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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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| ^ 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.]])) | [[http://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]])) (([[http://nar.oupjournals.org/cgi/content/full/31/13/3349|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/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 | ||
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| - | ==== References ==== | + | ===== References ===== |
