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P3S

Type: 
Bioinformatics & Cheminformatics
One line description: 
Protein structure similarity search
Annotation: 

Proteins can perform many different biological functions and so ensure most of the vital processes in the living organisms. From a chemical point of view, proteins are linear polymer chains made of only twenty kinds of amino acids. However, they can fold into various 3D structures resulting in huge functional diversity. The study of protein functions is one of the areas where similarity search in protein structure databases is widely used. The usage follows from the thesis that proteins having similar 3D structures also share similar biological function. Our tool P3S allows similarity search in protein structure databases. Currently it employs only the SProt similarity measure developed at Siret research group. However, support for other protein similarity measures is planned, for example the SABERTOOTH measure developed by AG Porto at the Universität zu Köln.

Developers: 
david.hoksza
jakub.galgonek

ICME

Research area: 
Multimedia
Paper due: 
12.12.2011
Publisher: 
IEEE
Location: 
Melbourne, Australia

PACBB

Research area: 
Bioinformatics & Chemoinformatics
Paper due: 
18.01.2014
Publisher: 
Advances in Intelligent and Soft Computing, Springer
Location: 
University of Salamanca, Spain

EDBT

Research area: 
Databases
Paper due: 
15.09.2011
Publisher: 
ACM
Location: 
Berlin, Germany

ICDE

Research area: 
Databases
Abstract due: 
11.07.2011
Publisher: 
IEEE
Location: 
Washington, USA

ACM Transaction on Database Systems

Research area: 
Databases
Publisher: 
ACM

Nucleic Acids Research

Research area: 
Bioinformatics & Chemoinformatics
Publisher: 
Oxford University Press

GAČR 201/05/P036

Name: 
Efficient metric search in large multimedia databases
Start year: 
2005
End year: 
2007

Finished, rated as excellent

Investigators
Investigator: 
tomas.skopal
Investigator role: 
Principal investigator

GAUK 57907

Name: 
Similarity search in biological databases
Start year: 
2007
End year: 
2008

In recent years volume of gene and protein banks (databases) grows rapidly. The reason for storing huge volumes of gene and protein sequences in one place is not only for browsing these sequences itself, but in the first place searching for similarities among stored sequences. Similar sequences indicate similar functionality which helps in finding functions of unknown genes.

Investigators
Investigator: 
david.hoksza
Investigator role: 
Principal investigator
Investigator: 
tomas.skopal
Investigator role: 
Team member
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