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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
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
1)
MolSurfer: 2D maps to navigate 3D structures of proteins and their complexes
2)
MolSurfer: a macromolecular interface navigator.
3)
Druggability Assessment in TRAPP using Machine Learning Approaches
4)
TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins
5)
TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets
6)
Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets
7)
RASPD+: Fast protein-ligand binding free energy prediction using simplified physicochemical features.
8)
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
9)
Substrate Access to Cytochrome P450cam: a Comparison of a Thermal Motion Pathway Analysis with Molecular Dynamics Simulation Data
10)
Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations.
11)
Machine learning analysis of tauRAMD trajectories to decipher molecular determinants of drug-target residence times.
12)
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

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