dynamic Effects on the Specificity of Transcription factors – chapter.0: “Homeodomain protein-DNA complexes”. |
| Mario Orsi | Queen Mary University London | Cancer cell membranes and their interaction with peptide amphiphiles |
| Arianna Fornili | Queen Mary University London | Modulation of myosin dynamics by Omecamtiv Mecarbil |
| Richard Sessions | University of Bristol | Further simulations investigating the mechanism of the SecA-YEG translocon |
| Alessandro Pandini | Brunel University London | Investigation of the role of ARNT dynamics in the stabilization of functional PAS domain heterodimers |
| Syma Khalid | University of Southampton | Large Scale Simulations of the Outer Membrane of Gram-Negative Bacteria |
| Agnes Noy | University of York | Predictive modelling on DNA minicircles for designing switchable gene-therapy vectors |
7th HECBioSim ARCHER Resource Allocation Panel Successful Applications - November 2015
| Applicant | Institution | Project Title |
| Irina Tikhonova | Queens University Belfast | Understanding how ligands migrate to the buried active site of the malaria M1 aminopeptidase. |
| Irina Tikhonova | Queens University Belfast | Simulations of peptide-drug conjugates to predict new vaginal microbicides |
| Charles Laughton | University of Nottingham | DNA Dynamics and Multiscale Genomics |
| Mark Sansom | University of Oxford | Energy Landscapes of Protein-Lipid Interactions using High-Throughput Molecular Dynamics Simulations. |
| Julien Michel | University of Edinburgh | Conservation of protein dynamics among cyclophilin isoforms: implications for rational design of isoform-selective ligands |
| Philip Biggin | University of Oxford | Accurate calculations of absolute binding free energies and enthalpy analysis of a broad-spectrum bromodomain inhibitor: Bromosporin |
| Mario Orsi | Queen Mary University London | Antimicrobial peptide amphiphiles and their interaction with biomembranes |
| Alessandro Pandini | Brunel University London | Analysis of the allosteric communication in HIF-2?–ARNT heterodimer |
| Arianna Fornili | Queen Mary University London | Prediction of ligand-binding hotspots of cardiac myosin |
| David Huggins | University of Cambridge | Identifying and Ranking Protein Binding Sites |
| Francesco Gervasio | University College London | Effects of oncogenic mutations on the free energy landscape of Protein Kinases. |
6th HECBioSim ARCHER Resource Allocation Panel Successful Applications - May 2015
| Applicant | Institution | Project Title |
| Charles Laughton | University of Nottingham | Development and application of ensemble simulation strategies for enhanced sampling and binding affinity prediction. |
| Philip Biggin | University of Oxford | Exploring the drug access pathway to P-glycoprotein |
| Cait MacPhee | University of Edinburgh | Interfacial protein folding |
| Mario Orsi | Queen Mary University London | Simulating the effect of lipid composition on membrane permeation |
| Mark Sansom | University of Oxford | Determining Biomembrane Organization via large MD Simulations: Viral and Bacterial Membranes |
| Richard Bryce | University of Manchester | Swarm enhanced sampling in molecular dynamics simulations of biomolecular systems |
| Michele Vendruscolo | University of Cambridge | Replica-averaged metadynamics simulations of alpha-synuclein |
| Jonathan Hirst | University of Nottingham | Large scale molecular dynamics simulations of bacterial pore formation by antibiotic peptides |
| Damian Jefferies | University of Southampton | Understanding the uptake mechanism of a last resort antibiotic Gram-negative bacteria: polymyxin B1 in E.coli |
5th HECBioSim ARCHER Resource Allocation Panel Successful Applications - February 2015
| Applicant | Institution | Project Title |
| Sarah Harris | University of Leeds | Atomistic MD simulations of supercoiled DNA |
| Michelle Sahai | University of Roehampton | Comparative modelling and molecular dynamics studies of the human and rat dopamine transporters and the effects of novel psychoactive drugs |
| Francesco Gervasio | University College London | Effects of oncogenic mutations on the free energy landscape of Protein Kinases. |
| David Huggins | University of Cambridge | Estimating Free-Energy Changes in Protein Folding Using a Direct Method (8.3MAUs) |
| Arianna Fornili | Queen Mary University London | Molecular Dynamics simulation of a two-headed fragment of cardiac Myosin: the Off-to-On state transition and the effect of RLC tail dynamics |
| Anna Croft | University of Nottingham | Radical Enzymes for Biotechnology |
| Richard Sessions | University of Bristol | Further simulations of SAGES exploring conformational and encapsulation phenomena |
| Edina Rosta | King's College London | Mechanistic Insights and the Role of Magnesium Ions in Topoisomerase II Catalytic Reactions |
