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projects:software [2014/06/25 13:09] – [Methods and software available at other research groups] wadeprojects:software [2025/02/13 12:17] (current) – richter
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 {{:projects:mcm_logo.jpg}} {{:projects:mcm_logo.jpg}}
-====== MCM software and databases ====== +===== MCM software and databases ===== 
-This page has links for webservers and software downloads. +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:tutorials|tutorials page]].+There are tutorials for some software on our [[tutorials:tutorials|tutorials page]]. For queries, send email to: [[mcmsoft@h-its.org|mcmsoft@h-its.org]]
  
-  ? [[http://sycamore.eml.org|SYCAMORE]] 
-  : SYstems biology's Computational Analysis and MOdeling Research Environment 
-  ? [[http://mcm.h-its.org/trapp/|TRAPP]] 
-  : a tool for analysis of transient binding pockets in proteins. 
-  ? [[http://pipsa.h-its.org|PIPSA]] 
-  : Webserver (and software download) for comparing electrostatic potential properties of proteins structures 
-  ? [[http://mcm.h-its.org/sda7/|SDA]] 
-  : Simulation of Diffusional Association - Brownian Dynamics Software 
-  ? [[http://projects.h-its.org/dbase/molsurfer/index.html|Molsurfer]] 
-  : Tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. 
-  ? [[http://projects.h-its.org/dbase/ps2/index.html|Prosat2]] 
-  : Select and group residue based annotations and explore them interactively on a 3D structure of a protein. 
-  ? [[http://projects.h-its.org/mcm/software/ramd|RAMD]] 
-  : The (RAMD) method can be used to carry out molecular dynamics simulations with an additional randomly oriented force applied to a molecule in the system. 
-    ? [[http://projects.eml.org/mcm/software/namd|NAMD]] 
-    : The Random Acceleration Molecular Dynamics (RAMD) method implemented in NAMD. 
-  ? [[http://projects.h-its.org/mcm/software/amber.html|AMBER]] 
-  : AMBER patches from the MCM group at HITS gGmbH (RAMD and NPSA) 
-  ? [[http://projects.h-its.org/mcm/software/ADS|ADS]] 
-  : Analytically Defined molecular Surfaces (used within Molsurfer). 
-  ? [[http://projects.h-its.org/mcmsoft/sda/ecm/doc/index.html|ECM]] 
-  : ECM is now part of the SDA distribution. 
  
