Table of Contents

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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 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
Google colab
commandline 		You can also run the commandline version in a google colab: https://colab.research.google.com/drive/1L7-KFFe69TG-tnoYQS3Yzomqxb8t2F1k#scrollTo=0rtGiKf7MtYh
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
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
ProSAT+
ProSAT+ Protein structure visualization and annotation tool.

References

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) , 13)
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
14)
SDA 7: A modular and parallel implementation of the simulation of diffusional association software
15)
webSDA: a web server to simulate macromolecular diffusional association.
16)
Protein Interaction Property Similarity Analysis.
17)
qPIPSA: Relating enzymatic kinetic parameters and interaction fields
18)
webpipsa: a web server for the comparison of protein interaction properties.
19)
SYCAMORE-a systems biology computational analysis and modeling research environment.