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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...
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Limitations of variant consequence predictors
 Břicháčková, Kateřina ; Daněček, Petr (advisor) ; Kolář, Michal (referee)
Thanks to numerous large-scale sequencing projects, the number of discovered genomic variants is increasing. The key step in analyzing the variant data is the functional annotation, since it helps researchers and clinicians to categorize, filter and prioritize the variants for further research. This thesis discusses five commonly-used variant consequence predictors, offers advice on how to use them and briefly goes through the algorithms they employ. Moreover, various data formats as well as the human reference genome and different genome annotations are described in the thesis. The correctness of the reference is of great importance as all the predictors rely on it. This thesis highlights some situations in which the results given by different predictors can vary. All the tests were made using the Ensembl gene annotation (release 92) and the GRCh38 reference assembly.
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1 Břicháčková, Klára
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