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Table of Contents
MCM software and databases
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
Current software of the Group
- KBbox
- KBbox: a Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding
- 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. Click to start hemoglobin example '1o1o' in Protein structure visualization and annotation tool. ProSAT+ is also listed on OMICs Tools collection
- 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
- RAMD in NAMD
- 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
- UHBD
- 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