[BiO BB] Best Practices in Virtual Screening
Barry Hardy
barry.hardy at vtxmail.ch
Thu Aug 16 13:38:32 EDT 2007
Perhaps the most frequent topic of discussion that I have seen
consistently arising in my recent conversations with drug discovery
researchers, is the topic of Virtual Screening and its complexities,
confusions, and varying validity and reliability. John Irwin and I
initiated the idea of a best practice initiative last Autumn
(http://barryhardy.blogs.com/cheminfostream/2006/10/could_we_take_a.html).
We realise this will take time but I believe it is an endeavour worth
undertaking that will be of significant benefit to both industry and
academic researchers. To this end we are supporting workshop and wiki
activity this Autumn to initiate such a program.
The Virtual Screening Community of Practice Workshop and Forum will take
place 15-16 October at Bryn Mawr, Philadelphia to further the above
goals. This activity will consist of the following components:
1. Workshop to share experiences on current practices in virtual
screening and to collaboratively develop best practices for comparison
studies. (morning/afternoon of October 15).
2. Conference session on latest method developments with presentations
and panel discussion. (October 16)
3. Poster Session (evening of October 16). NOTE: If interested in
presenting a poster, please send an abstract (ca. 300-500 words) for
review to eCheminfo (-at-) douglasconnect.com We have also left space on
the program schedule to feature a selection of the abstracts submitted
as oral presentations.
4. Virtual communication and collaboration approaches will be used pre-
and post-event to maximise the benefit of the workshop activity. In
particular a wiki will be opened prior to the workshop to commence
documentation of supporting materials and to start to populate the area
with initial suggestions, ideas, practices and methods. The wiki will
also support subsequent practice group activities and development
initiatives, including future ongoing meetings and workshops and
research and development projects. (Realising this activity needs to be
in progress for quite some time.)
The agenda of workshop will be designed so as to maximise interaction,
discussion, issue resolution, and action plans for cooperation. Workshop
activities will address the specific challenges:
* statistically significant relationships between docking scores and
ligand affinity
* practices and procedures for the operation of community-based
screening and docking comparisons including tests and interpretation of
results, in a way that everyone can agree is fair.
* peer review, data compilation, running of programs, judgement of results
* workflow descriptions for comparisons
* beyond conformational energetics in the rank ordering of diverse
compounds in high throughput virtual screening
* measurement and benchmarking
* binding mode prediction, virtual screening for lead identification,
rank-ordering by affinity for lead optimization
* atom typing, ligand preparation (ionic forms, tautomers, ...), ligand
conformer generation, protein preparation (protonation, residue
orientation, ...), ligand placement (top-down, bottom-up, fragment
based, group based, ...), energy calculation (force field type, grid
type, algorithm, ...), constraint handling (global and local
optimization strategy? process to escape local minima?), scoring
(single-objective, multi-objective, consensus, ...)
* separation of test set information from model development
* validation datasets, results and applicability domains
* objective comparisons of standardized test datasets
* extraction of data from the scientific literature
* methods and procedures for secure testing of commercial data that
could be acceptable to industry
* frameworks for computational model testing and validation
* impact of knowledge management approaches
* collaboration and community support structures and environments
We welcome the collaboration and participation of all academic,
government and industry practitioners in drug discovery in strengthening
the scientific foundations of this valuable set of cheminformatics
techniques.
More Information
Website: http://www.echeminfo.com/COMTY_screeningforumbm07
Pdf Download:
http://barryhardy.blogs.com/cheminfostream/files/eChemProgramBrynMawr07-web1.PDF
best regards
Barry Hardy
eCheminfo Community of Practice
Barry Hardy, PhD
Douglas Connect
Zeiningen, CH-4314
Switzerland
Tel: +41 61 851 0170
Blog: http://barryhardy.blogs.com/cheminfostream/
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