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

31 May 2017, UCL, London UK

We would like to invite you to participate in our upcoming one-day CompBioMed/BioExcel meeting on Free Energy Calculations from Molecular Simulation on Wednesday 31st May 2017. This event is free to attend (registration will close on Wednesday May 24th).

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.

Agenda:
08:30 Registration Opens
09:00 Introduction

Session 1: Methodology 1 (Chair: Bert De Groot)
09:15 Chris Oostenbrink (BOKU, Vienna, Austria):
Robust free-energy calculations from a small number of simulations
09:35 Berk Hess (KTH, Stockholm, Sweden)
Optimal sampling along reaction coordinates
09:55 Peter Coveney (UCL, London, UK)
Ensemble-based molecular dynamics: principles and applications
10:15 Davide Branduardi (Schrödinger Inc)
Schrödinger FEP+: calculating relative binding free energiesin lead optimization
10:35 25 min break

Session 2: Methodology 2 (Chair: Andrea Townsend-Nicholson)
11:00 Antonia Mey (University of Edinburgh, United Kingdom)
Current limits of binding free energy calculations
11:20 Hannah Bruce McDonald (University of Southampton, Southampton, UK)
Predicting water networks and relative ligand binding freeenergies in proteins using grand canonical Monte Carlo
11:40 Phil Biggin (Oxford University, Oxford, UK)
Predictions of ligand selectivity from absolute binding free energy calculations
12:00 Alexander Heifetz (Evotec, UK)
Accurate Assessment of Protein-Ligand Interaction Energy in Seconds with Quantum Mechanics
12:20 Lunch

Session 3: Workflows (Chair: David Wright)
13:20 Hannes Loeffler (Rutherford Laboratory, STFC, UK)
FESetup: automating relative alchemical free energy simulations
13:40 Gianni De Fabritiis (UPF, Barcelona, Spain)
HTMD: High-throughput molecular dynamics for molecular discovery
14:00 Erik Lindahl (KTH, Stockholm, Sweden)
Efficient high-throughput free energy calculation and parameterization with GROMACS & STaGE
14:20 Bert de Groot (MPI, Goettingen, Germany)
Large-scale stability and affinity estimates through alchemical freeenergy calculations using pmx.
14:40 25 min break

Session 4: Applications (Chair: Vytautas Gapsys)
15:05 Philip Fowler (Oxford University Hospitals NHS Foundation Trust, Oxford, UK)
De novo prediction of resistance to trimethoprim in Staphylococcus aureus.
15:25 Daniel Seeliger (Boehringer Ingelheim Pharma Biberach, Ingelheim am Rhein, Germany)
Towards free-energy calculations as routine applications in industrial drug discovery
15:45 Miguel Machuqueiro (University of Lisbon, Lisbon, Portugal)
pKa shifts in protein and membrane binding
16:05 Gary Tresadern (Janssen, Antwerp, Belgium)
Free Energy Perturbation Applied in Drug Discovery at Janssen: Learnings so far…
16:25 10 minute break

16:35 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)

17:20 Close

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)

Location:
This meeting takes 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.


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