Webinar: How to contribute to GROMACS code and documentation: where it is and how to use it (2018-10-30)
BioExcel’s webinar series continue with a presentation by Dr. Paul Bauer, Lindahl group. Register Abstract I’ll give a short overview about how to successfully contribute new content to the GROMACS project, going into detail for contribution policies and our code review and acceptance standards. I’ll explain how to find the necessary information in the GROMACS […]
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Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server.
Abstract Recently we published PROtein binDIng enerGY (PRODIGY), a web-server for the prediction of binding affinity in protein–protein complexes. By using a combination of simple structural properties, such as the residue-contacts made at the interface, PRODIGY has demonstrated a top performance compared with other state-of-the-art predictors in the literature. Here we present an extension of […]
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Interview with Professor Michael Levitt, 2013 Nobel Laureate in Chemistry
In 2013 the Nobel Prize in Chemistry was awarded jointly to three scientists who laid the foundations of computational biomolecular research – Martin Karplus, Michael Levitt and Arieh Warshel. The prize was awarded “for the development of multiscale models for complex chemical systems.” In this interview, we speak with one of them, Professor Michael Levitt […]
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Webinar: Open Force Field Initiative: The SMIRNOFF format and learned chemical perception (2018-10-10)
BioExcel’s webinar series continue with a presentation by Caitlin C. Bannan Mobley Group, UC Irvine – Chemistry Department Register Abstract The Open Force Field Initiative (openforcefield.org) is developing a machinery to automatically parameterize molecular mechanics force fields. An important part of this process will be automating chemical perception — the way force field parameters are […]
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Webinar: Immersive visual exploration of biomolecular systems in virtual reality – from static views to interactive dynamics (2018-10-04)
BioExcel’s webinar series continue with a presentation by Marc Baaden, CNRS (Centre National de la Recherche Scientifique). Register Abstract For several years now, my team pursues the goal to study complex molecular assemblies through interactive visualization, manipulation and analysis approaches to aid hypothesis generation and exploration of complex datasets. The UnityMol framework [1] forms a […]
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Webinar: Molecular simulation control and extension with gmxapi for GROMACS. (2018-09-19)
BioExcel’s webinar series continue with a presentation by Eric Irrgang, Kasson Lab Register Abstract gmxapi is a framework and front-end designed to support new methods in molecular simulation. A Python package provides a scriptable interface to manage ensembles of simulations. A C++ extension interface allows researchers to attach custom code to a high-performance GROMACS simulation. […]
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