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projects:software [2019/06/07 14:32]
richter
projects:software [2019/09/18 13:04] (current)
richter
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 {{:​projects:​mcm_logo.jpg}} {{:​projects:​mcm_logo.jpg}}
-=== MCM software and databases ===+===== MCM software and databases ​=====
 This page has links for webservers and software downloads provided by the Molecular and Cellular Modeling (MCM) group at the Heidelberg Institute for Theoretical Studies (HITS). This page has links for webservers and software downloads provided by the Molecular and Cellular Modeling (MCM) group at the Heidelberg Institute for Theoretical Studies (HITS).
 There are tutorials for some software on our [[tutorials:​tutorials|tutorials page]]. For queries, send email to: [[mcmsoft@h-its.org|mcmsoft@h-its.org]] There are tutorials for some software on our [[tutorials:​tutorials|tutorials page]]. For queries, send email to: [[mcmsoft@h-its.org|mcmsoft@h-its.org]]
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 ^ ::: | ::: | ::: | 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.eml.org|Sycamore webserver]] |
-^ 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.]])) ​ | [[http://​prosat.h-its.org/​prosat/​prosatexe?​pdbcode=1o1o|Hemoglobin example '​1o1o'​]] | +^ 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/​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]] |
 ^ KBbox | KBbox: a Toolbox of \\ Computational Methods for Studying \\ the Kinetics of Molecular Binding | Search term | Webserver |  | [[https://​kbbox.h-its.org|Search KBbox]] | ^ KBbox | KBbox: a Toolbox of \\ Computational Methods for Studying \\ the Kinetics of Molecular Binding | Search term | Webserver |  | [[https://​kbbox.h-its.org|Search KBbox]] |
  
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   : Scripts for pKa calculations with UHBD   : Scripts for pKa calculations with UHBD
   ​   ​
-==== References ====+===== References ​=====
  
  
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