Fragment-based virtual screening is an in-silico method that potentially identifies new startingpoints for drug molecules and provides an inexpensive and fast exploration of the relevantchemical space compared to its experimental counterpart. It focuses on docking small potentialbinding fragments to a binding pocket and is used to design improved binders by growing thefragments or joining fragments using suitable linkers. In this project, a fragment-based virtualscreening was evaluated by docking 21 fragments that are obtained from 4 different drugs. Here,the fragments were evaluated using SP score in place and SP and XP flexible docking methodsand were compared to the results of the two decoy fragment datasets. Three of the investigatedfragments are positioned at the top and docked with the correct poses and pockets when comparedto the corresponding substructure in the crystal structure and thus could be considered a successfulfragment starting points. Out of the two flexible docking methods used, the SP method providedadditional correct poses and pockets than XP in this limited dataset.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:uu-446388 |
| Date | January 2021 |
| Creators | Nawsheen, Sabia |
| Publisher | Uppsala universitet, Institutionen för läkemedelskemi |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
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