Workshop Objectives
The worshop will introduce HADDOCK (High Ambiguity Driven protein-protein DOCKing) which is an information-driven flexible docking approach for the modeling of biomolecular complexes, and PMX which is a service for users who need to do free energy calculations. PMX utilizes the Gromacs classical molecular dynamics simulation engine to perform calculations at the background. The workshop also covers advanced usage of Gromacs itself in particular on HPC environment.
Upon registration the participants are asked for special topics they are interested in which potentially could be covered at the workshop. It will be possible to follow a video stream of the lectures also remotely, but unfortunately we will not be able to support doing the hands-on remotely. Check closer to the event for detailed instructions, or contact us.
Registration
Please register for on-site or remote participation here. Registration deadline is 27th September 2019 by 12:00
BioExcel can provide a limited number of travel bursaries for participants. Instructions to apply can be found in the registration form.
Tentative Programme / to be updated
Wednesday, 9th October
12:00 Lunch
13:00 Gromacs - where are we now, what's new, what's coming in the future
13:30 Participant Introduction
14:00 Maximizing Gromacs performance for HTC and HPC
14:30 Hands on - Performance
15:00 Advanced simulation protocols in GROMACS
15:30 Hands on - Advanced simulation protocols
18:00 Light dinner and social program
21:00 End of Day 1
Thursday, 10th October
09:00 PMX - alchemical free energy calculation setup tools introduction
10:00 Hands on - PMX
12.00 Lunch
13:00 HADDOCK – Modelling intermolecular interactions
14:00 Hands on - HADDOCK
15:00 HADDOCK – advanced topics
17:00 End of Day 2
Friday, 11th October
09:00 Getting deeper into issues and questions that emerged during the workshop
10:00 Participant contributions
12:00 Closing
Speakers and organizers
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Dr. Christian Blau, Theoretical and Computational Biophysic
KTH Royal Institute of Technology -
Dr. Rodrigo Vargas Honorato, Computational structural biology group
Utrecht University
The event is organized in collaboration with BioExcel and CSC and supported by PRACE.
Language: English
