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