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Table of Contents
MCM software and databases
This page has links for webservers and software downloads. There are tutorials for some software on our tutorials page.
- SYCAMORE
- SYstems biology's Computational Analysis and MOdeling Research Environment
- TRAPP
- a tool for analysis of transient binding pockets in proteins.
- PIPSA
- Webserver (and software download) for comparing electrostatic potential properties of proteins structures
- SDA
- Simulation of Diffusional Association - Brownian Dynamics Software
- Molsurfer
- Tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures.
- Prosat2
- Select and group residue based annotations and explore them interactively on a 3D structure of a protein.
- RAMD
- The (RAMD) method can be used to carry out molecular dynamics simulations with an additional randomly oriented force applied to a molecule in the system.
- NAMD
- The Random Acceleration Molecular Dynamics (RAMD) method implemented in NAMD.
- AMBER
- AMBER patches from the MCM group at HITS gGmbH (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
- Information that belongs to the article: 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
- GRID for identifying energetically favorable binding sites on biological molecules Tutorial GRID at Molecular Discovery
Not updated software
- Prosat
- Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein. Currently out of date.
- DSMM
- Database of Simulated Molecular Motions
- TRAJAN
- A Tool to Analyze Trajectories from Molecular Simulations
- pka calculation
- Scripts for pKa calculations with UHBD