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projects:software [2020/03/06 14:38] – richterprojects:software [2026/06/18 09:42] (current) – wade
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-|  ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^ +| ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^ 
-^ 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]] | +^ 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]] | 
-^ 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]] | +^ 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]] |
-^ ::: | ::: | ::: | 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]] | ^ 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.]]))  | [[https://prosat.h-its.org|https://prosat.h-its.org]] \\ [[https://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]] \\ [[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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