About Us

Research in the Michel group focuses on the development of molecular simulations methods and use of biophysical experiments to study molecular recognition in biological molecules, and to develop novel rational drug design technologies.

Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory

paper

Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

paper

Blinded predictions of binding modes and energies of HSP90-alpha ligands for the 2015 D3R Grand Challenge

paper

Elucidation of Non-Additive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study

paper

Impact of Ser17 phosphorylation on the conformational dynamics of the oncoprotein MDM2

paper

FESetup: Automating Setup for Alchemical Free Energy Simulations

paper

Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate complexes

paper

Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2

paper

A Collective Variable for the Rapid Exploration of Protein Druggability

paper

Evaluation of Water Displacement Energetics in Protein Binding Sites with Grid Cell Theory

paper

Evaluation of Host/Guest Binding Thermodynamics of Model Cavities with Grid Cell Theory

paper

Current and Emerging Opportunities for Molecular Simulations in Structure-Based Drug Design

paper

Prediction of Small Molecule Hydration Thermodynamics with Grid Cell Theory

paper

Mechanisms of small-molecule binding to intrinsically disordered proteins

paper

The Impact of Small Molecule Binding on the Energy Landscape of the Intrinsically Disordered Protein c-Myc

paper

Targeting the von Hippel–Lindau E3 Ubiquitin Ligase Using Small Molecules To Disrupt the VHL/HIF-1a Interaction

paper

A Simple QM/MM Approach for Capturing Polarization Effects in Protein-Ligand Binding Free Energy Calculations

paper

Effects of Water Placement on Predictions of Binding Affinities for p38 MAPalpha Kinase Inhibitors

paper

A Remote Arene Binding Site on Prostate Specific Membrane Antigen Revealed by Antibody-Recruiting Small Molecules

paper

Rigorous free energy calculations in structure-based drug design

paper

Chemical Control Over Immune Recognition: A Class of Antibody-Recruiting Small Molecules (ARMs) that Target Prostate Cancer

paper

Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization

paper

News

Currently

September 2016 - Congratulation to George Gerogiokas for publishing Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory in J Phys Chem B.

September 2016-Congratulations to Antonia Mey who was awarded a poster prize for our work about binding free energy calculation at the UK's first conference of research software engineers. You can download the poster by clicking here.

August 2016 - Congratulation to Stefano Bosisio and Antonia Mey for publishing Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge in J Comput Aided Mol Des.

July 2016 - Congratulation to Antonia Mey, Jordi Juarez-Jimenez and Alexis Hennessy for publishing Blinded predictions of binding modes and energies of HSP90-alpha ligands for the 2015 D3R Grand Challenge in Bioorg. Med. Chem.

June 2016 - Julien's slides from the 2016 Workshop on Free energy Methods in Drug Design held in Boston last month are now available here.

June 2016 - Congratulation to Gaetano Calabro, Francis Powlesland and Antonia Mey for publishing Elucidation of Non-Additive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study in J Phys Chem B.

May 2016 First group dinner of the year to welcome new members.

Group dinner May 2016

May 2016 - Welcome to new visitor Prof. José Manuel Granadino Roldán from the University of Jaen in Spain. Jose will spend 4-month with us for a project on alchemical free energy calculations.

April 2016 - Congratulation to alumni Juan Bueren-Calabuig for publishing Impact of Ser17 phosphorylation on the conformational dynamics of the oncoprotein MDM2 in Biochemistry.

April 2016 - New group photo (finally!).

Group picture April 2016

April 2016 - Welcome to new group members Cesar Mendoza Martinez and Kanhaya Lal. Cesar previously completed a PhD in Chemistry at the Universidad Nacional Autonoma de Mexico. Kanhaya previously completed a masters degree in pharmacoinformatics at NIPER Hajipur.

March 2016 - Julien is co-organising in July an international conference sponsored by CCP-BioSim and CCPN. The topic of the meeting is on molecular simulation and experimental methods to study biomolecular interactions.

March 2016 - Julien has been promoted to Senior Lecturer.

March 2016 - Congratulations to Dr Cesar Mendoza-Martinez who has been awarded a Newton international fellowship supported by the Academy of Medical Sciences to work with the group. Cesar will join us from Mexico City in April.

March 2016 - Antonia Mey and Stefano Bosisio present in San Diego our submissions to the D3R and SAMPL5 challenges for blind predictions of binding modes, binding affinities and distribution coefficients.

January 2016 - Welcome to new group member Arun who previously completed a postdoc in biomolecular NMR at Umea University with Magnus Wolf-Watz.

