Symposium Leaders

Session Leader: Dr. Paul Hawkins, OpenEye Scientific
Facilitators: Dr. Indira Ghosh (JNU), Dr. Subba Rao (JNU), Dr. Sarma Jarp (GVKBio)
Seascape Learning

A. Shape/Electrostatics oriented research & key challenges –Dr. Indira Ghosh/Dr. Subba Rao or Dr. Sarma
Case study approach on a target using docking/scoring methods

B. Shape Screening and Lead-Hopping – Dr. Paul Hawkins

Since validation/comparison metrics are a significant piece of virtual screening, we will examine metrics, statistics and validation methods in virtual screening.  This is critical to compare and contrast between different methods, applications, parameter sets etc.

•An introduction to virtual screening
•Outline of the process of virtual screening
•How to validate a virtual screening tool
            How do we know if it works
            How do we assess future performance
                        ROC curves, AUC, p-values
•Virtual screening with shape
            Screening the right compounds
            Using OMEGA/ROCS
            Conformer database generation
                        Introduction to conformer generation
                        Introduction to OMEGA
                        Some common misconceptions about conformer sampling
            Shape and chemistry matching
                        Introduction to ROCS theory
                        Retrospective case studies
                        Prospective case studies
•Query generation and comparison using vROCS
            Multi-molecule queries
            Feature weighting
            Query comparison using statistical measures
C. Lead-Hopping with shape and electrostatics
            Introduction to electrostatics
            Introduction to EON
            ROCS & EON in lead-hopping
                        Retrospective examples
                        Prospective examples
Day 2

D. Hands-on work session
•Brief tutorial on new GUIs in vROCS, BROOD 2.0 and the extensions in VIDA (overlay and alignment, conformer generation)

•vROCS – generating multi-molecule queries, editing queries to alter both shape and color properties, series of validations with different queries, generate statistics to compare the queries

•BROOD – generate a query, edit its properties, set constraints, use protein information in the search, analyze results in VIDA

•VIDA extensions – generate conformations, perform shape-based overlays

Note: Exact schedule may vary a bit, however above items will be fully covered

 

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