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projects:software [2020/03/06 14:41]
richter
projects:software [2021/02/18 15:12] (current)
richter
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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]] |+^ 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'​]] | 
 +^ 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]] | ^ 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]] | ^ ::: | ::: | ::: | 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 ?+^ 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]] |  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]] | ^ ::: | ::: | ::: | $\tau$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://​arxiv.org/​abs/​2006.11066|Kokh DB et. al. A Workflow for Exploring Ligand Dissociation from a Macromolecule:​ Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories. arXiv 2020 arXiv:​2006.11066]])) | [[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://​arxiv.org/​abs/​2006.11066|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) submitted to JCP]])) | [[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]] | ^ 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]] | ^ ::: | ::: | ::: | 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]] |
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 ^ ::: | ::: | ::: | 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]] | ^ 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]] |
-^ 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'​]] | 
-^ 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]] | 
-^ KBbox | KBbox: a Toolbox of \\ Computational Methods for Studying \\ the Kinetics of Molecular Binding | Search term | Webserver |  | [[https://​kbbox.h-its.org|Search KBbox]] | 
  
  
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 ==== 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 are 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 from 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]]   ? [[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]]   : University of Houston Brownian Dynamics ​ [[https://​projects.h-its.org/​mcm/​projects/​uppsala/​tutorials/​|Tutorial]][[http://​www.chee.uh.edu/​faculty/​briggs|Contact]]
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