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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]])) | [[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 ? | + | ^ 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]] | |