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About the webinars
This series of webinars on compound design aims 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 mark.gardner [at] amgconsultants.co.uk.
Links to recordings of previous webinars
PKTool v3.0 - update of popular free tool for dose prediction and pharmacokinetic modelling
Mark Gardner covers new features in the new version of the BMGF PK Tool for human dose prediction. These include handling single dose compounds, using Cav (or AUC) as well as Cmin for dose prediction, estimating bioavailability, and new usability features such as annotation. After a brief run-through for experienced users, Gardner provides an overview explaining the use of the PK Tool for dose prediction, comparing allometric scaling with in vitro clearance estimates and how to use the tool to ask 'what if' questions.
Modelling pharmacokinetics with PKTool v2.0 - improvements to BMGF’s free tool
BMGF’s free PKTool has been updated to address feedback from the Global Health community. Mark Gardner from AMG Consultants took us through the improved tool and demonstrated how to predict human dosing from experimental data.
Advanced features of DataWarrior - creating workflows with macros
DataWarrior has become an invaluable free tool for visualising drug discovery data. Isabelle Giraud, from Idorsia (formerly Actelion), demonstrated some of its more advanced features that allow you to streamline your workflows and make the most of your data.
Drug Discovery Data Insights
CDD hosted a discussion between Andrew Leach (ChEMBL), Evan Bolton (PubChem), and Ashley Farley (BMGF) on how SAR Data from the freely available ChEMBL and PubChem resources is transforming the Drug Discovery Informatics landscape. The discussion considered the challenges of creating large-scale community resource from heterogeneous biological data.
Searching and Analysing 3D Protein-ligand structures using PDBe web services
Abhik Mukhopadhyay, EBI UK showed how to search and analyse 3D protein-ligand structures using Protein Data bank in Europe (PDBe) websites and services (www.pdbe.org). He also demonstrated some PDBe web services that medicinal and computational chemist will find useful in understanding how small molecules interact with proteins.
→ Abhik's slides
PK Solver - a free tool to analyse pharmacokinetic data and derive PK parameters for modelling
PK Solver is a Microsoft Excel add-in which complements the free BMGF-funded PK Tool for pharmacokinetic analysis and prediction. It takes raw data and calculates parameters such as half-life, volume, AUC. Mark Gardner (AMG Consultants) described how to set PK Solver up and how to use it. Mark also gave an update on plans to update the PK Tool to make it more user-friendly and add in some additional capabilities.
→ Mark's slides
Hit triaging and advancement to anti-wolbachial lead compounds
Continuing the theme of capitalising on HTS results, Mike Petrassi presented on developing anti-wolbachial lead compounds at CALIBR.
Processing malaria HTS results using KNIME
Greg Landrum, Knime, gave a tutorial on workflows developed for ligand-based virtual screening, based on results of a phenotypic HTS against malaria.
→ Workflows and data from Greg's presentation (instructions together with a copy of the slides)
→ Greg's slides
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).
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
→ Mark's slides
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
→ Chris' slides
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
→ Chris' slides
- 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
→ Caroline's slides
- A simple KNIME script to compare compound collections, Mark Gardner
→ Mark's slides
- Tips on R group analysis in DataWarrior, Mark Gardner
→ Mark's slides
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
→ Charlie's slides
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
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.