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 http://www.bonvinlab.org/software/haddock2.2
Feel free to create new topics related to your questions!

GROMACS

GROMACS is a free and open-source software suite for high-performance molecular dynamics and output analysis. It primarily targets bio-molecular simulations of thousands to millions of atoms, described by particle-based classical mechanics force fields. These simulations integrate the Newtonian equations of motion for billions of time steps, which permits scientists to understand behaviour on experimentally relevant time scales.

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

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.

PRODIGY

PRODIGY (PROtein binDIng enerGY prediction) is a web server that predicts binding affinities for protein-protein (PRODIGY) and protein-small ligand (PRODIGY-LIG) complexes To use PRODIGY you just need to provide the three-dimensional structure of your complex/complexes in PDB/mmCIF format or the ID of its PDB entry. The dG estimation for a typical complex is expected to take a few seconds.

SPOTON

SpotOn is a robust algorithm developed to identify and classify the interfacial residues as Hot-Spots (HS) and Null-Spots (NS) with a final accuracy of 0.95 and a sensitivity of 0.95 on an independent test set.

pmx

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

MDWeb

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

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.

CP2K in Biomolecular Simulation

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

Workshop Tutorials

This is a place to discuss tutorials during BioExcel workshops.

General Topics in Molecular Dynamics

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

Site Feedback

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