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projects:software [2023/10/19 11:20] richter |
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| ^ 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]] You can also run the commandline version in a google colab: https://colab.research.google.com/drive/1L7-KFFe69TG-tnoYQS3Yzomqxb8t2F1k#scrollTo=0rtGiKf7MtYh | |
| ^ ::: | ::: | ::: | Python Interface \\ Multipipsa | ::: | ::: | | ^ ::: | ::: | ::: | Python Interface \\ Multipipsa | ::: | ::: | | ||
| ^ ::: | ::: | ::: | 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]] | | ||
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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]] | ||
| - | :: Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein | + | : Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein |
| ? [[https://ligdig.h-its.org|LigDig]] | ? [[https://ligdig.h-its.org|LigDig]] | ||
| - | :: LigDig: a web server for querying ligand–protein interactions | + | : LigDig: a web server for querying ligand–protein interactions |
| ? [[http://projects.h-its.org/dbase/dsmm/|DSMM]] | ? [[http://projects.h-its.org/dbase/dsmm/|DSMM]] | ||
| - | :: Database of Simulated Molecular Motions | + | : Database of Simulated Molecular Motions |
| ? [[http://projects.h-its.org/mcm/software/trajanabs|TRAJAN]] | ? [[http://projects.h-its.org/mcm/software/trajanabs|TRAJAN]] | ||
| - | :: A Tool to Analyze Trajectories from Molecular Simulations | + | : A Tool to Analyze Trajectories from Molecular Simulations |
| ? [[http://projects.h-its.org/mcm/software/pka|pka calculation]] | ? [[http://projects.h-its.org/mcm/software/pka|pka calculation]] | ||
| - | :: Scripts for pKa calculations with UHBD | + | : Scripts for pKa calculations with UHBD |
| ? [[https://prosat.h-its.org|ProSAT+ ]] | ? [[https://prosat.h-its.org|ProSAT+ ]] | ||
| - | :: ProSAT+ Protein structure visualization and annotation tool. | + | : ProSAT+ Protein structure visualization and annotation tool. |
| - | | ||
| ===== References ===== | ===== References ===== | ||
