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projects:software [2021/02/18 15:12] richter |
projects:software [2023/10/19 06:59] richter |
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| | ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^ | | ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^ | ||
| - | ^ ProSAT+ | Protein structure visualization and \\ annotation tool. \\ Display protein annotations \\ (eg mutation data from uniprot) \\ on protein structures from RCSB. | PDB or Uniprot codes | Webserver | (([[http://dx.doi.org/10.1093/protein/gzw021|ProSAT+: visualizing sequence annotations on 3D structure.]])) | [[https://prosat.h-its.org|https://prosat.h-its.org]] \\ [[https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o1o|Hemoglobin example '1o1o']] | | ||
| ^ Molsurfer | Protein structure tool \\ to link a 2D projection of a \\ macromolecular interface to a 3D \\ view of the macromolecular structures \\ [[http://projects.h-its.org/mcm/software/ADS|ADS]] Analytically Defined molecular Surfaces \\ is used within Molsurfer | PDB/PQR files \\ or PDB codes | Webserver | (([[https://projects.h-its.org/dbase/molsurfer/doc/tibs.html|MolSurfer: 2D maps to navigate 3D structures of proteins and their complexes]])) (([[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168994/|MolSurfer: a macromolecular interface navigator.]])) | [[https://molsurfer.h-its.org]] \\ [[https://molsurfer.h-its.org/demo/1nca/result.html|Neuraminidase 1nca example]] | | ^ Molsurfer | Protein structure tool \\ to link a 2D projection of a \\ macromolecular interface to a 3D \\ view of the macromolecular structures \\ [[http://projects.h-its.org/mcm/software/ADS|ADS]] Analytically Defined molecular Surfaces \\ is used within Molsurfer | PDB/PQR files \\ or PDB codes | Webserver | (([[https://projects.h-its.org/dbase/molsurfer/doc/tibs.html|MolSurfer: 2D maps to navigate 3D structures of proteins and their complexes]])) (([[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168994/|MolSurfer: a macromolecular interface navigator.]])) | [[https://molsurfer.h-its.org]] \\ [[https://molsurfer.h-its.org/demo/1nca/result.html|Neuraminidase 1nca example]] | | ||
| ^ TRAPP v4 | Tool for the analysis, \\ including druggability analysis, \\ of TRAnsient binding Pockets in Proteins | Structures, Ligands, \\ Trajectories | Webserver | (([[https://pubs.acs.org/doi/10.1021/acs.jcim.9b01185 | Druggability Assessment in TRAPP using Machine Learning Approaches]])) | [[https://trapp.h-its.org|Run TRAPP analysis]] | | ^ TRAPP v4 | Tool for the analysis, \\ including druggability analysis, \\ of TRAnsient binding Pockets in Proteins | Structures, Ligands, \\ Trajectories | Webserver | (([[https://pubs.acs.org/doi/10.1021/acs.jcim.9b01185 | Druggability Assessment in TRAPP using Machine Learning Approaches]])) | [[https://trapp.h-its.org|Run TRAPP analysis]] | | ||
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| ^ ::: | ::: | ::: | 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]] | | ||
| - | ^ 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.eml.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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| ? [[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 | ||
| + | ? ProSAT+ Protein structure visualization and \\ annotation tool. | ||
| + | :[[https://prosat.h-its.org|ProSAT+ retired]] | ||
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| ===== References ===== | ===== References ===== | ||
