Welcome back after the summer break! In this issue we share new HADDOCK and BioBB releases as well as a revamped PMX webserver. Registration for our main conference closes very soon (31st August), so don't miss out! Registration is open for our Ambassador workshop in Athens, Greece in November. We present two new workflows based on BioBB with applications in drug discovery and feature a number of recent new publications, including a groundbreaking collaborative study highlighting the inherent 'physical code' of DNA.
`deeprank` scoring module - this module scores complexes using deeprank-gnn-esm, a graph neural network that predicts the fraction of native contacts (fnat) between two chains of an interface;
`rnascan` analysis module - this module performs a mutagenesis scan of each RNA base in the interface, following short energy minimisation, and outputs the difference in HADDOCK score between wild-type and mutated models.
Benchmarks, new tutorials, new workflows:
Two new Jupyter notebooks that can be launched directly in Colab:
Protein-DNA notebook - this tutorial demonstrates how to set up a HADDOCK3 workflow dedicated to predicting the 3D structure of a protein-DNA complex using pre-defined restraints (derived from the literature) and symmetry restraints.
Protein-glycan notebook - this tutorial demonstrates the use of HADDOCK3 for predicting the structure of a protein-glycan complex using information about the protein binding site. Includes the optional step of building the glycan structure using the GLYCAM server.
Taking place in the beautiful city of Brno, Czech Republic from 27 to 30 September this promises to be an outstanding event for the biomolecular research community.
With >30 invited and selected speakers and >130 registered participants to date, you are still in time to join us.
Submit your abstract and present your work as a poster (full instructions on the conference webpage)
See live demos and learn more about our core codes from the experts who will be present at our BioExcel booth during the conference and get support with your application to access LUMI supercomputerHPC resources.
We have a number of sightseeing options in and around Brno which you can sign up for before the start of the conference.
We have developed an automated drug design pipeline using the BioBB ecosystem, which is divided into Molecular Dynamics (MD) simulation workflows and Virtual Screening (VS) workflows. You can now access repositories containing documentation and tutorials for each workflow which can be run locally or in Google Colab. The software is public and free for academic use. Check it out!
Ambassador Program workshop: Aegean edition
Registration is open for the Aegean edition workshop will take place in Athens, Greece from 18 to 20 November and will focus on the use of GROMACS, HADDOCK and BioBB.
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