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-====== 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]]
  
-==== Current software of the Group ==== 
-  ? [[http://kbbox.h-its.org/toolbox|KBbox]] 
-  : KBbox: a Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding 
-  ? [[http://mcm.h-its.org/ligdig|LIGDIG]] 
-  : LigDig: a web server for querying ligand–protein interactions 
-  ? [[http://sycamore.eml.org|SYCAMORE]] 
-  : SYstems biology's Computational Analysis and MOdeling Research Environment 
-  ? [[http://mcm.h-its.org/trapp/|TRAPP]] 
-  : Tool for analysis of transient binding pockets in proteins 
-  ? [[http://pipsa.h-its.org|PIPSA]] 
-  : Webserver (and software download) for comparing electrostatic potentials (or other molecular interaction fields) of protein structures 
-  ? [[http://mcm.h-its.org/sda7/|SDA]] 
-  : Simulation of Diffusional Association - Brownian Dynamics Software 
-  ? [[http://mcm.h-its.org/websda|webSDA]] 
-  :Webserver for Simulation of Diffusional Association 
  
-  ? [[http://mcm.h-its.org/lrip-riplig|L-RIP and RIPlig]] +| ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^ 
-  : Two non-equilibrium MD approaches  for the  identification of slow conformational changes of a protein binding site​ +^ 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]] | 
-  ? [[http://molsurfer.h-its.org|Molsurfer]] +^ 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]] | 
-  : Tool to link a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures +^ 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]] | 
-  ? [[http://prosat.h-its.org/|ProSAT]]<sup>+</sup> +^ 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]] | 
-  : Display protein annotations on protein structures. Click to start hemoglobin example '1o1o' in [[http://prosat.h-its.org/prosat/prosatexe?pdbcode=1o1o|Protein structure visualization and annotation tool]]. ProSAT<sup>+</sup> is also listed on [[https://omictools.com/protein-structure-annotation-tool-plus-tool|OMICs Tools collection]] +^ 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]] | 
-  ? [[https://www.h-its.org/downloads/ramd/|RAMD]] +^ 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]] | 
-  : 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 +^ ::: | ::: | ::: | Python Interface \\ Multipipsa | ::: | ::: | 
-  ? [[https://www.h-its.org/downloads/ramd/|RAMD in NAMD]] +^ ::: | ::: | ::: | 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  | 
-  : The RAMD method implemented in NAMD +^ ::: | ::: | ::: | 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]] | 
-  ? [[http://projects.h-its.org/mcm/software/ADS|ADS]] +^ 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 ? 
-  : Analytically Defined molecular Surfaces (used within Molsurfer) +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]] |  
-  ? [[http://mcm.h-its.org/sda/doc/doc_sda7/ecm.html|ECM]] +^ ::: | ::: | ::: | 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]] | 
-  : ECM is now part of the SDA distribution+^ ::: | ::: | ::: | 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]] |
  
  
-==== 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]]
   : 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 available at other research groups ==== +==== Methods and software developed with participation of members of MCM 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 by Ariane Nunes-Alves (MCM) and merged.  [[literature|Literature]],  [[tutorials:tutorials|Tutorial]], [[http://farmamol.uah.es/soft/gCOMBINE/|gCOMBINE binaries]]
-  ? [[|UHBD]] +
-  : University of Houston Brownian Dynamics  [[tutorials: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]] +
-  : 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+
   ? [[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
-  ? [[http://projects.h-its.org/mcm/software/trajanabs|TRAJAN]] +  ? [[https://ligdig.h-its.org|LigDig]] 
-  : A Tool to Analyze Trajectories from Molecular Simulations+  : 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]] 
 +  : Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein 
 +  ? [[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 
 +  ? [[https://prosat.h-its.org|ProSAT+ ]]  
 +  : ProSAT+  Protein structure visualization and annotation tool. 
   ? [[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
 +  ? [[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]]
 +  : A Tool to Analyze Trajectories from Molecular Simulations
 +
 +===== References =====
  
  

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