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| projects:software [2024/05/06 14:42] – richter | projects:software [2025/02/13 12:17] (current) – richter |
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| ^ ::: | ::: | ::: | 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]] | | ^ ::: | ::: | ::: | 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]] | |
| ^ MD-IFP | MD trajectory analysis using protein-ligand 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]])) | 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) J. Chem. Phys. 153(12):125102 \\ [[https://github.com/HITS-MCM/MD-IFP]] | | ^ MD-IFP | MD trajectory analysis using protein-ligand 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]])) | 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) J. Chem. Phys. 153(12):125102 \\ [[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]] \\ [[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]] | | ^ ::: | ::: | ::: | 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]] | |
