Wednesday February 21st 16:00 CET
Processing malaria HTS results using Knife: a tutorial
Speaker: Greg Landrum, Knime
We're pleased to welcome Greg Landrum, Knime, back for a return visit. He will give a tutorial on workflows developed for ligand-based virtual screening, based on results of a phenotypic HTS against malaria. Join us to learn how to use these and other freely available tools in the first of the 2018 series.
Wednesday, March 21st
Hit triaging and advancement to Anti-Wolbachial lead compounds
Speaker: Mike Petrassi, CALIBR
Continuing the theme of capitalising on HTS results, Mike Petrassi will present the next webinar on developing anti-Wolbachial lead compounds at CALIBR.
Registration details coming soon.
Links to recordings of previous meetings
- TB Drug Accelerator: December’s webinar is a joint event with Collaborative Drug Discovery. Dr. Dale Kempf (AbbVie) and Dr. Ben Gold (Cornell), members of the TB Drug Accelerator Program, discussed the challenges of tuberculosis drug discovery: identifying new ways to target resistant disease, develop new tools and drugs that accelerate treatment. Moderated by Dr. Peter Warner (BMGF).
- SwissDrugDesign: a free web-based environment for docking, virtual screening, target prediction and more design tools; Vincent Zoete and Antoine Daina, Swiss Institute of Bioinformatics
- Picking the best of the free drug discovery ADMET prediction models; Mark Gardner, AMG Consultants
- SwissADME: a web tool to support pharmacokinetic optimization for drug discovery; Vincent Zoete and Antoine Daina, Swiss Institute of Bioinformatics
- Heterocyclic Quinolones – privileged pharmacophore targeting both Mycobacterium tuberculosis and malaria; Gemma Nixon, University of Liverpool
- Using Jupyter as an electronic notebook to store and share computational chemistry, Chris Swain, Cambridge MedChem Consulting
- Transforming ‘hits’ into ‘leads’ - Two malaria drug discovery case studies, Claire Le Manach and Tanya Paquet, University of Cape Town.
- An introduction to the free BMGF PK tool, Mark Gardner, AMG consultants (Start - 44:00)
- Using the PK tool in human dose prediction, Gavin Whitlock, Sandexis (44:00 - End)
- Predicting physicochemical properties with OCHEM and using chemistry in patents, Igor Tetko, Helmholtz Zentrum Munchen and BigChem GmbH
- 20 million public patent-extracted chemical structures: a look at the gift horse, Christopher Southan, GtoPDB and Centre for Integrative Physiology, University of Edinburgh
- Solubility prediction: Outcomes & insights from the "Solubility Challenge" competition, Jonathan Goodman, University of Cambridge
- How Confident can we be in ADME Predictions? Matt Segall, Optibrium
- Freely available databases with applications in Drug Design, Caroline Low
- A simple KNIME script to compare compound collections, Mark Gardner
- Tips on R group analysis in DataWarrior, Mark Gardner
The ChEMBL Database for Drug Discover and Design, Anna Gaulton, EMBL-EBI
Two ChEMBL use cases: (1) Using ChEMBL data to produce a Quantitative Estimate of Drug-likeness; (2) Using ChEMBL data to derive transformations and models for de novo design, Jérémy Besnard, ExScientia
- Open source malaria project, Mat Todd, University of Sydney
- An introduction to the open-source workflow tool KNIME and applications in drug discovery, Greg Landrum, KNIME
- KNIME use case: Property calculation and chemical space diagrams in DNDi's Drug Booster project, Ben Perry, DNDi
Ben's workflow & guide
- KNIME use case: ‘Know Your Molecule’ searching ChEMBL with KNIME & interpreting the data, Mark Gardner, AMG
Mark's guide & workflow
- DataWarrior advanced data analysis, Isabelle Giraud, Actelion
- Using the RSC Medicinal Chemistry Toolkit in Drug Discovery Projects, Andy Davis, AZ
Visceral leishmaniasis Target Candidate Profile & screen sequence, Charlie Mowbrary, DNDi
Malaria Target Candidate Profiles, stage gates and implications for successful malaria drug discovery, Paul Willis, MMV
- Application of PK Tools in the optimisation of a series for the treatment of leishmaniasis, Gavin Whitlock, Sandexis
- Hints and tips to working with DataWarrior, Isabelle Giraud, Actelion
This series of webinars on compound design will continue throughout 2017. The aim is to share experiences of compound design in global health projects (malaria, TB, NTD), covering a range of topics including the use of freely available design tools, quality criteria such as target candidate profiles, screen sequences and case histories. If you are interested in making a presentation, please contact %20mark.gardner [at] amgconsultants.co.uk.
Information on this page is provided by AMG Consultants. The information is advisory only and represents the views of AMG Consultants. The information does not represent the views of MMV nor of the Bill & Melinda Gates Foundation. None of these organisations accept responsibility or liability for the tools or for the consequences of any actions taken on the basis of the information provided on the use of the tools. The information, both the guides and links provided are correct at time of publication. AMG Consultants will make reasonable efforts to maintain the content but accept no liability for any changes to the tools or the free status of those tools at any point in the future. AMG Consultants are aware that other similar tools exist and no favourable or unfavourable opinion should be inferred from the inclusion or exclusion of any particular tool to this website.