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| projects:software [2023/10/19 13:16] – [Not updated software] 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]] | |
| : ProSAT+ Protein structure visualization and annotation tool. | : ProSAT+ Protein structure visualization and annotation tool. |
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| ==== Not updated software ==== | |
| * [[http://projects.h-its.org/mcm/software/amber.html|AMBER patches]] | |
| * AMBER patches from the MCM group at HITS for RAMD and NPSA | |
| * [[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 | |
| * [[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 | |
| * [[https://ligdig.h-its.org|LigDig]] | |
| * LigDig: a web server for querying ligand–protein interactions | |
| * [[http://projects.h-its.org/dbase/dsmm/|DSMM]] | |
| * Database of Simulated Molecular Motions | |
| * [[http://projects.h-its.org/mcm/software/trajanabs|TRAJAN]] | |
| * A Tool to Analyze Trajectories from Molecular Simulations | |
| * [[http://projects.h-its.org/mcm/software/pka|pka calculation]] | |
| * Scripts for pKa calculations with UHBD | |
| * [[https://prosat.h-its.org|ProSAT+ ]] | |
| * ProSAT+ Protein structure visualization and annotation tool. | |
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| ===== References ===== | ===== References ===== |
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