2012 Accelrys North American User Group Meeting - Save the Date

Agenda

The User Forums will feature a single track with presentations delivered by expert Pipeline Pilot users and developers. The program will also feature a Tips & Tricks session lead by Accelrys Pipeline Pilot developers in addition to a Pet Peeves session that will allow you to provide us with feedback on what you'd like to see changed in Pipeline Pilot.

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Note: Please note that timings, topics, speakers and titles are subject to change.

Wednesday, October 16th - Princeton, NJ

Time Description
9:30 am Coffee & Registration
10:00 am Welcome & Introduction
Dave Rogers, Accelrys
10:15 am Contour® Technology and its Application to Drug Discovery
Suresh Singh, Director, Vitae Pharmaceuticals
10:45 am Pipeline Pilot Expert User Presentation
11:15 am Easing the Path to Quality Statistical Models
Dana Honeycutt, Principal Scientist, Statistics and Data Modeling, Accelrys
12:00 pm Networking Lunch
1:15 pm New Chemistry Functionality, Science and Enhancements in AEP 9.0
David Foss, Advisory Software Scientist, Accelrys
2:00 pm Pipeline Pilot Tips & Tricks
Fred Coughlin, Lead Field Applications Scientist, Accelrys
2:45 pm Pipeline Pilot Pet Peeves
Rob Brown, Sr. Director, Product Marketing, Accelrys
Andy Leuthe, Sr. Director, Product Marketing, Accelrys
3:30 pm Close

 

Thursday, October 17th - Boston, MA

Time Description
9:30 am Coffee & Registration
10:00 am Welcome & Introduction
Dave Rogers, Accelrys
10:15 am Not Just for Science: A Migration Tale
Jennifer Heymont, Bioinformatician, Eisai
10:45 am Pipeline Pilot Expert User Presentation
11:15 am Easing the Path to Quality Statistical Models
Dana Honeycutt, Principal Scientist, Statistics and Data Modeling, Accelrys
12:00 pm Networking Lunch
1:15 pm New Chemistry Functionality, Science and Enhancements in AEP 9.0
David Foss, Advisory Software Scientist, Accelrys
2:00 pm Pipeline Pilot Tips & Tricks
Fred Coughlin, Lead Field Applications Scientist, Accelrys
2:45 pm Pipeline Pilot Pet Peeves
Rob Brown, Sr. Director, Product Marketing, Accelrys
Andy Leuthe, Sr. Director, Product Marketing, Accelrys
3:30 pm Close

 

 

Tuesday, October 22nd - San Mateo, CA

Time Description
9:30 am Coffee & Registration
10:00 am Welcome & Introduction
Matt Hahn, CTO, Accelrys
10:15 am Gilead Sciences Structure Portal – An Integrated Solution to Organize and Disseminate 3D Structural Project Data
Johannes Voigt, Senior Research Scientist, Gilead
10:45 am Accessing Synthetic Chemistry Space Using Pipeline Pilot
Warren Wade, Director, Medicinal Chemistry, BioBlocks, Inc.
11:15 am Easing the Path to Quality Statistical Models
Dana Honeycutt, Principal Scientist, Statistics and Data Modeling, Accelrys
12:00 pm Networking Lunch
1:15 pm New Chemistry Functionality, Science and Enhancements in AEP 9.0
Moises Hassan, Principal Software Development Scientist, Accelrys
2:00 pm Pipeline Pilot Tips & Tricks
Lucy Cesar, Principal Field Applications Scientist, Accelrys
2:45 pm Pipeline Pilot Pet Peeves
Rob Brown, Sr. Director, Product Marketing, Accelrys
Andrew LeBeau, Advisory Product Manager, Accelrys
3:30 pm Close

 

 

Abstracts


Welcome to Pipeline Pilot User Forum
Princeton & Boston: Dave Rogers, Accelys
San Mateo: Matt Hahn, CTO, Accelrys

Abstract: This session will introduce new and advanced Pipeline Pilot users to the planned sessions for the day.


Contour® Technology and its Application to Drug Discovery
Suresh Singh, Director, Vitae Pharmaceuticals

Abstract: A state-of-the-art structure based drug design technology called Contour® was developed to discover drug-like molecules against high resolution protein crystal structures. The technology consists of a de novo growth algorithm that intelligently selects fragments and assembles molecules in the context of the binding site. The growth algorithm with its programming capability offers flexibility and a large number of possible combinations to assemble molecular fragments to generate molecules. The grown molecules are scored by a novel directional contact based scoring function. The Contour scoring function predicts affinities of molecules with high correlation both on the training and validation sets. The technology originally contained a JAVA based molecular graphics interface. This infrastructure now is integrated into Discovery Studio (DS) for the front-end and Pipeline Pilot (PP) protocols for the back-end. The details of the integration of Contour technology into a DS/PP interface and the application of Contour to design a clinically useful human renin inhibitor will be presented.


