A Domain Specific Data Management Architecture for Protein Structure Data

2006 ◽  
Author(s):  
Yanchao Wang ◽  
Rajshekhar Sunderraman ◽  
Hao Tian
Keyword(s):  
Protein Structure ◽  
Data Management ◽  
Structure Data ◽  
Specific Data ◽  
Domain Specific ◽  
Management Architecture ◽  
Protein Structure Data

scholarly journals A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions

2013 ◽  
Vol 14 (1) ◽  
pp. 111 ◽  
Author(s):  
Emma M Rath ◽  
Dominique Tessier ◽  
Alexander A Campbell ◽  
Hong Ching Lee ◽  
Tim Werner ◽  
...  
Keyword(s):  
Protein Structure ◽  
High Resolution ◽  
Structure Data ◽  
Protein Structure Data

Inferring Functional Annotation for Human Genes from Gene-PDB Structure Mapping

2012 ◽  
Vol 195-196 ◽  
pp. 391-396
Author(s):  
Xi Chen ◽  
Hao Jiang ◽  
Wai Ki Ching ◽  
Li Min Li
Keyword(s):  
Protein Structure ◽  
Structure Data ◽  
Gene Function ◽  
Function Analysis ◽  
Protein Structures ◽  
3D Structure ◽  
Structure Mapping ◽  
Gene Similarity ◽  
Gene Function Analysis ◽  
Protein Structure Data

Protein 3D structure is one of the main factors in reecting gene functions. The availability of protein structure data in Protein Data Bank (PDB) allows us to conduct gene function analysis based on protein structure data. However, the molecules in PDB, whose structures having been determined, are always not corresponding to a unique gene. That is to say, the mapping from a gene to the PDB is not one-to-one. This feature complicates the situation and increases the difculty of gene function analysis. In this paper, we attempt to tackle this problem and also study the problem of predicting gene function from protein structures based on the gene-PDB mapping. We rst obtain the gene-PDB mapping, which is used to represent a gene by the structure set of all its corresponding PDB molecules. We then dene a new gene-gene similarity measurement based on the structure similarity between PDB molecules, and we further show that this new measurement matches with the gene functional similarity. This means that the measurement we dened here can be used effectively for gene function prediction.

scholarly journals Fit3D: a web application for highly accurate screening of spatial residue patterns in protein structure data

2015 ◽  
Vol 32 (5) ◽  
pp. 792-794 ◽  
Author(s):  
Florian Kaiser ◽  
Alexander Eisold ◽  
Sebastian Bittrich ◽  
Dirk Labudde
Keyword(s):  
Protein Structure ◽  
Structure Data ◽  
Web Application ◽  
Protein Structure Data
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