Home > Search Results: keywords:"P2Rank"
Search:
Search Tips :: Advanced Search
Search collections:
Sort by: Display results: Output format:
National Repository of Grey Literature 2 records found  Search took 0.01 seconds. 
Use of residue-level annotations for structural prediction of protein-ligand binding sites
 Břicháčková, Kateřina ; Hoksza, David (advisor) ; Galgonek, Jakub (referee)
The number of experimentally resolved protein structures in the Protein Data Bank has been growing fast in the last 20 years, which motivates the develop- ment of many computational tools for protein-ligand binding sites prediction. Binding sites prediction from protein 3D structure has many important applica- tions; it is an essential step in the complex process of rational drug design, it helps to infer the side-effects of drugs, it provides insight into proteins biological functions and it is helpful in many other fields, such as protein-ligand docking and molecular dynamics. As far as we know, there has not been a study that would systematically investigate general properties of known ligand binding sites on a large scale. In this thesis, we examine these properties using existing experimen- tal and predicted residue-level annotations of protein sequence and structure. We present an automated pipeline for statistical analysis of these annotations, based on hypothesis testing and effect size estimation. It is implemented in Python and it is easily extensible by user-defined annotations. The usage is demonstrated on 33 existing annotations and 4 different datasets. The practical significance of the results is tested with P2Rank prediction method. We hope that the results as well as the pipeline...
Detailed record
Structure- and sequence-based identification of functionally important amino acids in a protein family
 Peclinovská, Iveta ; Novotný, Marian (advisor) ; Pleskot, Roman (referee)
A group of small GTPases consist of over twenty protein families in the super class P-loop. It has a very diverse cell functions. Small GTPases regulate the formation of vesicular follicles, cytoskeleton and nuclear transport. They participate also on cell proliferation and signaling. The aim of my work is to find important amino acids that define family and distinguish each other. I focus on families Arf, Rab, Ran, Ras and Rho. At the Rho family I am also devoted to classes Rho, Rac and Cdc42. Amino acids are identified using bioinformatic programs selected Consurf and Sca5. The objective is also to test P2RANK specialized tool developed at the Charles University in Prague that predict ligand binding sites from protein structure in different families. Founding amino acids can have a big role in the functional divergence of individual families and classes of small GTPases and can be the basis for future study example for the proliferation of cancerous cells. 1.1 Keywords Powered by TCPDF (www.tcpdf.org)
Detailed record

Interested in being notified about new results for this query?
Subscribe to the RSS feed.
Digital Repository :: Search :: Submit :: Personalize :: Help
Powered by Invenio v1.1.2
Maintained by admin.invenio@techlib.cz
This site is also available in the following languages:
Česky  English