Difference between revisions of "HSSP curve"
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+ | [[File:Hssp curve.png | 200px | left | Different thresholds for HSSP-curve]] |
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+ | [[File:Threshholds.png | 200px | center | Different thresholds for HSSP-curve]] |
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== Core Functionalities == |
== Core Functionalities == |
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| + | = Progress = |
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| + | <div style=" text-align:left; width: 60% ; overflor:auto; height:10em border:2px"> |
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| + | {| class="wikitable" |
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| + | |- |
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| + | ! scope="col" width="70%" | Task !! scope="col" width="30%" | Implemented |
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| + | |- |
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| + | | Core Functionality || No |
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| + | |- |
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| + | | Drag nodes || No |
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| + | |- |
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| + | | Display additional info on mouse-over || No |
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| + | |- |
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| + | | Edit graph and export changes || No |
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| + | |- |
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| + | | PBseq format compatibility || No |
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| + | |- |
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| + | | Connect (.ct) format compatibility || No |
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| + | |} |
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| + | </div> |
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Revision as of 11:31, 20 November 2014
Introduction to HSSP curve?
HSSP is a derived database merging structural (3-D) and sequence (1-D) information. For each protein of known 3-D structure from the Protein Data Bank (PDB), the database has a multiple sequence alignment of all available homologues and a sequence profile characteristic of the family. The list of homologues is the result of a database search in SwissProt using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). The database is updated frequently. The listed homologues are very likely to have the same 3-D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of aligned sequence families, but also a database of implied secondary and tertiary structures covering 29% of all SwissProt-stored sequences.
Existing visualisations
Core Functionalities
Progress
| Task | Implemented |
|---|---|
| Core Functionality | No |
| Drag nodes | No |
| Display additional info on mouse-over | No |
| Edit graph and export changes | No |
| PBseq format compatibility | No |
| Connect (.ct) format compatibility | No |
References
http://en.wikipedia.org/wiki/Homology-derived_Secondary_Structure_of_Proteins
http://www.ncbi.nlm.nih.gov/pubmed/?term=UniqueProt%3A+creating+representative+protein+sequence+sets
