•  

Toolkit Presentation Focused on Shape and Spicoli

A session at JCUP IV

Friday 7th June, 2013

11:45am to 12:45pm (CJT)

The theory that similar ligands often bind to the same protein binding site drives much of the utility of ligand-based virtual screening approaches. A corollary of this idea is that similar binding pockets might bind the same ligand. This makes the comparison of ligand binding sites is a generally useful tool, with possible applications ranging from examining the effects of induced fit, to comparing related proteins to explore selectivity, and even searching for off-target effects or drug repurposing campaigns. We have recently applied the same shape-based approach that has proven very successful in the ligand-based virtual screening realm to this problem of binding site comparison in a new tool, SiteHopper, which can rapidly define binding sites by shape and surface chemical features. These binding site definitions, called "patches", can be collected from public or internal sources into a database, which then can be searched using as a query the specific pocket of interest, yielding a hitlist of aligned similar pockets. Due to the generality of this method, we have chosen to implement SiteHopper as a series of python scripts using the toolkits, rather than as a compiled application, to further allow modification by users to their specific needs and interests. More detail will be provided as to the specifics of the shape-based definition of a binding site, our philosophy on toolkits, and examples of possible uses for SiteHopper.

About the speaker

This person is speaking at this event.
Paul Hawkins

Applications Science Group Leader, OpenEye Scientific Software

Next session in Ohtemachi SunSky Room

1pm New Frontiers at OpenEye: The Cloud by Joe Corkery

Coverage of this session

Sign in to add slides, notes or videos to this session

JCUP IV

Japan Japan, Tokyo

6th7th June 2013

Tell your friends!

When

Time 11:45am12:45pm CJT

Date Fri 7th June 2013

Where

Ohtemachi SunSky Room, Asahi Seimei Ohtemachi Building

Short URL

lanyrd.com/schyph

Official event site

www.eyesopen.com/events/jcup4

View the schedule

Share

See something wrong?

Report an issue with this session