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Virtual Screening & Docking - Comparative Methodology & Best Practice Forum and Workshop
13 October 2008
facilitated by Barry Hardy |
This activity will take place at the Community of Practice Meeting, Autumn 2008, Bryn Mawr College, Philadelphia.
It continues ongoing best practice activity in virtual screening initiated at earlier eCheminfo meetings with the goal of contributing to building best practice-based community resources and assessments. Places are available to attend the screening workshop program only OR it may be participated in as a conference attendee.
This Community of Practice Workshop and Forum will 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. A wiki-supported Knowledge Café format will be used.
Best Practice Workshop (Oct 13)
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
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.
Knowledge Cafe Methodology
The following approach will be used for the format of the Cafés:
1. The Knowledge Café format will be explained to all participants prior to the start of the event. The workshop will be divided into component sections, each having their own theme and goal, which the group will work through sequentially during the workshop.
2. Each workshop section will involve a Knowledge Café-based discussion as a primary component. The group will first be divided into smaller groups at separate tables. Each table will be assigned a topic and a facilitator who will remain at their table during the discussion. The number of seats at each table will be chosen to ensure an equal division of the group between topics.
3. Members of the group will be free to select a seat at their table of choice, with the constraint that a seat is available. Following a brief introduction by the facilitator, the group will be free to discuss the topic with each other, with the only constraint being of staying reasonably close to the table topic, and allowing everyone to make their points.
4. Following ca. 30 minutes of conversations, participants will be required to change tables and start a second or third round of conversations.
5. All participants will join together for a final group discussion which will include short summaries by each facilitator and questions and discussions by the group.
6. Each facilitator will enter a summary of their notes into the group-based wiki.
7. A final post-workshop step will allow contributions based on further reflections by the group in the 4 weeks following the workshop.
Program & Schedule
MONDAY 13 OCTOBER
07.30 Registration & Welcome Coffee Opens, Thomas Great Hall
Best Practice Workshop 09.00 – 18.15 [Dalton 300]
09.00 Introduction and Overview
09.30 Discussion of practices for ligand-based screening
11.00 Coffee Break
11.30 Discussion of practices for scoring
13.00 Lunch
14.00 Discussion of practices for target-based screening
15.45 Coffee Break
16.15 Discussion of practices for scoring
17.15 Discussion of rules and execution of comparison studies
18.30 Drinks and Dinner, Wyndham Alumnae House
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