May 11, 2016
||The Harvard Faculty Club|
20 Quincy Street, Cambridge, MA, 02138, United States
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Protein Homology 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 aligning and super-positioning protein multimers. A method for superposing proteins that is strictly based on structural motifs will be described.
Organizing Structural Project Data and Protein Family Modeling
The course describes the MOE Project automated protocol for organizing, managing and sharing data sets across a drug discovery organization. Topics include an overview of the Project Search application used for generating, searching and combining queries, an XML editor for generating specialized protein family databases, and analysis of receptor-ligand contacts through Protein-Ligand Interaction Fingerprints (PLIF) analysis.
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