Open Notebook Science for Malaria Drug Discovery and Solubility Modeling

Jean-Claude Bradley

September 30, 2010

Drexel Chemistry Mini Symposium

Associate Professor of ChemistryDrexel University

Industry is Sharing More

Opportunities for Competitive Collaboration

Some Initiatives Promoting More Openness in Drug Discovery

Motivation: Faster Science, Better Science

TRUST

PROOF

UsefulChem Project:UsefulChem Project: Open Primary Open Primary Research in Drug Design using Web2.0 Research in Drug Design using Web2.0

toolstools

Docking

Synthesis

Testing

Rajarshi GuhaIndiana U

JC BradleyDrexel U

Phil RosenthalUCSF

(malaria)

Dan ZaharevitzNCI

(tumors)

Tsu-Soo TanNanyang Inst.

Malaria Target: falcipain-2 involved in hemoglobin metabolism

Dana.org

The Ugi Reaction

Outcome of Guha-Bradley-Outcome of Guha-Bradley-Rosenthal collaborationRosenthal collaboration

References to papers, blog posts, lab notebook pages, raw

data

The Ugi reaction: can we predict precipitation?

Can we predict solubility in organic solvents?

Crowdsourcing Solubility Data

ONS Challenge Judges

ONS Submeta Award Winners

Solubilities collected in a Google Spreadsheet

Rajarshi Guha’s Live Web Query using Google Viz API

Data provenance: From Wikipedia to…

…the lab notebook and raw data

Interactive NMR spectra using JSpecView and JCAMP-DX

(Andy Lang, Tony Williams)

Open Data JCAMP spectra for education

(Andy Lang, Tony Williams, Robert Lancashire)

Raw Data As Images

Splatter?

Some liquid

YouTube for demonstrating experimental YouTube for demonstrating experimental set-upset-up

The importance of raw data availability

Missed in a prior publication on

solubility for this compound

The Intersection of Open Notebooks (Bradley/Todd) and IP implications

Open Notebook could have blocked patent

if done earlier

Convenient web services for solubility measurement and

prediction

(Andrew Lang)

Other Web Services…

(Andrew Lang)

General Transparent Solubility Prediction

Semi-Automated Semi-Automated Measurement of solubility via Measurement of solubility via

web service analysis of web service analysis of JCAMP-DX files JCAMP-DX files

(Andy Lang)(Andy Lang)

Integration of Multiple Web Services to Recommend Solvents

for Reactions

(Andrew Lang)

Solubility Prediction (Andy Lang uses Abraham Model)

Reaction Attempts Book

Reaction Attempts Book: Reactants listed Alphabetically

For all Formats of ONS Projects