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
Feel free to create new topics related to your questions!
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.
The CPMD category is meant for discussing topics related to the use of the
software in biological oriented applications, and in particular its QM/MM interface
This is the help forum for DISVIS, a
that allows you to visualizes and quantify the information content of distance restraints between macromolecular complexes
This is the help forum for POWERFIT, a
that allows you to automatically fits high-resolution atomic structures in cryo-EM densities.
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 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.
This topic is for any discussion related to Hybrid Methods. It is the main forum for general discussion of the Hybrid Methods interest group, but it's open for anyone to participate.
Integrative Modelling IG
This category is for all discussions related Integrative Structural Biology and Modelling, offering a forum to discuss various approaches and software. Please also register at
to receive our newsletter.
Molecular Dynamics Entry Level Users IG
This category is for discussions amongst members of the Molecular Dynamics Novice Users Interest Group that do not relate directly to GROMACS, HADDOCK or CPMD. If your question relates to one of these codes, please use the code-specific forums on this site.
Free Energy IG
This category is for all discussions related to the Free Energy Interest Group. Its primary audience is members of the IG but this forum is open for anyone to contribute.
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.
Discussion about this site, its organization, how it works, and how we can improve it.