November 2015 - New publication in JCIM, FESetup: Automating Setup for Alchemical Free Energy Simulations.

November 2015 There is a PhD studentship opportunity in the group for BBSRC eligible students, see above for details.

October 2015 - Welcome to new group members Alessio, Lisa, Alexis and David.

September 2015 - Welcome to new group members Joan, Jordi and Harris.

August 2015 - Well done to Gaetano for passing his PhD viva !

George's viva July 2015 George's viva July 2015

July 2015 - Congratulations to George for passing his PhD viva !

George's viva July 2015 George's viva July 2015

June 2015 - Congratulations to Gaetano for publishing a new article in JCTC. This work, Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate complexes, was carried out in collaboration with Sushil Kumar Mishra from the Koca lab (Central European Institute of Technology, Brno) who visited us last year, and Hannes Loeffler from STFC Daresbury.

June 2015 - Congratulations to Juan for publishing his postdoctoral research work on MDM2 protein dynamics in PloS Computational Biology , Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2. You can watch below some of the simulations performed on this cancer drug target.

May 2015 - Congratulations to Remi and Kevin, whose recent article on the protein druggability estimator JEDI is on the cover of the latest issue of JCTC.

April 2015 - There are several vacancies in the group, see details above.

April 2015 - Congratulations to Gaetano, Remi and George, that are all starting postdocs in other labs next month. Gaetano will join the group of David Mobley at the University of California, Irvine. Remi will join the group of Prof Phil Biggin at the University of Oxford, and George will join the group of Dr Elsa Sanchez-Garcia at the Max Planck Institut für Kohlenforschung in Mulheim.

March 2015 - Welcome to new post-doctoral associate Antonia Mey. Antonia joins us from FU Berlin where she completed a postdoc in the Computational Molecular Biology Group with Frank Noe.

February 2015 - Julien is co-organising with Cecilia Clementi (Rice), Gianpaolo Gobbo (Mathematics), Ben Leimkuhler (Mathematics) and Frank Noe (Berlin) a conference on molecular simulations at Edinburgh on April 09-10. See the link for details: New Frontiers in the Characterization of Molecular Systems.

February 2015 - Congratulations to Jordi Juárez-Jiménez who has been awarded a Marie Curie individual fellowship to work with the group. Jordi will join us from Barcelona later this year.

January 2015 - Congratulations to Remi for passing his PhD viva !

Remi's viva January 2015

Remi's viva January 2015 Remi's viva January 2015

January 2015 - Congratulations to Remi and Kevin for a new publication in JCTC, A Collective Variable for the Rapid Exploration of Protein Druggability.

January 2015 - Congratulations to George for his new publication in PCCP, Evaluation of Water Displacement Energetics in Protein Binding Sites with Grid Cell Theory.

December 2014 - We thank the BBSRC and UCB for the award of a CASE studentship.

October 2014 Welcome to new final year MChem. students Richard and Giulia.

September 2014 Goodbye to Juan Bueren-Calabuig that has moved on to a postdoc position at Dundee. The group also welcomes new PhD students Pattama and Stefano.

August 2014 - The group visits the Council Chamber of the Glasgow City Chambers during the MGMS M3 conference. Congratulations to Remi for winning a prize for his poster on 'Protein druggability: the JEDI approach'.

Group picture August 2014

August 2014 There is a postdoctoral vacancy in the group, see above for details.

June 2014 - New publication in JCTC, Evaluation of Host/Guest Binding Thermodynamics of Model Cavities with Grid Cell Theory.

June 2014 - There are vacancies in the group, see above for details.

May 2014 - The 3rd annual CCP-BioSim conference, Frontiers of Biomolecular Simulation, was held at the University of Edinburgh from Wednesday 21st to Friday 23rd of May 2014. Details are available here.

May 2014 - Hi Ludwig !

Botlzmann Vienna May 2014

April 2014 - Welcome to visitor Dr Sushil Kumar Mishra from the Central European Institute of Technology, Masaryk University, Czech republic.

April 2014 - New group picture.

Group picture April 2014

April 2014 - Welcome to new PhD student Kevin who joins the group from the University of Barcelona on a ERC funded project.

January 2014 - New publication in PCCP, Current and Emerging Opportunities for Molecular Simulations in Structure-Based Drug Design.

January 2014 - Our recent article on Grid Cell Theory is on the cover of the latest issue of JCTC.

December 2013 - Congratulations to George for his new publication in JCTC, Prediction of Small Molecule Hydration Thermodynamics with Grid Cell Theory.

