This is a group for scientists working on biomolecular (proteins/nucleic acids) structures but with little or no experience of setting up simulations. That would be users who are mostly interested in simulations in standard conditions (constant temperature and pressure, explicit solvent, no ligands) seeking to solve specific biochemical questions (effects of mutations in stability, simple conformational changes) using biomolecular simulations.
The IG targets mainly users of portals for automated simulations such as those offered by IRB: MDWeb(http://mmb.irbbarcelona.org/MDWeb), a platform to setup, run and analyse protein structure molecular dynamics, FlexServ(http://mmb.irbbarcelona.org/FlexServ), to run a complete set of flexibility analyses on protein structure MD trajectories, NAFlex(http://mmb.irbbarcelona.org/NAFlex), a platform to build, setup, run and analyse nucleic acids molecular dynamics simulations and MCDNA (NEW! http://mmb.irbbarcelona.org/MCDNA), to build and study the structure and dynamics of DNA and chromatin fibers.
In addition, those IG users will have access to a set of already computed MD simulations stored in a couple of databases: MoDEL(http://mmb.irbbarcelona.org/MoDEL), with almost 2000 different protein structures trajectories and BigNASim(http://mmb.irbbarcelona.org/BigNASim), with 150 nucleic acid trajectories covering 150 µs simulation time.
Webinars and slides
Below are some of the BioExcel webinars that focus on Entry Level users:
- 2018-04-11: MC_DNA: A web server for the detailed study of the structure and dynamics of DNA and chromatin fibers (Joint MuG-BioExcel Webinar #2)
- 2017-07-20: NAFlex, a web server for the study of nucleic acid flexibility (Joint MuG-BioExcel Webinar #1)
- 2016-10-12: PRODIGY, a web server to predict binding affinities in protein-protein complexes
- 2016-05-19: Mutation free energy calculations with pmx
- 2016-05-10: Atomistic Molecular Dynamics Setup with MDWeb
- 2016-04-15: Integrative modelling of biomolecular complexes with HADDOCK
- 2017-10-11: MDStudio, microservice based molecular dynamics workflows
- 2017-07-17: BioExcel and OpenPHACTS: Building pharmacological workflow blocks for virtual screening
- 2016-11-16: Large-scale analytical workflows on the cloud using Galaxy and Globus
- 2017-02-08: Assessing Structure Quality in the PDB Archive
- 2017-03-15: Accessing Cloud and HTC Resources in BioExcel
- 2017-03-08: How to choose compute resources for your team
To be informed of upcoming BioExcel webinars, sign up for the BioExcel newsletter.
Below are some of the BioExcel publications and deliverables relating to Entry Level users:
- BioExcel Deliverable 2.1 – State of the art and gap analysis
- BioExcel Deliverable 2.2 – First Release of Workflow Blocks and Portals
- BioExcel Summer School
- BioExcel Community Forum
- BioExcel Spring School
- BioExcel Workflows
- PATC Course: Simulation Environments for Life Sciences
BioExcel Support Forum
Anyone can ask questions on BioExcel’s support forum (ask.bioexcel.eu) about Entry Level users web servers, webinars and courses. Subscribe to the Entry Level users IG category to follow relevant discussions, contribute and post your own questions.