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Drug Binding Affinities Workshop
12 October 2009
Co-chaired by Scott Brown (Abbott Laboratories) Abstract & Bio.... , Zheng Yang (GlaxoSmithKline Pharmaceuticals) Bio...., Ruhong Zhou (IBM) Bio.... and Judith Lalonde (Bryn Mawr College) Bio.... |
Morning Technical Session:
The morning workshop section will focus on the technical aspects of setting up and running MM-PB/GB-SA binding affinity calculations. The session will adopt the “community of practice approach” previously used at eChemInfo meetings involving wiki-supported small group discussions. The session will start with a 15 minute overview and then will be divided into three discussions:
1) MM (Molecular Mechanics), Force-field use in the calculations
A. Amber
B. Others
C. Partial charges
2) PB/GB, Solvation Models
A. Explicit Models
B. PB, OpenEye- ZAP
C. GB, various calculations of effective Born radii
a. Amber (GB-HCT) and (GB-OBC)
b. Charmm (GB-MV) and (GB-SW)
c. Others, ACE, AGBNP, FACTS
3) SA, Surface Area Representation
A. Solvent Accessible Surface Area
B. Volume Integration
C. Other
Afternoon Case Studies Session:
The afternoon section will present case studies of successful and not so successful MM-PB/GB-SA applications. Each case study will be presented by an expert user and will be followed by round table guided discussions. These discussions will also be captured on the wiki.
Presentations:
Dong Xu (University of California, San Diego), MM-GBSA-based Calculation of Binding Energies of Hemagglutinin-glycan interactions involved in Avian Flu Virus Infection Initiation Abstract & Bio....
Scott Brown (Abbott Laboratories), MMPBSA as a Tool for Prospective Drug-Discovery Research Abstract & Bio....
Natasja Brooijmans (Wyeth Research), Docking and MM/GBSA Re-scoring in Lead Identification Abstract & Bio....
The workshop day will be completed with a documentation of issues and actions including practice group actions beyond the workshop.
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Workshop Format
* Virtual communication and collaboration approaches will be used pre- and post-event to maximise the benefit of the workshop. In particular a wiki will be used prior to the workshop to commence group documentation of supporting materials and to start to populate the workshop program with suggestions, ideas and methods.
* During the workshop extensive use of facilitated small group discussions using a knowledge café format will be used.
* The results of all discussions will be collected by workshop facilitators and entered into the practice group wiki, to support subsequent group activities and development initiatives, including future practice group meetings and research and development projects.
Program & Schedule
MONDAY 12 OCTOBER
07.30 Registration & Welcome Coffee Opens, Thomas Great Hall
09:00 Welcome and Overview, Judith LaLonde (Bryn Mawr College)
09:15 Background and Overview on MM, Ruhong Zhou (IBM)
09:30 Break-out Discussions on MM
10:00 Background and Overview on Solvation Models, Scott Brown (Abbott Laboratories)
10:15 Break-out Discussions on Solvation Models
11:00 Coffee Break
11:30 Background and Overview on Surface Area, Judith LaLonde (Bryn Mawr College)
11:45 Break-out Discussions on Surface Area
13:00 Lunch
14:00 Case Studies Introduction, Zheng Yang (GlaxoSmithKline Pharmaceuticals)
14:05 Dong Xu (University of California, San Diego), MM-GBSA-based Calculation of Binding Energies of Hemagglutinin-glycan interactions involved in Avian Flu Virus Infection Initiation
15:00 Scott Brown (Abbott Laboratories), MM-PBSA as a Tool for Prospective Drug-Discovery Research
15:45 Coffee Break
16:15 Natasja Brooijmans (Wyeth Research), Docking and MM/GBSA Re-scoring in Lead Identification
17:00 Round Table Discussion, Zheng Yang (GlaxoSmithKline Pharmaceuticals)
18.30 Refreshments and Dinner [Wyndham Alumnae House]
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