On 15-16 October 2007 we will hold an eCheminfo Community of Practice Workshop and Forum at Bryn Mawr College, Philadelphia to discuss and advance best practice in virtual screening and docking, to develop co-created best practices for comparison studies, and to review latest developments in method development and applications related to drug discovery.
This activity will consist of three parts:
1. Workshop to develop co-created best practices for comparison studies. (morning/afternoon of October 15).
2. Conference session on latest method developments with presentations and panel discussion. (morning of October 16)
3. Hands-on Workshop sessions with screening software (afternoon of October 16)
1. Best Practice Workshop (Oct 15)
This workshop will have an agenda to:
· share experiences on current practices for comparative studies in virtual screening
· engage in group-based discussion and detailed documentation and agreement of best practices for conducting comparison studies
· to co-create requirements for a comparison study which will subsequently be conducted by the community of practice
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.
- use of wiki-based approaches for practice development
- 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
(Follow continuation for more information...)
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