July 2013 - Julien has been awarded a five year Starting Grant from the European Research Council for the project "EBDD- Beyond structure: integrated computational and experimental approach to Ensemble-Based Drug Design".

June 2013 - Congratulations to alumna Anna, who was awarded a poster prize at the Summer School on ab initio Molecular Dynamics for Biomolecules in S. Stefano di Sessanio (Italy) for her graduate research project on dynamic allostery.

June 2013 - Congratulations to recent alumna Jodie, who will pursue next a Postgraduate Certificate in Education in London. The group also welcomes summer project students Chang and Changyoung.

May 2013 - The Computers in Chemistry Division of the American Chemical Society has awarded Julien an OpenEye Outstanding Junior Faculty Award in Computational Chemistry.

April 2013 - New group picture.

Group picture April 2013

March 2013 - Welcome to new postdoc Juan who joins the group from the University of Florida on a EPSRC funded project.

November 2012 - New article in JACS, Luminescent, Enantiopure, Phenylatopyridine Iridium-Based Coordination Capsules.

November 2012 - The 2nd annual CCP-BioSim conference, Frontiers of Biomolecular Simulation, will be held at the University of Nottingham from Monday 25th to Wednesday 27th March 2013. Details are available here.

October 2012 - Julien is co-organising with CCP-BioSim a workshop on free energy calculations for protein-ligand interactions, this November at the University of Southampton. Details are available here.

October 2012 - Welcome to Jodie who will pursue a research project as part of her MSc in Medicinal and Biological Chemistry.

September 2012 - New article in Biochem Soc Trans, Mechanisms of small-molecule binding to intrinsically disordered proteins.

September 2012 - Welcome to new EASTBIO PhD student Haris.

August 2012 - We thank the EPSRC for the award of a research grant.

July 2012 - New article in PLoS ONE, The Impact of Small Molecule Binding on the Energy Landscape of the Intrinsically Disordered Protein c-Myc.

July 2012 - Our research is featured on the cover of the 2012 PRACE digest magazine.


PRACE digest 2012

July 2012 - Congratulations to recent alumna, Anna who will pursue a PhD at the University of Oxford.

Group dinner July 2012

Group dinner before the summer holidays.

May 2012 - Welcome to Iva who will pursue with us a research project as part of her MSc in Drug Discovery and Translational Biology.

May 2012 - Congratulations to George for receiving a prize for best poster presentation at the 2012 NAIS workshop on State-of-the-Art Algorithms for Molecular Dynamics.

March 2012 - We thank the Royal Society for the award of a Research Grant.

March 2012 - New article in JACS, Targeting the von Hippel–Lindau E3 Ubiquitin Ligase Using Small Molecules To Disrupt the VHL/HIF-1a Interaction.

Feb 2012 - Upcoming talks: Julien has been invited to speak at the Biochemical society meeting on Intrinsically Disordered Proteins in York UK ; the CCP-BioSim/CMS 2012 meeting in Cirencester, UK ; the Frontiers in Water Biophysics 2012 meeting in Perugia, Italy.

Jan 2012 - Upcoming talks: Julien has been invited to speak at the 52nd Sanibel Symposium in St-Simons Island, USA ; the 2012 NAIS workshop on State-of-the-Art Algorithms for Molecular Dynamics in Edinburgh ; the 2012 Workshop on Free Energy Methods in Drug Design in Boston, USA.

Jan 2012 - Congratulations to recent alumna Rucha, who will pursue a PhD at the University of Cambridge.

Oct 2011 - Welcome to Anna who will pursue with us her final year Masters degree research project.

Sep 2011 - A warm welcome to new PhD students Gaetano, George and Remi.

Sep 2011 - Congratulations to Sriram who has been offered a PhD studentship at the Max Planck Institute for Heart and Lung Research.

Sep 2011 - We thank Evotec for funding our research.

July 2011 -We thank NVIDIA for supporting our research.

May 2011 - Julien is giving a talk next month at the ScotCHEM 2011 Computational Chemistry symposium.

May 2011 - Welcome to Rucha and Sriram who join the group for their Masters degree project.

May 2011 - We thank the European Commission for funding our research.

Jan 2011 - Welcome to Richard who joins the group for his BSc Honours degree final year project.

Jan 2011 - Our work on the water placement algorithm JAWS is on the cover of the most recent issue of the Journal of Chemical Theory and Computation.

Dec 2010 - The group website goes live, in anticipation of the official opening of the lab next month, many thanks to the Royal Society for making this possible.