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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.
- 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
- Molsurfer
- Tool to link 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 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
- NAMD
- The RAMD method implemented in NAMD
- AMBER
- 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
- 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