Difference between revisions of "HSSP curve"

From Protein Prediction 2 Winter Semester 2014
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== Introduction ==
 
== Introduction ==
   
What is HSSP curve
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What is HSSP curve?
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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.
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References:
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http://en.wikipedia.org/wiki/Homology-derived_Secondary_Structure_of_Proteins
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http://www.ncbi.nlm.nih.gov/pubmed/?term=UniqueProt%3A+creating+representative+protein+sequence+sets
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http://en.wikipedia.org/wiki/Protein_superfamily

Revision as of 11:18, 20 November 2014

Introduction

What is 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.

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 http://en.wikipedia.org/wiki/Protein_superfamily