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 | Webserver | 3) | Run TRAPP analysis |
| TRAPP v3 | Tool for analysis of transient binding pockets in proteins | Structures, Ligands, Trajectories | Standalone Software | 4) | Download TRAPP |
| Webserver | 5) | Run TRAPP analysis, old version | |||
| 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 | Search KBbox | |
| RAMD / $\tau$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. Originally this was implemented from the MCM group in Amber 8 (not maintained). Recently the Amber group has provided the functionality integrated in Amber 20 see RAMD additional information | NAMD simulation setup | NAMD Plugin | 8) 9) | Included in NAMD distribution (plugin directory) also here with additional resources Download |
| $\tau$RAMD scripts | 10) 11) | Includes RAMD plugin with additional scripts Download |
|||
| GROMACS RAMD implementation | 12) | https://github.com/HITS-MCM/gromacs-ramd RAMD in GROMACS Tutorial |
|||
| MD-IFP | MD trajectory analysis using protein-ligand Interaction Fingerprints | Trajectories Test dataset provided | Jupyter Notebooks | 13) | IFP analysis of dissociation trajectories for 3 compounds of HSP90 reported in the paper D. B. Kokh, B. Doser, S. Richter, F. Ormersbach, X. Cheng , R.C. Wade “A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories” (2020) J. Chem. Phys. 153(12):125102 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 | 14) | Download SDA |
| Webserver | 15) | Run webSDA | |||
| PIPSA / webPIPSA | Comparing electrostatic potentials (or other molecular interaction fields) of protein structures | Protein Structures of the same fold | Standalone Software | 16) 17) | Download PIPSA/Multipipsa |
| Python Interface Multipipsa |
|||||
| Webserver | 18) | Run Pipsa Analysis | |||
| Sycamore | SYstems biology's Computational Analysis and MOdeling Research Environment | Kinetic Data | Webserver | 19) | Sycamore webserver |
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)
- metaPocket2
- Webserver to identify pockets on protein surfaces to predict binding sites for ligands
Methods and software developed with participation of members of MCM are available at other research groups
- COMBINE analysis
- Comparative Binding Energy Analysis, extended from Ariane Nunes-Alves (MCM) and merged. Literature Tutorial gCOMBINE binaries
- UHBD
- GRID
- Computational method for identifying energetically favorable binding sites on biological molecules Tutorial
Not updated software
- AMBER patches
- AMBER patches from the MCM group at HITS for RAMD and NPSA
- 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
- LigDig
- LigDig: a web server for querying ligand–protein interactions
- DSMM
- Database of Simulated Molecular Motions
- TRAJAN
- A Tool to Analyze Trajectories from Molecular Simulations
- pka calculation
- Scripts for pKa calculations with UHBD
- ProSAT+
- ProSAT+ Protein structure visualization and annotation tool.
References
13)
https://pubs.aip.org/aip/jcp/article-abstract/153/12/125102/1062851/A-workflow-for-exploring-ligand-dissociation-from?redirectedFrom=fulltext|Kokh DB et. al. (2020) A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories. J. Chem. Phys. 153(12):125102
