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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 provided by the Molecular and Cellular Modeling (MCM) group at the Heidelberg Institute for Theoretical Studies (HITS). 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]]. For queries, send email to: [[mcmsoft@h-its.org|mcmsoft@h-its.org]] 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]]
  
  
-|  ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^ +| ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^ 
-^ 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]] | +^ COMBINE analysis / \\ ensembleCombine | Prediction of Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis (COMBINE analysis was originally developed for and can also be used for the prediction of binding free energies) | Binding Analysis  | Standalone Program | (([[https://doi.org/10.1021/acs.jcim.1c00639|Prediction of the Drug–Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis]]))  | [[https://kbbox.h-its.org/toolbox/tutorials/generation-of-quantitative-structure-kinetics-relationships-qskrs-using-comparative-binding-energy-combine-analysis/ | Tutorial]] \\ [[https://github.com/HITS-MCM/ensembleCOMBINE|GitHub]] | 
-^ ::: | ::: | ::: | Webserver |  (([[https://academic.oup.com/nar/article/45/W1/W325/3744539|TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets]]))  | [[https://trapp.h-its.org|Run TRAPP analysis]] | +^ KBbox | KBbox: a Toolbox of \\ Computational Methods for Studying \\ the Kinetics of Molecular Binding | Search term | Webserver | (([[https://doi.org/10.1021/acs.jcim.9b00485|KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding]])) | [[https://kbbox.h-its.org|Search KBbox]] |
-^ 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 |  (([[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]] | ^ 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]] |
-^ 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. \\ \\ [[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 ? +^ MD-IFP | MD trajectory analysis using protein-ligand or protein-protein 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]])) | Includes example of IFP analysis of dissociation trajectories for 3 compounds of HSP90 reported in Kokh et al.  (2020) J. Chem. Phys. 153(12):125102; as well as an example for IFP analysis for a protein-protein complex reported in D'Arrigo et al. (2024) Commun Biol 7(1):1159  \\ [[https://github.com/HITS-MCM/MD-IFP]] | 
-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]] |  +^ 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]] |
-^ ::: | ::: | ::: | $\tau$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]] | +
-^ 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]] | +
-^ ::: | ::: | ::: | 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]] | ^ 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 | ::: | ::: | ^ ::: | ::: | ::: | 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]] | ^ ::: | ::: | ::: | 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.eml.org|Sycamore webserver]] | +^ RAMD / \\ tauRAMD| 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 implementations in other software, see: \\ [[tauRamdDescription|see RAMD additional information]] | MD 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 ? 
-^ 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 |  (([[http://dx.doi.org/10.1093/protein/gzw021|ProSAT+: visualizing sequence annotations on 3D structure.]]))  | [[http://prosat.h-its.org/prosat/prosatexe?pdbcode=1o1o|Hemoglobin example '1o1o']] | +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]] |  
-^ 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/demo/1nca/result.html|Neuraminidase 1nca example]] | +^ ::: | ::: | ::: | tauRAMD 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]] | 
-^ KBbox | KBbox: a Toolbox of \\ Computational Methods for Studying \\ the Kinetics of Molecular Binding | Search term | Webserver |  | [[https://kbbox.h-its.org|Search KBbox]] | +^ ::: | ::: | ::: | 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]] | 
 +^ 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 ]] | 
 +^ 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]] | 
 +^ TRAPP v4 | Tool for the analysis, \\ including druggability analysis, \\ of TRAnsient binding Pockets in Proteins   | Structures, Ligands, \\ Trajectories | Standalone Software | (([[https://pubs.acs.org/doi/10.1021/acs.jcim.9b01185 | Druggability Assessment in TRAPP using Machine Learning Approaches]])), (([[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://trapp.h-its.org|Run TRAPP analysis]] |
  
  
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   ? [[http://ligin.weizmann.ac.il/space/programs/|LIGIN]]   ? [[http://ligin.weizmann.ac.il/space/programs/|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)    : 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]] 
-  : 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 ==== +==== Methods and software developed with participation of members of MCM available at other research groups ==== 
-  ? [[https://projects.h-its.org/mcm/software/|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 by Ariane Nunes-Alves (MCM) and merged.  [[literature|Literature]],  [[tutorials:tutorials|Tutorial]], [[http://farmamol.uah.es/soft/gCOMBINE/|gCOMBINE binaries]]
-  ? [[https://projects.h-its.org/mcm/projects/uppsala/tutorials/|UHBD]] +
-  : 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]] 
-  +  ? [[https://projects.h-its.org/mcm/projects/uppsala/tutorials/|UHBD]] 
 +  : University of Houston Brownian Dynamics , [[https://projects.h-its.org/mcm/projects/uppsala/tutorials/|Tutorial]][[http://www.chee.uh.edu/faculty/briggs|Contact]] 
 + 
      
 ==== Not updated software ==== ==== Not updated software ====
-  ? [[http://projects.h-its.org/mcm/software/amber.html|AMBER patches]] +  ? [[http://projects.h-its.org/mcm/software/amber.html|AMBER patches]]  
-  : AMBER patches from the MCM group at HITS for RAMD and NPSA +  : AMBER patches from the MCM  group at HITS for RAMD and NPSA   
-  ? [[http://projects.h-its.org/dbase/ps2/index.html|ProSAT2]] +  ? [[http://projects.h-its.org/dbase/dsmm/|DSMM]] 
-  : Select and group residue-based annotations and explore them interactively on a 3D structure of a protein+  : Database of Simulated Molecular Motions 
 +  ? [[https://ligdig.h-its.org|LigDig]] 
 +  : LigDig: a web server for querying ligand–protein interactions 
 +  ? [[http://projects.biotec.tu-dresden.de/metapocket/|metaPocket2]] 
 +  : Webserver to identify pockets on protein surfaces to predict binding sites for ligands 
   ? [[http://projects.h-its.org/dbase/pdba/index.html|ProSAT]]   ? [[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   : Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein
-  ? [[https://ligdig.h-its.org|LigDig]] +  ? [[http://projects.h-its.org/dbase/ps2/index.html|ProSAT2]]  
-  : LigDig: a web server for querying ligand–protein interactions +  : Select and group residue-based annotations and explore them interactively on a 3D structure of a protein 
-  ? [[http://projects.h-its.org/dbase/dsmm/|DSMM]] +  ? [[https://prosat.h-its.org|ProSAT+ ]]  
-  : Database of Simulated Molecular Motions+  : ProSAT+  Protein structure visualization and annotation tool.  
 +  ? [[http://projects.h-its.org/mcm/software/pka|pka calculation]] 
 +  : Scripts for pKa calculations with UHBD 
 +  ? [[http://sycamore.h-its.org|Sycamore webserver]] 
 +  : Sycamore | SYstems biology's Computational Analysis and MOdeling Research Environment for Kinetic Data (([[https://academic.oup.com/bioinformatics/article/24/12/1463/196145|SYCAMORE-a systems biology computational analysis and modeling research environment.]]))
   ? [[http://projects.h-its.org/mcm/software/trajanabs|TRAJAN]]   ? [[http://projects.h-its.org/mcm/software/trajanabs|TRAJAN]]
   : A Tool to Analyze Trajectories from Molecular Simulations   : A Tool to Analyze Trajectories from Molecular Simulations
-  ? [[http://projects.h-its.org/mcm/software/pka|pka calculation]] + 
-  : Scripts for pKa calculations with UHBD +===== References =====
-   +
-==== References ====+
  
  

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