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John Irwin is Adjunct Associate Professor in the Department of Pharmaceutical Chemistry at the University of California San Francisco. John works on methods to discover new reagents for biological targets using target- and ligand-based methods. He applies these methods to various projects, and particiates in numerous collaborations.
John develops the ZINC database of commercially available compounds for virtual screening, the DUDE database for benchmarking virtual screening methods, the DOCK Blaster family of products for web-based virtual screening, and the SEA method of comparing proteins by the ligands they bind.
Short bio: John received his Ph.D. for work with Jack Dunitz in chemical crystallography in 1991 at ETH Zurich. He worked at a startup molecular modeling company before joining Gerard Bricogne's group at the Medical Research Council's Laboratory of Molecular Biology in Cambridge UK, developing software for new macromolecular crystallographic structure solution and refinement methods (BUSTER and SHARP). He spent a year and a half as a staff scientist at EMBL-EBI also in Cambridge working on the PDB cleanup project before moving to Northwestern University Medical School in 2000. He has been working on DOCK, ZINC, and SEA since 2000. 30
I am interested in fragment-based approaches applied to drug design and substrate discovery:
- Fragment-based screening against AmpC Beta-Lactamase: how to expand our exploration of chemical space using fragment molecules?
- Analyzing the potential of fragment molecules as tools for enzyme function prediction: the Amidohydrolase Superfamily as a case study. These two projects involve fragment docking, enzymatic assays and X-ray crystallography.
Khanh has a Bachelor’s Degree in Biochemistry and a former student of PINC at San Francisco State University. She loves chemistry and had 2 years of experience of working in a Organic Chemistry lab. She is interesting in computation-based approach for drug discovery.
I am the Systems and Infrastructure Administrator of the Irwin Lab and Keiser Lab. I have a Red Hat certificate in Systems Administration and my main interests lie in hoarding data with ZFS, dreaming of LTO-8 Ultriums, and backing up via Backblaze B2.
I am a graduate student in computer science in San Francisco State University. I am interning as a software engineer in Irwin lab. My jobs includes:
1. Learned and handled Flask web server framework and PostgreSQL database system.
2. Install R shiny, JupyterHub, and Docker to provide graphical and interactive user interface in sandbox environment.
3. Implemented a searching program with indexing and parallel execution to speed up searching on SMILE files.
4. Developed pipeline to utilize indexing, partition, and parallel query of Postgres 10 on ZINC database to speed up searching.
Former Scientific Programmer
He is now working at BioMarin Pharmaceuticals Inc., San Rafael. Teague was the author of the ZINC 12 and ZINC 15 interfaces, as well as many other tools and databases in the lab.
Now a software engineer at Hitachi Corp, Santa Clara, CA.
Went on to work at IBM Almaden Research, currently involved in a startup in stealth mode.
Currently at Flurry, a mobile analytics company in San Francisco.
Now a graduate student at Harvard University.