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# 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 Link Refer- ence(s) Tool for analysis of transient binding pockets in proteins Structures, Ligands, Trajectories Standalone Software 1) Download TRAPP Webserver 2) Run TRAPP analysis Tool for druggability analysis of transient binding pockets in proteins Structures, Ligands, Trajectories Webserver not yet released Two non-equilibrium MD approaches for the identification of slow conformational changes of a protein binding site​ Protein structure Standalone also used within TRAPP 3) L-RIP and RIPlig 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 additional information see $\tau$RAMD additional information NAMD simulation setup NAMD Plugin 4) 5) Included in NAMD distribution (plugin directory) also here (additional resources) Download RAMD scripts 6) 7) Includes RAMD plugin with additional scripts Download 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 8) Download SDA Webserver 9) Run webSDA Comparing electrostatic potentials (or other molecular interaction fields) of protein structures Protein Structures of the same fold Standalone Software 10) 11) Download PIPSA/Multipipsa Python Interface Multipipsa Webserver 12) Run Pipsa Analysis SYstems biology's Computational Analysis and MOdeling Research Environment Kinetic Data Webserver 13) Sycamore webserver Protein structure visualization and annotation tool. Display protein annotations (eg mutation data from uniprot) on protein structures from RCSB. PDB or Uniprot codes Webserver 14) Hemoglobin example '1o1o' 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 15) 16) Neuraminidase 1nca example KBbox: a Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding Search term Webserver Search KBbox

### Some software has been migrated to other research groups

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)
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

Comparative Binding Energy Analysis Literature Tutorial gCOMBINE
University of Houston Brownian Dynamics TutorialContact
Computational method for identifying energetically favorable binding sites on biological molecules Tutorial

### Not updated software

AMBER patches from the MCM group at HITS for RAMD and NPSA
Select and group residue-based annotations and explore them interactively on a 3D structure of a protein
Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein
LigDig: a web server for querying ligand–protein interactions
Database of Simulated Molecular Motions
A Tool to Analyze Trajectories from Molecular Simulations
Scripts for pKa calculations with UHBD