Category Topics

BioExcel Feedback

Welcome to BioExcel feedback category. Here you can provide feedback on future development of our core softwares (GROMACS,HADDOCK,BioBB and PMX) and on BioExcel activities.
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BioExcel Webinar

Here you ask questions to the BioExcel Webinar speakers. After each BioExcel Webinar, you can discuss the webinar topic with speaker for one week.
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HADDOCK

The HADDOCK category is meant for discussing any topic related to the use of the HADDOCK software, either as a local installation or via the HADDOCK web portal. For details about HADDOCK please refer to https://www.bonvinlab.org/software/haddock2.4
Feel free to create new topics related to your questions!
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BioBB

BioBB is a software library for interoperable biomolecular simulation workflows.
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pmx

Automated protein structure and topology generation for alchemical perturbations. Web-server, source code, and examples at pmx.mpibpc.mpg.de/ .
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GROMACS

Find the GROMACS forum at http://gromacs.bioexcel.eu
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SPOTON

This is the forum for the SpotOn web portalwhich implements a robust algorithm developed to identify and classify the interfacial residues as Hot-Spots (HS) and Null-Spots (NS).
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PDB-tools

This is the forum for the PBD-tools web portal that allows to define workflows to manipulate PDB files and is designed to be a swiss-knife for the PDB format.
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MDWeb

MDWeb - Molecular dynamics on the web provides a web interface to set up molecular dynamics simulations at https://mmb.irbbarcelona.org/MDWeb/
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Workflows

This category is for all discussions related to the Workflows Interest Group. Its primary audience is members of the IG but this forum is open for anyone to contribute.
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QM/MM for Biomolecular Simulation

Challenges combining quantum mechanics and molecular mechanics using CP2K and GROMACS
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DISVIS

This is the help forum for DISVIS, a software and web portal that allows you to visualizes and quantify the information content of distance restraints between macromolecular complexes
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General Topics in Molecular Dynamics

General musings about molecular dynamics that do not relate directly to GROMACS, HADDOCK or CPMD
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POWERFIT

This is the help forum for POWERFIT, a software and web portal that allows you to automatically fits high-resolution atomic structures in cryo-EM densities.
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Site Feedback

Discussion about this site, its organization, how it works, and how we can improve it.
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PRODIGY

This is the forum for the PRODIGY web portal ( that predicts binding affinities for protein-protein (PRODIGY) and protein-small ligand (PRODIGY-LIG) complexes and also allows to classify an interface as biological or crystallographic.
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