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projects:software [2023/10/19 11:18] – richterprojects: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]] |
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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 =====
  
  

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