[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 
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 

More Information
Website: http://www.echeminfo.com/COMTY_screeningforumbm07
Pdf Download: 

best regards
Barry Hardy
eCheminfo Community of Practice

Barry Hardy, PhD
Douglas Connect
Zeiningen, CH-4314
Tel: +41 61 851 0170
Blog: http://barryhardy.blogs.com/cheminfostream/

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