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| projects:software [2023/10/19 11:20] – richter | projects:software [2024/05/06 14:42] (current) – richter |
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| ^ 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]] | |
| ==== 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 |
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| ? [[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. |
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| ===== References ===== | ===== References ===== |
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