You are here: start » projects » software

This is an old revision of the document!

Table of Contents

mcm_logo.jpg

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 v4 Tool for the analysis,
including druggability analysis,
of TRAnsient binding Pockets in Proteins 		Structures, Ligands,
Trajectories 		Webserver 1) Run TRAPP analysis
TRAPP v3 Tool for analysis of transient
binding pockets in proteins 		Structures, Ligands,
Trajectories 		Standalone Software ( TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins)) Download TRAPP
Webserver 2) 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 		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.

see RAMD additional information 		NAMD simulation setup NAMD Plugin 4) 5) Included in NAMD
distribution (plugin directory)
also here with
additional resources
Download
$\tau$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
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
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) https://prosat.h-its.org
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) https://molsurfer.h-its.org
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 TutorialContact
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)
Druggability Assessment in TRAPP using Machine Learning Approaches
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)
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.
15)
MolSurfer: 2D maps to navigate 3D structures of proteins and their complexes
16)
MolSurfer: a macromolecular interface navigator.

Trace: • software

Navigation
Print/export