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- Publications
- Influence
A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing
- D. E. Gordon, Gwendolyn M. Jang, +122 authors N. Krogan
- Medicine
- Nature
- 30 April 2020
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million… Expand
ZINC - A Free Database of Commercially Available Compounds for Virtual Screening
- J. J. Irwin, B. Shoichet
- Computer Science, Medicine
- J. Chem. Inf. Model.
- 2005
TLDR
Benchmarking sets for molecular docking.
- N. Huang, B. Shoichet, J. J. Irwin
- Chemistry, Medicine
- Journal of medicinal chemistry
- 16 November 2006
Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross… Expand
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
- Michael M. Mysinger, Michael Carchia, John J. Irwin, B. Shoichet
- Chemistry, Medicine
- Journal of medicinal chemistry
- 20 June 2012
A key metric to assess molecular docking remains ligand enrichment against challenging decoys. Whereas the directory of useful decoys (DUD) has been widely used, clear areas for optimization have… Expand
Relating protein pharmacology by ligand chemistry
- Michael J. Keiser, B. Roth, B. Armbruster, P. Ernsberger, J. J. Irwin, B. Shoichet
- Chemistry, Medicine
- Nature Biotechnology
- 1 February 2007
The identification of protein function based on biological information is an area of intense research. Here we consider a complementary technique that quantitatively groups and relates proteins based… Expand
ZINC ? A Free Database of Commercially Available Compounds for Virtual Screening.
- J. J. Irwin, B. Shoichet
- Chemistry
- 19 April 2005
Automated docking with grid‐based energy evaluation
- E. Meng, B. Shoichet, I. Kuntz
- Chemistry
- 1 May 1992
The ability to generate feasible binding orientations of a small molecule within a site of known structure is important for ligand design. We present a method that combines a rapid, geometric docking… Expand
Predicting new molecular targets for known drugs
- Michael J. Keiser, V. Setola, +14 authors B. Roth
- Biology, Medicine
- Nature
- 17 September 2009
Although drugs are intended to be selective, at least some bind to several physiological targets, explaining side effects and efficacy. Because many drug–target combinations exist, it would be useful… Expand
Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs.
- X. Wang, G. Minasov, B. Shoichet
- Biology, Medicine
- Journal of molecular biology
- 28 June 2002
Pressured by antibiotic use, resistance enzymes have been evolving new activities. Does such evolution have a cost? To investigate this question at the molecular level, clinically isolated mutants of… Expand
Rapid behavior—based identification of neuroactive small molecules in the zebrafish
- David Kokel, J. Bryan, +10 authors R. Peterson
- Biology, Medicine
- Nature chemical biology
- 23 December 2009
Neuroactive small molecules are indispensable tools for treating mental illnesses and dissecting nervous system function. However, it has been difficult to discover novel neuroactive drugs. Here, we… Expand
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