Not Just for Science: A Migration Tale
Jennifer Heymont, Bioinformatician, Eisai

Abstract: Although our department most commonly uses Pipeline Pilot in support of scientists and scientific applications, two years ago we were tasked with a new challenge: provide informatics support for the Help Desk to drive the site's migration to Windows 7. In response we developed an application suite that not only enabled us to meet the migration deadline but could also be retooled after the migration was complete to support routine Help Desk workflows. We have continued to build onto the initial application, and our Help Desk today has greener processes, build times that are reduced by over 50%, and more pro-active maintenance of user machines, all supported by Pipeline Pilot.


Gilead Sciences Structure Portal – An Integrated Solution to Organize and Disseminate 3D Structural Project Data
Johannes Voigt, Senior Research Scientist, Gilead

Description: This web-based application allows easy perusal of 3D structural data by the entire research project team. The key concept is the use of the same XYZ-space for related projects/target families. Thus, all in-house and published X-ray structures as well as modeled structures can be easily compared.  Current implementation includes kinase and protease structural domains. Since structures are loaded into a viewer on demand, there is no size limit to the overall structure collection.

Browsing and selecting molecules is aided by 2D-structure image links and hierarchical organization into subsections like targets, target families, chemotypes and for kinases hinge binding motifs. Text, substructure, and similarity searches can be made and model annotations are stored. 3D visualization supports both DS Viewer 3.1 (Accelrys) and Pymol 1.4 (Schrödinger) and the web GUI is driven by Pipeline Pilot.


Accessing Synthetic Chemistry Space Using Pipeline Pilot
Warren Wade, Director, Medicinal Chemistry, BioBlocks, Inc.

Abstract: The Syntheverse™ is the synthetically accessible region of virtual compound space that can be assembled readily using available reagents and tractable reaction schemes. The emphasis on synthetic viability and reagent availability provides a straightforward synthetic plan and an estimate of relative difficulty for alternative proposed solutions. However, even with limits on compound size and medicinally preferred functional groups, the Syntheverse™ is too large for practical enumeration. Using Pipeline Pilot, we have developed methods to generate and query large virtual libraries (> 1011 members) to identify high-value subsets for further screening. Applications to drug discovery will be used as examples.


Easing the Path to Quality Statistical Models
Dana Honeycutt, Principal Scientist, Statistics and Data Modeling, Accelrys

Abstract: Validation of a statistical model has multiple aspects, from testing that the model fits the training data (in a way that is better than a null model), to ensuring that the prediction quality for test data is adequate, to rating the confidence of predictions on new samples. Here I present ways that we have enhanced Pipeline Pilot and related products to encourage and make simpler various facets of model validation. Specifics include (1) "self-validating learners" that incorporate cross-validation (or other types of validation) and null model comparison into the model building process; (2) applicability domain measures that are automatically captured upon model building and reported when making predictions; (3) a wizard-like QSAR/QSPR workflow application built on Pipeline Pilot that leads the scientist step-by-step through best practices for data pre-processing and model building, validation, and distribution of models for wider use within the organization.


New Chemistry Functionality, Science and Enhancements in AEP 9.0
Princeton & Boston: David Foss, Advisory Software Scientist, Accelrys
San Mateo: Moises Hassan, Principal Software Development Scientist, Accelrys

Abstract: Several enhancements have been made for the Pipeline Pilot Chemistry Collection in 9.0. Among them are harmonized chemistry perception and mapping functionality, a completely revamped depiction module, enhanced molecule-to-name and name-to-molecule functionality, and new scientific capabilities.


Pipeline Pilot Tips and Tricks
Princeton & Boston: Fred Coughlin, Lead Field Applications Scientist, Accelrys
San Mateo: Lucy Cesar, Principal Field Applications Scientist, Accelrys

Abstract: This session will cover tips and tricks for Pipeline Pilot users based upon our newest version of Pipeline Pilot. Working with customers day in and day out, we've built up a vast knowledge of problems that users have encountered and how to address those problems. After attending this session users will enhance their Pipeline Pilot skills considerably and should feel more comfortable tackling new challenges.


Pipeline Pilot Pet Peeves
Boston & Princeton:
Rob Brown, Sr. Director, Product Marketing, Accelrys
Andy Leuthe, Sr. Director, Product Marketing, Accelrys

San Mateo: Andrew LeBeau, Advisory Product Manager, Accelrys

Abstract: This is the time to inform Accelrys about your “Pet Peeves”, i.e. those little things that crop up from time to time that you wished would work differently, but usually not in a way that would make you file a support ticket. In this session we will also look forward and discuss new areas of development and solicit input from the audience.