Software

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: mcmsoft@h-its.org

 

LIGDIG
LigDig: a web server for querying ligand–protein interactions
SYCAMORE
SYstems biology’s Computational Analysis and MOdeling Research Environment
TRAPP
Tool for analysis of transient binding pockets in proteins
PIPSA
Webserver (and software download) for comparing electrostatic potentials (or other molecular interaction fields) of protein structures
SDA
Simulation of Diffusional Association – Brownian Dynamics Software
webSDA
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
Molsurfer
Tool to link a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures
ProSAT+
 Display protein annotations on protein structures.
RAMD
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
The RAMD method implemented in NAMD
AMBER patches
AMBER patches from the MCM group at HITS for RAMD and NPSA
ADS
Analytically Defined molecular Surfaces (used within Molsurfer)
ECM
ECM is now part of the SDA distribution

Migrated to other research groups

LIGIN
Software for molecular docking using surface complementarity, see: Sobolev, V., Wade, R.C., Vriend, G. & Edelman, M. Molecular docking using surface complementarity, PROTEINS, 25, 120-129 (1996)
metaPocket2
Webserver to identify pockets on protein surfaces to predict binding sites for ligands

Methods and software available at other research groups

COMBINE analysis
Comparative Binding Energy Analysis Literature Tutorial gCOMBINE
UHBD
University of Houston Brownian Dynamics TutorialContact
GRID
Computational method for identifying energetically favorable binding sites on biological molecules Tutorial

Not updated software

ProSAT2
Select and group residue-based annotations and explore them interactively on a 3D structure of a protein
ProSAT
Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein
DSMM
Database of Simulated Molecular Motions
TRAJAN
A Tool to Analyze Trajectories from Molecular Simulations
pka calculation
Scripts for pKa calculations with UHBD