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Shoichet Lab: Home

Recent results from the lab. D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Wang, et al., Science. Discovery of new GPCR ligands to illuminate new biology. BL Roth, JJ Irwin, BK Shoichet, Nature Chem. Biol. In silico design of novel probes for the atypical opioid receptor MRGPRX2. K Lansu, J Karpiak, et al., Nature Chem. Biol. Structure-based discovery of opioid analgesics with reduced side effects. A Manglik, H Lin, D Aryal, et al., Nature. H Lee, M Fischer, ...

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Shoichet Lab: Home | bkslab.org Reviews

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Recent results from the lab. D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Wang, et al., Science. Discovery of new GPCR ligands to illuminate new biology. BL Roth, JJ Irwin, BK Shoichet, Nature Chem. Biol. In silico design of novel probes for the atypical opioid receptor MRGPRX2. K Lansu, J Karpiak, et al., Nature Chem. Biol. Structure-based discovery of opioid analgesics with reduced side effects. A Manglik, H Lin, D Aryal, et al., Nature. H Lee, M Fischer, ...

<META> KEYWORDS

1 shoichet laboratory

2 overview

3 projects

4 people

5 publications

6 take aways

7 dock

8 dock blaster

9 zinc

10 dud e

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Shoichet Lab: Home | bkslab.org Reviews

https://bkslab.org

Recent results from the lab. D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Wang, et al., Science. Discovery of new GPCR ligands to illuminate new biology. BL Roth, JJ Irwin, BK Shoichet, Nature Chem. Biol. In silico design of novel probes for the atypical opioid receptor MRGPRX2. K Lansu, J Karpiak, et al., Nature Chem. Biol. Structure-based discovery of opioid analgesics with reduced side effects. A Manglik, H Lin, D Aryal, et al., Nature. H Lee, M Fischer, ...

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mailman.bkslab.org

mailman.docking.org Mailing Lists

Mailman.docking.org Mailing Lists. Below is a listing of all the public mailing lists on mailman.docking.org. Click on a list name to get more information about the list, or to subscribe, unsubscribe, and change the preferences on your subscription. To visit the general information page for an unadvertised list, open a URL similar to this one, but with a '/' and the list name appended. List administrators, you can visit the list admin overview page. To find the management interface for your list.

sea.bkslab.org

SEA

Similarity ensemble approach (SEA). The Similarity ensemble approach relates proteins based on the set-wise chemical similarity among their ligands. It can be used to rapidly search large compound databases and to build cross-target similarity maps. How to use SEA. You can try SEA yourself via the online SEA search tool. SEA is a collaborative project provided by the Keiser Laboratory. In the Institute for Neutrodegenerative Diseases. Laboratories in the Department of Pharmaceutical Chemistry.

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bkslab.org

1

Shoichet Lab: Publications

http://www.bkslab.org/publications.php

Farrell MS, McCorvy JD, Huang XP, Urban DJ, White KL, Giguere PM, Doak AK, Bernstein AI, Stout KA, Park SM, Rodriguiz RM, Gray BW, Hyatt WS, Norwood AP, Webster KA, Gannon BM, Miller GW, Porter JH, Shoichet BK, Fantegrossi WE, Wetsel WC, Roth BL. In Vitro. Characterization of the Alkaloid Nuciferine. PloS ONE. 3), e0150602 (2016). [ Pubmed. Irwin J, Shoichet BK. Docking Screens for Novel Ligands Conferring New Biology. J. Med. Chem. 4), 1580-1598 (2016). [ Pubmed. UCSF Pharmacy - Recent Research. Duan D,...

2

Shoichet Lab: Links

http://www.bkslab.org/links.php

Uppsala Software Factory Manuals. Relibase - Searching protein-ligand databases. SPIN - Protein Protein Interfaces. NIMH Psychoactive Drug Screening Program. Computational Molecular Biology at NIH. Digital library of UCSF.

3

Shoichet Lab: People

http://www.bkslab.org/people.php

Brian K. Shoichet, Ph. D. Shoichet, channeling William F. Buckley, offers a vigorous defense of docking and high-throughput screening for the graduate student retreat (interviewedby Emily Crawford, channeling Steven Colbert). Shoichet, in a public interview, tries desperately to sound less confused than he actually is. Recent reviews, book chapters, and papers:. Shoichet BK. No free energy lunch. Nat Biotechnol. 10), 1109-10 (2007). [ Pubmed. 13-14), 607-15 (2006). [ Pubmed. 40-43 (2004). [ Pubmed. I am ...

4

Shoichet Lab: Take aways

http://www.bkslab.org/take-away.php

Model Systems and Decoys can be used to test and ideally improve Molecular Docking Scoring Functions. Here we provide two types of decoys which address two major problems in molecular docking "Hit List" Decoys are experimentally determined non-binders that are predicted to bind, and "Geometric" Decoys are known ligands predicted to bind with an incorrect configuration-greater than 3 angstrom RMSD from the crystallographic pose-in the binding site. Binders / Apparent non-binders:. T4 lysozyme L99A binders.

5

Shoichet Lab: Projects

http://www.bkslab.org/projects.php

We are currently pursuing four major parallel and overlapping projects in the lab:. Design and Experimental Testing of Docking Algorithms. Discovery of Novel Inhibitors by Docking. Structure, Function, and Inhibition of β-lactamases. A Relationship Between Enzyme Stability and Function.

