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projects:software [2023/10/19 10:01] – richterprojects:software [2024/05/06 14:42] (current) – richter
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 ^ ::: | ::: | ::: | $\tau$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://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]] |
 ^ ::: | ::: | ::: | 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]] |
 ^ ::: | ::: | ::: | 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.h-its.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.h-its.org|Sycamore webserver]] |
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 ==== 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/ps2/index.html|ProSAT2]] 
   : Select and group residue-based annotations and explore them interactively on a 3D structure of a protein   : Select and group residue-based annotations and explore them interactively on a 3D structure of a protein
   ? [[http://projects.h-its.org/dbase/pdba/index.html|ProSAT]]   ? [[http://projects.h-its.org/dbase/pdba/index.html|ProSAT]]
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   : ProSAT+  Protein structure visualization and annotation tool.    : ProSAT+  Protein structure visualization and annotation tool. 
  
-  +
 ===== References ===== ===== References =====
  
  

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