Algorithms for protein-ligand binding site discovery
| Thesis title in Czech: | Algoritmy pro detekci vazebních míst u protein-ligand interakcí |
|---|---|
| Thesis title in English: | Algorithms for protein-ligand binding site discovery |
| Key words: | Strukturální Bioinformatika, Vazební místa pro Ligandy, Strojové učení |
| English key words: | Structural Bioinformatics, Protein-ligand binding sites, Machine learning |
| Academic year of topic announcement: | 2012/2013 |
| Thesis type: | diploma thesis |
| Thesis language: | angličtina |
| Department: | Department of Theoretical Computer Science and Mathematical Logic (32-KTIML) |
| Supervisor: | Mgr. Roman Neruda, CSc. |
| Author: | hidden - assigned and confirmed by the Study Dept. |
| Date of registration: | 31.08.2012 |
| Date of assignment: | 31.10.2012 |
| Confirmed by Study dept. on: | 29.01.2013 |
| Date and time of defence: | 10.09.2013 00:00 |
| Date of electronic submission: | 02.08.2013 |
| Date of submission of printed version: | 02.08.2013 |
| Date of proceeded defence: | 10.09.2013 |
| Opponents: | RNDr. František Mráz, CSc. |
| Advisors: | doc. RNDr. David Hoksza, Ph.D. |
| Guidelines |
| Virtually all processes in living organisms are conducted by proteins. Proteins perform their function by binding to other proteins (protein-protein interactions) or small molecules - so called ligands (protein-ligand interactions). Active sites for protein-ligand interactions are pockets in protein structure where ligand can bind. In this thesis we will look into possibility of application of artificial intelligence methods to improve current algorithms for pocket detection and characterization. The student will get familiar with current approaches and will propose his own ones,which will be compared with existing solutions. The thesis will most likely build on existing representation of protein pockets that will be used within a new algorithm. |
| References |
| [1] Structural Bioinformatics, 2nd ed. , Jenny Gu, Philip E. Bourne http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1118210565.html
[2] Intelligent Bioinformatics: The Application of Artificial Intelligence Techniques to Bioinformatics Problems, Edward Keedwell, Ajit Narayanan http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470021756.html [3] From Protein Structure to Function with Bioinformatics, Daniel John Rigden (Ed.) http://www.springer.com/biomed/book/978-1-4020-9057-8 [4] Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures., Ghersi D, Sanchez R. http://www.ncbi.nlm.nih.gov/pubmed/21537951 [5] Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery., Pérot S, Sperandio O, Miteva MA, Camproux AC, Villoutreix BO. http://www.ncbi.nlm.nih.gov/pubmed/21537951 |