Category Topics

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!
396

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
8

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.
6

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.
9

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).
1

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.
0

pmx

Automated protein structure and topology generation for alchemical perturbations. Web-server, source code, and examples at pmx.mpibpc.mpg.de/ .
3

MDWeb

MDWeb - Molecular dynamics on the web provides a web interface to set up molecular dynamics simulations at https://mmb.irbbarcelona.org/MDWeb/
21

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.
4

QM/MM for Biomolecular Simulation

Challenges combining quantum mechanics calculations with CP2K and molecular mechanics simulations with GROMACS. For pure CP2K support, see cp2k.org/howto:forum .
1

Workshop Tutorials

This is a place to discuss tutorials during BioExcel workshops.
1

General Topics in Molecular Dynamics

General musings about molecular dynamics that do not relate directly to GROMACS, HADDOCK or CPMD
5
31

Site Feedback

Discussion about this site, its organization, how it works, and how we can improve it.
2

GROMACS

Find the GROMACS forum at http://gromacs.bioexcel.eu
11

BioBB

BioBB is a software library for interoperable biomolecular simulation workflows.
1