 +|  ^ 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 \\ [[http://projects.h-its.org/mcm/software/ADS|ADS]] Analytically Defined molecular Surfaces \\ is used within Molsurfer | PDB/PQR files \\ or PDB codes | Webserver |  (([[https://projects.h-its.org/dbase/molsurfer/doc/tibs.html|MolSurfer: 2D maps to navigate 3D structures of proteins and their complexes]]))  (([[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168994/|MolSurfer: a macromolecular interface navigator.]]))  | [[https://molsurfer.h-its.org]] \\ [[https://molsurfer.h-its.org/demo/1nca/result.html|Neuraminidase 1nca example]] |
 +^ TRAPP v4 | Tool for the analysis, \\ including druggability analysis, \\ of TRAnsient binding Pockets in Proteins  | Structures, Ligands, \\ Trajectories | Webserver | (([[https://pubs.acs.org/doi/10.1021/acs.jcim.9b01185 | Druggability Assessment in TRAPP using Machine Learning Approaches]])) | [[https://trapp.h-its.org|Run TRAPP analysis]] |
 +^ TRAPP v3 | Tool for analysis of transient \\ binding pockets in proteins  | Structures, Ligands, \\ Trajectories | Standalone Software | (([[https://pubs.acs.org/doi/abs/10.1021/ci4000294 | TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins]])) | [[https://www.h-its.org/downloads/trapp/|Download TRAPP]] |
 +^ ::: | ::: | ::: | Webserver | (([[https://academic.oup.com/nar/article/45/W1/W325/3744539 | TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets]])) | [[https://trapp3.h-its.org|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 |  (([[https://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00101|Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets]]))  | [[http://mcm.h-its.org/lrip-riplig|L-RIP and RIPlig]] |
 +^ RASPD+ | Fast protein-ligand binding free energy prediction using simplified physicochemical features | Structures, \\ Ligands | Standalone Software | (([[https://www.frontiersin.org/articles/10.3389/fmolb.2020.601065/full|RASPD+: Fast protein-ligand binding free energy prediction using simplified physicochemical features.]])) | [[https://github.com/HITS-MCM/RASPDplus | GitHub ]] |
 +^ KBbox | KBbox: a Toolbox of \\ Computational Methods for Studying \\ the Kinetics of Molecular Binding | Search term | Webserver |  | [[https://kbbox.h-its.org|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 \\ [[tauRamdDescription|see RAMD additional information]] | NAMD simulation setup | NAMD Plugin |  (([[https://www.ncbi.nlm.nih.gov/pubmed/11061976|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]])) (([[https://link.springer.com/article/10.1007/s008940050053|Substrate Access to Cytochrome P450cam: a Comparison of a Thermal Motion Pathway Analysis with Molecular Dynamics Simulation Data]]))  | Included in NAMD \\ distribution (plugin directory) \\ also here with \\ additional resources \\ [[https://www.h-its.org/downloads/ramd|Download]] | 
 +^ ::: | ::: | ::: | $\tau$RAMD scripts |  (([[https://pubs.acs.org/doi/10.1021/acs.jctc.8b00230|Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations.]])) (([[https://www.frontiersin.org/articles/10.3389/fmolb.2019.00036/full|Machine learning analysis of tauRAMD trajectories to decipher molecular determinants of drug-target residence times.]]))  | Includes  RAMD plugin \\ with additional scripts \\ [[https://www.h-its.org/downloads/ramd|Download]] |
 +^ ::: | ::: | ::: | GROMACS RAMD\\ implementation | (([[https://pubs.aip.org/aip/jcp/article-abstract/153/12/125102/1062851/A-workflow-for-exploring-ligand-dissociation-from?redirectedFrom=fulltext|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]])) | [[https://github.com/HITS-MCM/gromacs-ramd]] \\  [[https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-gromacs/|RAMD in GROMACS Tutorial]] |
 +^ MD-IFP | MD trajectory analysis using protein-ligand Interaction Fingerprints | Trajectories \\ Test dataset provided | Jupyter Notebooks | (([[https://pubs.aip.org/aip/jcp/article-abstract/153/12/125102/1062851/A-workflow-for-exploring-ligand-dissociation-from?redirectedFrom=fulltext|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]])) | 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 \\ [[https://mcm.h-its.org/sda/doc/doc_sda7/ecm.html|ECM]] is part of the SDA distribution \\ and allows the \\ calculation of partial charges. | Structures of \\ Solutes | Standalone Software |  (([[https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.23971|SDA 7: A modular and parallel implementation of the simulation of diffusional association software]]))  | [[https://www.h-its.org/downloads/sda7/|Download SDA]] \\ [[https://mcm.h-its.org/sda7/doc/doc_sda7/index.html|Documentation of SDA]]   |
 +^ ::: | ::: | ::: | Webserver |  (([[http://dx.doi.org/10.1093/nar/gkv335|webSDA: a web server to simulate macromolecular diffusional association.]]))  | [[https://websda.h-its.org|Run webSDA]] |
 +^ PIPSA / \\ webPIPSA | Comparing electrostatic potentials \\ (or other molecular interaction fields)\\ of protein structures | Protein Structures \\ of the same fold | Standalone Software |  (([[https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.1204|Protein Interaction Property Similarity Analysis. ]])) (([[http://www.biomedcentral.com/1471-2105/8/373/|qPIPSA: Relating enzymatic kinetic parameters and interaction fields]]))  | [[https://projects.h-its.org/mcmsoft/pipsa/4.0.2/availability.html|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 |  (([[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447742/|webpipsa: a web server for the comparison of protein interaction properties.]]))  | [[https://pipsa.h-its.org|Run Pipsa Analysis]] |
 +^ Sycamore | SYstems biology's Computational \\ Analysis and MOdeling Research Environment | Kinetic Data | Webserver |  (([[https://academic.oup.com/bioinformatics/article/24/12/1463/196145|SYCAMORE-a systems biology computational analysis and modeling research environment.]]))  | [[http://sycamore.h-its.org|Sycamore webserver]] |
  
