Free Energy Calculations from Molecular Simulation: Applications in Life and Medical Sciences

Free Energy Calculations from Molecular Simulation: Applications in Life and Medical Sciences

31 May 2017, UCL, London UK

On this page you will find all the training material from our one-day CompBioMed/BioExcel meeting on Free Energy Calculations from Molecular Simulation on Wednesday 31st May 2017.

In recent years, it has become possible to calculate free energies of various binding processes between compounds and proteins with high levels of accuracy and precision, as well as speed and reliability. This meeting will assess the state of the art, through the participation of leading practitioners from academia and industry who will discuss methods, applications and experimental validation.

You can view all the abstracts from the speakers by following this link

For YouTube videos of the presentations, please click on the links in the agenda below. Some videos are not available due to confidentiality of the presentation.


Session 1: Methodology 1 (Chair: Bert De Groot)
Chris Oostenbrink (BOKU, Vienna, Austria):
Robust free-energy calculations from a small number of simulations
Berk Hess (KTH, Stockholm, Sweden)
Optimal sampling along reaction coordinates
Peter Coveney (UCL, London, UK)
Ensemble-based molecular dynamics: principles and applications
Davide Branduardi (Schrödinger Inc)
Schrödinger FEP+: calculating relative binding free energiesin lead optimization

Session 2: Methodology 2 (Chair: Andrea Townsend-Nicholson)
Antonia Mey (University of Edinburgh, United Kingdom)
Current limits of binding free energy calculations
Hannah Bruce McDonald (University of Southampton, Southampton, UK)
Predicting water networks and relative ligand binding freeenergies in proteins using grand canonical Monte Carlo
Phil Biggin (Oxford University, Oxford, UK)
Predictions of ligand selectivity from absolute binding free energy calculations
Alexander Heifetz (Evotec, UK)
Accurate Assessment of Protein-Ligand Interaction Energy in Seconds with Quantum Mechanics

Session 3: Workflows (Chair: David Wright)
Gary Tresadern (Janssen, Antwerp, Belgium)
Free Energy Perturbation Applied in Drug Discovery at Janssen: Learnings so far…
Gianni De Fabritiis (UPF, Barcelona, Spain)
HTMD: High-throughput molecular dynamics for molecular discovery
Erik Lindahl (KTH, Stockholm, Sweden)
Efficient high-throughput free energy calculation and parameterization with GROMACS & STaGE
Bert de Groot (MPI, Goettingen, Germany)
Large-scale stability and affinity estimates through alchemical freeenergy calculations using pmx.

Session 4: Applications (Chair: Vytautas Gapsys)
Philip Fowler (Oxford University Hospitals NHS Foundation Trust, Oxford, UK)
De novo prediction of resistance to trimethoprim in Staphylococcus aureus.
Daniel Seeliger (Boehringer Ingelheim Pharma Biberach, Ingelheim am Rhein, Germany)
Towards free-energy calculations as routine applications in industrial drug discovery
Miguel Machuqueiro (University of Lisbon, Lisbon, Portugal)
pKa shifts in protein and membrane binding

16:15 Panel discussion (Chair: Peter Coveney)
Sarah Skerratt (Convergence, UK)
Brad Sherborne (Merck, USA)
Franca Fraternali (King’s College London, UK)
Davide Branduardi (Schrödinger Inc)
Bert de Groot (MPI, Goettingen, Germany)
Erik Lindahl (KTH, Stockholm, Sweden)

Organising Committee:
Peter Coveney (UCL, London, UK)
Bert de Groot (MPI, Goettingen, Germany)
Vytautas Gapsys (MPI, Goettingen, Germany)
Rossen Apostolov (KTH, Stockholm, Sweden)
David Wright (UCL, London, UK)
Andrea Townsend-Nicholson (UCL, London, UK)

This meeting took place in Chandler House, 2 Wakefield St, Bloomsbury, London WC1N 1PF, registration will be in Room B02, and the talks will be given in Room G10. So please head to Room B02 in Chandler House.

This event was live-streamed via our Youtube channel, and are still available to watch. Please note that some talks were omitted from the live stream due to their confidential content and are not available.

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