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
TRAPP v3	Tool for analysis of transient binding pockets in proteins	Structures, Ligands, Trajectories	Standalone Software	¹⁾	Download TRAPP
TRAPP v3	Tool for analysis of transient binding pockets in proteins	Structures, Ligands, Trajectories	Webserver	²⁾	Run TRAPP analysis
TRAPP v4	Tool for druggability analysis of transient binding pockets in proteins	Structures, Ligands, Trajectories	Webserver		not yet released
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	³⁾	L-RIP and RIPlig
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. 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 / $\tau$RAMD		NAMD simulation setup	$\tau$RAMD scripts	⁶⁾ ⁷⁾	Includes RAMD plugin with additional scripts Download
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	⁸⁾	Download SDA
SDA / webSDA		Structures of Solutes	Webserver	⁹⁾	Run webSDA
PIPSA / webPIPSA	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	¹⁰⁾ ¹¹⁾	Download PIPSA/Multipipsa
			Webserver	¹²⁾	Run Pipsa Analysis
Sycamore	SYstems biology's Computational Analysis and MOdeling Research Environment	Kinetic Data	Webserver	¹³⁾	Sycamore webserver
ProSAT+	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'
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	¹⁵⁾ ¹⁶⁾	Neuraminidase 1nca example
KBbox	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

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 Literature Tutorial gCOMBINE
UHBD: University of Houston Brownian Dynamics Tutorial Contact
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

References

¹⁾

TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins

²⁾

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets

³⁾

Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets

⁴⁾

How do substrates enter and products exit the buried active site of cytochrome P450cam ? 1. Random expulsion molecular dynamics to investigate ligand access channels and mechanisms

⁵⁾

Substrate Access to Cytochrome P450cam: a Comparison of a Thermal Motion Pathway Analysis with Molecular Dynamics Simulation Data

⁶⁾

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations.

⁷⁾

Machine learning analysis of tauRAMD trajectories to decipher molecular determinants of drug-target residence times.

⁸⁾

[https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.23971|SDA 7: A modular and parallel implementation of the simulation of diffusional association software]

⁹⁾

webSDA: a web server to simulate macromolecular diffusional association.

¹⁰⁾

Protein Interaction Property Similarity Analysis.

¹¹⁾

qPIPSA: Relating enzymatic kinetic parameters and interaction fields

¹²⁾

webpipsa: a web server for the comparison of protein interaction properties.

¹³⁾

SYCAMORE-a systems biology computational analysis and modeling research environment.

¹⁴⁾

ProSAT+: visualizing sequence annotations on 3D structure.