Entry Level users IG


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, and NAFlex(http://mmb.irbbarcelona.org/NAFlex), a platform to build, setup, run and analyse nucleic acids molecular dynamics simulations.

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.

For entry level users interested in small molecule docking, the SEABED web server (http://www.bsc.es/SEABED) integrates a variety of docking and QSAR techniques in a user-friendly environment, going beyond the basic docking and QSAR web tools, implementing extended functionalities like receptor preparation, library editing, flexible ensemble docking, hybrid docking/QSAR experiments or virtual screening on protein mutants.

Webinars and slides

Below are some of the BioExcel webinars that focus on Entry Level users:

Web Servers:

Biomolecular Workflows:

Biomolecular Databases:

Computational infrastructures:

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Publications

Below are some of the BioExcel publications and deliverables relating to Entry Level users:

BioExcel activities

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.