MOE Workshop Series
NORTH AMERICA
Small Molecule - 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.
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Antibody Modeling and Protein Engineering
Protein Engineering / Protein Properties / Protein Contacts / Developability / Molecular surfaces / Hot spot analysis / Antibody modeling
This workshop 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 molecular surfaces and visualizing protein-protein contacts in 3D. Antibody properties will be evaluated using specialized calculated protein property descriptors and analyzing protein patches. The application of protein engineering tools for affinity and property optimization of antibodies in the context of developability will be studied. Antibody homology modeling optimization examples will include identifying glycosylation sites and their selective modification using a specialized MOE Project antibody database. All the steps necessary for high throughput antibody homology modeling workflow from sequence to structure to property calculations for developability analysis will be described.
3dpredict: Scalable High Quality Developability Predictions
Antibody structure prediction / Conformational ensembles / Descriptor calculations / Property prediction / Developability / Cloud computing
Predicting potential liabilities such as aggregation or viscosity is a key step in monoclonal antibody development. Computational property prediction methods are routinely used in the selection and optimization of candidate antibodies. High-quality property prediction involves prediction of ensembles of 3D structures at specified pH to reduce sensitivity to single conformational states. We will present 3dpredict/Ab, a solution that enables ensemble-based predictions of antibody developability descriptors and putative liabilities. 3dpredict/Ab allows for out-of-the-box SaaS automation and integration of such complex simulations of hundreds or thousands of sequences, making them accessible and efficient.
Biologics: Protein Alignments, Modeling and Docking
Alignments and superposition / Loop and linker modeling / Protein-Protein docking / Protein-Ligand Interaction Fingerprints (PLIFs) / Epitope analysis / Homology modeling / Solubility analysis / QSAR modeling / 2D hot spot mapping
This workshop covers methods for aligning protein sequences, superposing structures, loop modeling, building fusion protein models, and conducting protein-protein docking. In particular, a method for grafting and refining antibody CDR loops and using a knowledge-based approach to scFv fusion protein modeling using the Linker Modeler application will be described. Protein-protein docking of an antibody to an antigen and epitope mapping will also be discussed. Finally, a complete workflow for generating a QSAR model for predicting and analyzing protein/biologics solubility will be described.
Structure-Based Drug Design: Docking, Fragment Replacement, 3D Virtual Library Enumeration and Protein Family Analysis
Pharmacophore Modeling / Docking / Fragment-Based Design / Scaffold Replacement / R-Group Screening / Project Search / Protein-Ligand Interaction Fingerprints (PLIF)
This workshop explores advanced structure-based drug design (SBDD) workflows used in drug discovery projects. Participants will learn about key topics, including pharmacophore query generation, protein-ligand docking, scaffold replacement, and R-group screening. The session will cover the application of pharmacophore searching in drug design, as well as methods for querying 3D project databases. Additionally, participants will generate and analyze protein-ligand interaction fingerprints (PLIF) to support their design strategies.
Structure-Based Drug Design and Ligand Modification
Molecular surfaces and maps / Ligand interactions / Torsion Analysis / Ligand optimization / Capturing design ideas / Docking / Protein alignments and superposition
This workshop covers MOE applications for interactive structure-based design. Examples include active-site visualization, protein-ligand contact analysis, and ligand modification/optimization in the receptor pocket. Important milestones will be recorded through Capture for review and to allow for sharing the design session with colleagues. The docking module and its application to assess ligand flexibility will be discussed. A protocol for aligning and superposing protein complexes in the context of protein selectivity will be studied.
Small Molecule Virtual Screening
Virtual screening compound libraries / Descriptors / Molecular Fingerprints / QSPR modeling / Database filtering / Pharmacophore modeling / Pharmacophore-guided docking / Template-based docking / Compound design
This workshop covers the suite of MOE applications which can be applied to small-molecule virtual screening. Topics include the preparation of small molecule databases for virtual screening, filtering databases based on substructure matching and property values, building QSAR/QSPR models and fingerprint similarity models as database filters, pharmacophore query creation and searching, and small-molecule docking. These tools are used in conjunction to present a complete virtual screening workflow. The creation of de novo structures using the MOE Scaffold Replacement and MOE Medchem transformation applications is also covered.