This is an old revision of the document!
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
| Description | Input | Type | Main Refer- ence(s) | Link | |
|---|---|---|---|---|---|
| Molsurfer | Protein structure tool to link a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures ADS Analytically Defined molecular Surfaces is used within Molsurfer | PDB/PQR files or PDB codes | Webserver | 1) 2) | https://molsurfer.h-its.org Neuraminidase 1nca example |
| TRAPP v4 | Tool for the analysis, including druggability analysis, of TRAnsient binding Pockets in Proteins | Structures, Ligands, Trajectories | Standalone Software | 3), 4) | Download TRAPP |
| Webserver | 5) | Run TRAPP analysis | |||
| L-RIP / RIPLig | Two non-equilibrium MD approaches for the identification of slow conformational changes of a protein binding site | Protein structure | Standalone also used within TRAPP | 6) | L-RIP and RIPlig |
| RASPD+ | Fast protein-ligand binding free energy prediction using simplified physicochemical features | Structures, Ligands | Standalone Software | 7) | GitHub |
| KBbox | KBbox: a Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding | Search term | Webserver | 8) | Search KBbox |
| RAMD / tauRAMD | 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. For implementations in other software, see: see RAMD additional information | NAMD simulation setup | NAMD Plugin | 9) 10) | Included in NAMD distribution (plugin directory) also here with additional resources Download |
| tauRAMD scripts | 11) 12) | Includes RAMD plugin with additional scripts Download |
|||
| GROMACS RAMD implementation | 13) | https://github.com/HITS-MCM/gromacs-ramd RAMD in GROMACS Tutorial |
|||
| MD-IFP | MD trajectory analysis using protein-ligand or protein-protein Interaction Fingerprints | Trajectories Test dataset provided | Jupyter Notebooks | 14) | Includes example of IFP analysis of dissociation trajectories for 3 compounds of HSP90 reported in Kokh et al. (2020) J. Chem. Phys. 153(12):125102; as well as an example for IFP analysis for a protein-protein complex reported in D'Arrigo et al. (2024) Commun Biol 7(1):1159 https://github.com/HITS-MCM/MD-IFP |
| SDA / webSDA | Simulation of Diffusional Association - Brownian Dynamics Software ECM is part of the SDA distribution and allows the calculation of partial charges. | Structures of Solutes | Standalone Software | 15) | Download SDA Documentation of SDA |
| Webserver | 16) | Run webSDA | |||
| PIPSA / webPIPSA | Comparing electrostatic potentials (or other molecular interaction fields) of protein structures | Protein Structures of the same fold | Standalone Software | 17) 18) | Download PIPSA/Multipipsa |
| Python Interface Multipipsa |
|||||
| Google colab commandline | You can also run the commandline version in a google colab: https://colab.research.google.com/drive/1L7-KFFe69TG-tnoYQS3Yzomqxb8t2F1k#scrollTo=0rtGiKf7MtYh | ||||
| Webserver | 19) | Run Pipsa Analysis | |||
| COMBINE analysis / ensembleCombine | Prediction of Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis (COMBINE analysis was originally developed for and can also be used for the prediction of binding free energies) | Binding Analysis | Standalone Program | 20) | Tutorial GitHub |
Some software has been 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)
Methods and software developed with participation of members of MCM available at other research groups
- COMBINE analysis
- Comparative Binding Energy Analysis, extended by Ariane Nunes-Alves (MCM) and merged. Literature, Tutorial, gCOMBINE binaries
- GRID
- Computational method for identifying energetically favorable binding sites on biological molecules Tutorial
- UHBD
Not updated software
- AMBER patches
- AMBER patches from the MCM group at HITS for RAMD and NPSA
- DSMM
- Database of Simulated Molecular Motions
- LigDig
- LigDig: a web server for querying ligand–protein interactions
- metaPocket2
- Webserver to identify pockets on protein surfaces to predict binding sites for ligands
- ProSAT
- Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein
- ProSAT2
- Select and group residue-based annotations and explore them interactively on a 3D structure of a protein
- ProSAT+
- ProSAT+ Protein structure visualization and annotation tool.
- pka calculation
- Scripts for pKa calculations with UHBD
- Sycamore webserver
- Sycamore | SYstems biology's Computational Analysis and MOdeling Research Environment for Kinetic Data 21)
- TRAJAN
- A Tool to Analyze Trajectories from Molecular Simulations
