February 23, 2017
||St Johns Innovation Centre|
Cowley Road, Cambridge, Cambridgeshire, CB4 0WS, United Kingdom
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Applications of Pharmacophores in Drug Design
The course describes the application of pharmacophores in drug discovery projects and encompasses a range of topics from pharmacophore query generation to pharmacophore refinement and searching of structural databases. A new approach based on Extended Hückel Theory (EHT) for producing pharmacophore models with encoded interaction energies in the context of ligand-based and structure-based projects will be described. The generation and analysis of protein-ligand interaction fingerprints (PLIF) will be presented along with the application of PLIF for producing pharmacophore queries. A method for combining pharmacophore models and PLIF with linear and binary QSAR models for consensus modeling will also be described.
Protein Alignments, Superpositions, Homology Modeling and Loop Modeling
The course covers protein alignments and homology modeling in MOE. The homology modeling section covers the complete sequence to structure workflow, including template searching, query alignment, adjustment of the alignment between the sequence and the template, homology model building and refinement, along with applications for assessing model quality. Refinement of protein loops and loop conformations using the Loop Modeler and LowModeMD conformational searching will be discussed. Protein contacts will be evaluated after alignment and superposition of protein multimers. A method for superposing proteins that is strictly based on structural motifs will be described.
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