Molecular docking is a computational tool commonly applied in drug discovery projects
and fundamental biological studies of protein-ligand interactions. Traditionally, molecular docking is used to address one of three following questions: (i) given a ligand molecule and a protein receptor, predict the binding mode (pose) of the ligand within the context of a receptor, (ii) screen a collection of small-molecules against a receptor and rank ligands
by their likelihood of being active, and (iii) given a ligand molecule and a target receptor, predict the binding affinity of the two. Here, we focus on the first two questions, namely ranking and pose prediction. Currently, state-of-the-art docking algorithms predict poses within 2A of the native pose in a rate lower than ∼60% and in many cases, below 40%. In ranking, their ability to identify active ligands is inconsistent and generally suffers from high false-positive rate. In this thesis we present novel algorithms to enhance the ability of molecular docking to address these two questions. These algorithms do not substitute traditional docking but rather being applied on top of them to provide synergistic effect.
Our algorithms improve pose predictions by 0.5-1.0A and ranking order for 23% of the targets in gold-standard benchmarks. As importantly, the algorithms improve the consistence of the posing and ranking predictions over diverse sets of targets and screening libraries. In addition to the posing and ranking, we present the pharmacophore concept. A pharmacophore is an ensemble of physiochemical descriptors associated with a biological target that elucidates common interaction patterns of ligands with that target. We introduce a novel pharmacophore inference algorithm and demonstrate its utilization in molecular docking. This thesis is outlined as follow. First we introduce the molecular docking approach for pose prediction and ranking. Second, we discuss the pharmacophore concept and
present algorithms for pharmacophore inference. Third, we demonstrate the utilization of pharmacophores for pose prediction by re-scoring candidate poses generated by docking algorithms. Finally, we present algorithms to improve ranking by reducing bias in scoring functions employed by docking algorithms.
| Identifer | oai:union.ndltd.org:LACETR/oai:collectionscanada.gc.ca:OTU.1807/34955 |
| Date | 07 January 2013 |
| Creators | Wallach, Izhar |
| Contributors | Lilien, Ryan |
| Source Sets | Library and Archives Canada ETDs Repository / Centre d'archives des thèses électroniques de Bibliothèque et Archives Canada |
| Language | en_ca |
| Detected Language | English |
| Type | Thesis |
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