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zinc15.docking.org

ZINC

http://zinc15.docking.org/rings/home

About ZINC 15 Resources. Current Status / In Progress. Like us on Facebook. Rings are members of substances. And a common way of thinking about molecules in medicinal chemistry. Why are ZINC results "estimates"? Supported by NIGMS via GM71896. Questions, Discussion, Bug reports, Feature requests. Labs and UC Regents. Originally generated at 2017-03-08 23:43:26.297703 in 0.05034s on zinc15.docking.org using ZINC15 0.20161202.1.

zinc15.docking.org

ZINC

http://zinc15.docking.org/atccodes/home

About ZINC 15 Resources. Current Status / In Progress. Like us on Facebook. Describe drugs by the organ or system they act on and their therapeutic, chemical or pharmacological properties. Why are ZINC results "estimates"? Supported by NIGMS via GM71896. Questions, Discussion, Bug reports, Feature requests. Labs and UC Regents. Originally generated at 2017-03-08 23:43:26.320918 in 0.03615s on zinc15.docking.org using ZINC15 0.20161202.1.

zinc15.docking.org

ZINC

http://zinc15.docking.org/observations/home

About ZINC 15 Resources. Current Status / In Progress. Like us on Facebook. And vice versa) The best affinity observation for each gene - substance pair is captured in activity. Why are ZINC results "estimates"? Supported by NIGMS via GM71896. Questions, Discussion, Bug reports, Feature requests. Labs and UC Regents. Originally generated at 2017-03-08 23:43:26.333394 in 0.04765s on zinc15.docking.org using ZINC15 0.20161202.1.

zinc15.docking.org

ZINC

http://zinc15.docking.org/predictions/home

About ZINC 15 Resources. Current Status / In Progress. Like us on Facebook. SEA predictions connect substances. And vice versa), using the Similarity Ensemble Approach. Why are ZINC results "estimates"? Supported by NIGMS via GM71896. Questions, Discussion, Bug reports, Feature requests. Labs and UC Regents. Originally generated at 2017-03-08 23:43:26.296261 in 0.06050s on zinc15.docking.org using ZINC15 0.20161202.1.

zinc15.docking.org

ZINC

http://zinc15.docking.org/genes/home

About ZINC 15 Resources. Current Status / In Progress. Like us on Facebook. Within specific organism classes. Using the Uniprot Gene symbol. Why are ZINC results "estimates"? Supported by NIGMS via GM71896. Questions, Discussion, Bug reports, Feature requests. Labs and UC Regents. Originally generated at 2017-03-08 23:43:26.334645 in 0.02099s on zinc15.docking.org using ZINC15 0.20161202.1.

zinc15.docking.org

ZINC

http://zinc15.docking.org/majorclasses/home

About ZINC 15 Resources. Current Status / In Progress. Like us on Facebook. Major target classes group target subclasses. Which in turn group genes. Which in turn group orthologs. Which in turn contain activities. Why are ZINC results "estimates"? Supported by NIGMS via GM71896. Questions, Discussion, Bug reports, Feature requests. Labs and UC Regents. Originally generated at 2017-03-08 23:43:26.336487 in 0.04435s on zinc15.docking.org using ZINC15 0.20161202.1.

zinc15.docking.org

ZINC

http://zinc15.docking.org/organisms/home

About ZINC 15 Resources. Current Status / In Progress. Like us on Facebook. Is classified by the organism class to which it belongs. Why are ZINC results "estimates"? Supported by NIGMS via GM71896. Questions, Discussion, Bug reports, Feature requests. Labs and UC Regents. Originally generated at 2017-03-08 23:43:26.331635 in 0.04134s on zinc15.docking.org using ZINC15 0.20161202.1.

zinc15.docking.org

ZINC

http://zinc15.docking.org/subclasses/home

About ZINC 15 Resources. Current Status / In Progress. Like us on Facebook. Target subclasses are finer divisions of major target classes. Why are ZINC results "estimates"? Supported by NIGMS via GM71896. Questions, Discussion, Bug reports, Feature requests. Labs and UC Regents. Originally generated at 2017-03-08 23:43:26.297037 in 0.05249s on zinc15.docking.org using ZINC15 0.20161202.1.

zinc15.docking.org

ZINC

http://zinc15.docking.org/substances/home

About ZINC 15 Resources. Current Status / In Progress. Like us on Facebook. Resolve Substances From Text/File. Substances are molecules that are loaded from catalogs. They have observations against genes, the best of which is captured by activities. Why are ZINC results "estimates"? Supported by NIGMS via GM71896. Questions, Discussion, Bug reports, Feature requests. Labs and UC Regents.

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bkslab.org

Shoichet Lab: Home

Recent results from the lab. D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Wang, et al., Science. Discovery of new GPCR ligands to illuminate new biology. BL Roth, JJ Irwin, BK Shoichet, Nature Chem. Biol. In silico design of novel probes for the atypical opioid receptor MRGPRX2. K Lansu, J Karpiak, et al., Nature Chem. Biol. Structure-based discovery of opioid analgesics with reduced side effects. A Manglik, H Lin, D Aryal, et al., Nature. H Lee, M Fischer, ...

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