-==== Migrated to other research groups ====+ 
 + 
 +==== Some software has been migrated to other research groups ====
   ? [[http://ligin.weizmann.ac.il/space/programs/|LIGIN]]   ? [[http://ligin.weizmann.ac.il/space/programs/|LIGIN]]
-  : Information that belongs to the article: Sobolev, V., Wade, R.C., Vriend, G. & Edelman, M. Molecular docking using surface complementarity, PROTEINS, 25, 120-129 (1996) +  : 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) 
   ? [[http://projects.biotec.tu-dresden.de/metapocket/|metaPocket2]]   ? [[http://projects.biotec.tu-dresden.de/metapocket/|metaPocket2]]
   : Webserver to identify pockets on protein surfaces to predict binding sites for ligands    : Webserver to identify pockets on protein surfaces to predict binding sites for ligands 
  
-==== Methods and software available at other research groups ==== +==== Methods and software developed with participation of members of MCM are available at other research groups ==== 
-  ? [[|COMBINE analysis]] +  ? [[https://github.com/accsc/COMBINE|COMBINE analysis]] 
-  : Comparative Binding Energy Analysis [[literature|Literature]]  [[tutorials:tutorials|Tutorial]] [[http://farmamol.uah.es/index.php/en/2-uncategorised/4-gcombine|gCOMBINE]] +  : Comparative Binding Energy Analysis, extended from Ariane Nunes-Alves (MCM) and merged.  [[literature|Literature]]  [[tutorials:tutorials|Tutorial]] [[http://farmamol.uah.es/soft/gCOMBINE/|gCOMBINE binaries]] 
-  ? [[|UHBD]] +  ? [[https://projects.h-its.org/mcm/projects/uppsala/tutorials/|UHBD]] 
-  : University of Houston Brownian Dynamics  [[tutorials:tutorials|Tutorial]][[http://www.chee.uh.edu/faculty/briggs|Contact]]+  : University of Houston Brownian Dynamics  [[https://projects.h-its.org/mcm/projects/uppsala/tutorials/|Tutorial]][[http://www.chee.uh.edu/faculty/briggs|Contact]]
   ? [[http://www.moldiscovery.com/soft_grid.php|GRID]]   ? [[http://www.moldiscovery.com/soft_grid.php|GRID]]
   : Computational method for identifying energetically favorable binding sites on biological molecules  [[tutorials:tutorials|Tutorial]]    : Computational method for identifying energetically favorable binding sites on biological molecules  [[tutorials:tutorials|Tutorial]] 
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 ==== Not updated software ==== ==== Not updated software ====
-  ? [[http://projects.h-its.org/dbase/pdba/index.html|Prosat]] +  ? [[http://projects.h-its.org/mcm/software/amber.html|AMBER patches]]  
-  : Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein. Currently out of date.+  : AMBER patches from the MCM  group at HITS for RAMD and NPSA   
 +  ? [[http://projects.h-its.org/dbase/ps2/index.html|ProSAT2]]  
 +  : Select and group residue-based annotations and explore them interactively on a 3D structure of a protein 
 +  ? [[http://projects.h-its.org/dbase/pdba/index.html|ProSAT]] 
 +  : Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein 
 +  ? [[https://ligdig.h-its.org|LigDig]] 
 +  : LigDig: a web server for querying ligand–protein interactions
   ? [[http://projects.h-its.org/dbase/dsmm/|DSMM]]   ? [[http://projects.h-its.org/dbase/dsmm/|DSMM]]
   : Database of Simulated Molecular Motions   : Database of Simulated Molecular Motions
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   ? [[http://projects.h-its.org/mcm/software/pka|pka calculation]]   ? [[http://projects.h-its.org/mcm/software/pka|pka calculation]]
   : Scripts for pKa calculations with UHBD   : Scripts for pKa calculations with UHBD
 +  ? [[https://prosat.h-its.org|ProSAT+ ]] 
 +  : ProSAT+  Protein structure visualization and annotation tool. 
 +
 +
 +===== References =====
  
  

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