MOE Workshop Series
VIRTUAL WORKSHOPS
Small Molecules – Peptides – Biologics
Registration Fees
There is no cost to attend but pre-registration is required as seats are limited. Registrations will be processed and accepted first-come, first-served. No previous MOE software experience is required to attend.
Stay tuned, more to come!
Peptide Modeling, Conformational Searching and Docking
Structure preparation / Non-natural amino acids / Conformational searching / Distance restraints / Peptide-protein docking / Protein-ligand interaction fingerprints
The course covers methods for analyzing and optimizing peptide-protein interactions in the active site. Topics related to peptide-protein structure preparation, peptide sequence optimization using natural and non-natural acids and conformational analysis will be discussed. Peptide-protein docking and protein-ligand interactions to analyze contact points will be described. The course will also cover advanced conformational searching using distance restraints.
Organizing Protein Structural Families and Data Mining
MOE project / specialized protein families / project search / Organizing and centralizing project data / protein family modeling
The course covers MOE-Project, the automatic protocol for organizing SBDD project data. Topics include preparing protein data, using a graphical interface to create a project database of aligned and superposed protein structures, applying the MOE Project Search panel to mine the project data and analysis of molecular interactions using Protein-Ligand Interaction Fingerprints (PLIF).
Antibody Modeling and Protein Engineering
Protein Engineering / Protein Properties / Developability / Hot Spot Analysis / Antibody Modeling / Humanization / Molecular Surfaces
The course covers approaches for structure-based antibody design and includes protein-protein interactions analysis, in silico protein engineering, affinity modeling and antibody homology modeling. The interaction of a co-crystallized antibody-antigen complex will be studied by generating and examining the molecular surfaces and visualizing protein-protein interactions in 3D and 2D. Antibody properties will be evaluated using specialized calculated protein property descriptors and analyzing protein patches. The application of protein engineering tools for homology modeling and conducting property optimization of antibodies in the context of developability will be studied. Antibody optimization examples will include identification of glycosylation sites and analysis of correlated pairs using a specialized antibody database. An approach for humanizing antibody homology models will be discussed. All the steps necessary for producing and assessing antibody homology models will be described.
Biologics: Protein Alignments, Modeling and Docking
Protein Alignments and Superposition / Loop and Linker Modeling / Homology Modeling / Protein- Protein Docking / Protein Solubility Analysis / 2D Hot Spot Mapping / PLIF / Biologics QSAR Modeling
The course covers methods for aligning protein sequences, superposing structures, homology modeling fusion proteins and conducting protein-protein docking. In particular, an approach for aligning and superposing multiple structures will be described for determining structural and surface protein variations in relation to protein property modulation. A method for grafting and refining antibody CDR loops as well as using a knowledge-based approach to scFv fusion protein modeling using the MOE linker application will be described. An approach to generate homology models of a murine antigen structure from a human template as well as protein-protein docking of an antibody to an antigen will be discussed. A QSAR model for predicting and analyzing protein/biologics solubility will be described.