| Robert Glen | University of Cambridge | Simulation and Experimental Approaches to Gain Structural Insight into Histo-blood group Binding by the E. coli Fimbrial Adhesin, FedF and A knowledge based approach into parametrising small molecule force-fields using crystallographic data |
| Michele Vendruscolo | University of Cambridge | Replica-averaged metadynamics simulations of alpha-synuclein |
| Andrei Pasliakov | University of Dundee | The Mechanism of Proton Pumping in Respiratory Complex |
| Philip Biggin | University of Oxford | Absolute Binding Free Energy Calculations for Epigenetic Mark Readers |
4th HECBioSim ARCHER Resource Allocation Panel Successful Applications - September 2014
| Applicant | Institution | Project Title |
| Jiayun Pang | University of Greenwich | Dynamical Control of Radical Intermediates in the Vitamin B12-Dependent Enzymes |
| Sarah Harris | University of Leeds | Atomistic MD simulations of supercoiled DNA - Extension request |
| Jonathan Hirst | University of Nottingham | Large scale molecular dynamics simulations of bacterial pore formation by antibiotic peptides |
| Philip Biggin | University of Oxford | Accurate calculations of absolute binding free energies and enthalpic/entropic contributions for anticancer compounds. |
| Jon Essex | University of Southampton | Development of dual-resolution models for membrane proteins |
| Richard Sessions | University of Bristol | Multiple simulations of surface patches from self assembling nanocages (SAGES) to elucidate the factors determining curvature and closure in these novel structures. |
| Michele Vendruscolo | University of Cambridge | Conformational sampling of alpha-synuclein by means of NMR-restrained bias exchange metadynamics simulations |
| John Christodoulou | University College London | The computational study of co-translational folding and misfolding on the ribosome |
| Mark Sansom | University of Oxford | Big Membrane Simulations: Receptor Clustering for Signalling and Virus Interactions |
| Edina Rosta | King's College London | Study of the mechanism of MEK phosphorylation by RAF |
| Mario Orsi | Queen Mary University of London | Atomistic simulation of mixed lipid membranes |
| Christo Christov | Northumbria University at Newcastle | Atomistic Modelling conformational dynamics of enzymes |
| Tatyana Karabencheva | Northumbria University at Newcastle | Molecular dynamics simulations of enzyme-ligand complexes |
3rd HECBioSim ARCHER Resource Allocation Panel Successful Applications - June 2014
| Applicant | Institution | Project Title |
| Philip Biggin | University of Oxford | Understanding the Gating of GABAA Receptors. |
| Francesco Gervasio | University College London | Allosteric communication within the B-Raf dimer and the effect of inhibitors |
| Agnes Noy (Sarah Harris) | University of Leeds | Atomistic MD simulations of supercoiled DNA |
| Charles Laughton | University of Nottingham | Optimising peptide-based inhibitors of the TRF1-TIN2 interaction by high-throughput molecular dynamics simulation and MM-GBSA analysis. |
| Marieke Schor (Cait MacPhee) | University of Edinburgh | Interfacial protein folding |
| Andrei Pisliakov | University of Dundee | Molecular Dynamics Simulations of Respiratory Complex I: Identifying the Proton Transfer Pathways |
2nd HECBioSim ARCHER Resource Allocation Panel Successful Applications - February 2014
| Applicant | Institution | Project Title |
| Julien Michel | University of Edinburgh | Exploration of the N-terminal MDM2 lid dynamics using umbrella sampling calculations |
| Edina Rosta | King's College London | Role of dimerization in the activation mechanism of RAF kinases |
1st HECBioSim ARCHER Resource Allocation Panel Successful Applications - September 2013
| Applicant | Institution | Project Title |
| Julien Michel | University of Edinburgh | Computer Simulations of the N-terminal MDM2- lid dynamics and the impact of ligand binding |
| Philip Biggin | University of Oxford | Towards the open state of the ionotropic glutamate receptor |
| Peter Bond | University of Cambridge | A Simulation and Experimental Approach to Reconstructing the Bacterial Pilus Substrate Recognition Machinery |
| Martyn Winn | Science and Technologies Facilities Council | Simulations of the intra-cellular domains of EGFR |
| Charles Laughton | University of Nottingham | Ensemble simulations to improve the quality of ligand-protein binding affinity calculations |
| Philip Fowler | University of Oxford | Crowding and Complexity: Simulation Studies of Biologically realistic Membrane Models |
| Sarah Harris | University of Leeds | Atomistic MD simulations of supercoiled DNA |
| Syma Khalid | University of Southampton | Small molecule potentials of mean force through an E. coli membrane |