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projects:software [2020/03/06 14:36]
richter
projects:software [2020/07/23 08:22] (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]] | +^ 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]])) ​ +^ 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]] | 
- | [[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 ?+^ 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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