This page has links for webservers and software downloads provided by the Molecular and Cellular Modeling (MCM) group at the Heidelberg Institute for Theoretical Studies (HITS). There are tutorials for some software on our tutorials page. For queries, send email to: firstname.lastname@example.org
LigDig: a web server for querying ligand–protein interactions
SYstems biology’s Computational Analysis and MOdeling Research Environment
Tool for analysis of transient binding pockets in proteins
Webserver (and software download) for comparing electrostatic potentials (or other molecular interaction fields) of protein structures
Simulation of Diffusional Association – Brownian Dynamics Software
Webserver for Simulation of Diffusional Association
- L-RIP and RIPlig
Two non-equilibrium MD approaches for the identification of slow conformational changes of a protein binding site
Tool to link a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures
Display protein annotations on protein structures.
KBbox is a toolbox of computational methods for studying the kinetics of molecular binding. It also provides an updated list of examples of published work for these methods, along with detailed tutorials to guide less experienced researchers.
The Random Acceleration Molecular Dynamics (RAMD) method can be used to carry out molecular dynamics simulations with an additional randomly oriented force applied to a molecule in the system
τ-random acceleration molecular dynamics (τRAMD) is a protocol based on the RAMD method for the ranking of drug candidates by their residence time and obtaining insights into ligand-target dissociation mechanism.
Migrated to other research groups
Methods and software available at other research groups
Not updated software
Select and group residue-based annotations and explore them interactively on a 3D structure of a protein
Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein
Database of Simulated Molecular Motions
A Tool to Analyze Trajectories from Molecular Simulations
- pka calculation
Scripts for pKa calculations with UHBD