Zobrazeno 1 - 10
of 358
pro vyhledávání: '"Shoichet, BK"'
Autor:
Shoichet, Brian, Barelier, S, Eidam, O, Fish, I, Hollander, J, Figaroa, F, Nachane, R, Irwin, JJ, Shoichet, BK, Siegal, G
Publikováno v:
Shoichet, Brian; Barelier, S; Eidam, O; Fish, I; Hollander, J; Figaroa, F; et al.(2014). Increasing chemical space coverage by combining empirical and computational fragment screens. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/4gs2r4cx
Most libraries for fragment-based drug discovery are restricted to 1,000-10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverag
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=od_______325::c004eac8d709504245dc55cd858d1f33
http://www.escholarship.org/uc/item/4gs2r4cx
http://www.escholarship.org/uc/item/4gs2r4cx
Autor:
Babbitt, Patricia, Sali, Andrej, Jacobson, Matthew, Shoichet, Brian, Dong, GQ, Calhoun, S, Fan, H, Kalyanaraman, C, Branch, MC, Mashiyama, ST, London, N, Jacobson, MP, Babbitt, PC, Shoichet, BK
Publikováno v:
Babbitt, Patricia; Sali, Andrej; Jacobson, Matthew; Shoichet, Brian; Dong, GQ; Calhoun, S; et al.(2014). Prediction of substrates for glutathione transferases by covalent docking. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/6p17g9gg
Enzymes in the glutathione transferase (GST) superfamily catalyze the conjugation of glutathione (GSH) to electrophilic substrates. As a consequence they are involved in a number of key biological processes, including protection of cells against chem
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=od_______325::460ebc32804e7e9268f20463a6a5f0d2
http://www.escholarship.org/uc/item/6p17g9gg
http://www.escholarship.org/uc/item/6p17g9gg
Autor:
Shoichet, Brian, Owen, SC, Doak, AK, Ganesh, AN, Nedyalkova, L, McLaughlin, CK, Shoichet, BK, Shoichet, MS
Publikováno v:
Shoichet, Brian; Owen, SC; Doak, AK; Ganesh, AN; Nedyalkova, L; McLaughlin, CK; et al.(2014). Colloidal drug formulations can explain "bell-shaped" concentration-response curves. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/8g1474cn
Drug efficacy does not always increase sigmoidally with concentration, which has puzzled the community for decades. Unlike standard sigmoidal curves, bell-shaped concentration-response curves suggest more complex biological effects, such as multiple-
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=od_______325::07b00bce0752cbe1de7dc40fcf5b459d
http://www.escholarship.org/uc/item/8g1474cn
http://www.escholarship.org/uc/item/8g1474cn
Publikováno v:
Shoichet, Brian; Barelier, S; Boyce, SE; Fish, I; Fischer, M; Goodin, DB; et al.(2013). Roles for Ordered and Bulk Solvent in Ligand Recognition and Docking in Two Related Cavities. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/76p0r2ch
A key challenge in structure-based discovery is accounting for modulation of protein-ligand interactions by ordered and bulk solvent. To investigate this, we compared ligand binding to a buried cavity in Cytochrome c Peroxidase (CcP), where affinity
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=od_______325::06c47bec54cb676f6499c6e807d2c56c
http://www.escholarship.org/uc/item/76p0r2ch
http://www.escholarship.org/uc/item/76p0r2ch
Autor:
Shoichet, Brian, Weiss, DR, Ahn, S, Sassano, MF, Kleist, A, Zhu, X, Strachan, R, Roth, BL, Lefkowitz, RJ, Shoichet, BK
Publikováno v:
Shoichet, Brian; Weiss, DR; Ahn, S; Sassano, MF; Kleist, A; Zhu, X; et al.(2013). Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/0286z2v7
A prospective, large library virtual screen against an activated β2-adrenergic receptor (β2AR) structure returned potent agonists to the exclusion of inverse-agonists, providing the first complement to the previous virtual screening campaigns again
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=od_______325::aa285edc944e25eb312ace1b1edf88d8
http://www.escholarship.org/uc/item/0286z2v7
http://www.escholarship.org/uc/item/0286z2v7
Publikováno v:
Shoichet, Brian; Merski, M; & Shoichet, BK. (2013). The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/1rk2m8bt
Simplified model binding sites allow one to isolate entangled terms in molecular energy functions. Here, we investigate the effects on ligand recognition of the introduction of a histidine into a hydrophobic cavity in lysozyme. We docked 656040 molec
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=od_______325::6084e211dac924ef7026e4f34f2c8dca
http://www.escholarship.org/uc/item/1rk2m8bt
http://www.escholarship.org/uc/item/1rk2m8bt
Publikováno v:
Shoichet, Brian; Sassano, MF; Doak, AK; Roth, BL; & Shoichet, BK. (2013). Colloidal aggregation causes inhibition of G protein-coupled receptors. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/67v7w96d
Colloidal aggregation is the dominant mechanism for artifactual inhibition of soluble proteins, and controls against it are now widely deployed. Conversely, investigating this mechanism for membrane-bound receptors has proven difficult. Here we inves
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=od_______325::41e84dc8f19b8c49217c06395569527b
http://www.escholarship.org/uc/item/67v7w96d
http://www.escholarship.org/uc/item/67v7w96d
Publikováno v:
Shoichet, Brian; Lin, H; Sassano, MF; Roth, BL; & Shoichet, BK. (2013). A pharmacological organization of G protein-coupled receptors. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/12p556c5
Protein classification typically uses structural, sequence or functional similarity. Here we introduce an orthogonal method that organizes proteins by ligand similarity, focusing on the class A G-protein-coupled receptor (GPCR) protein family. Compar
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=od_______325::e04943e58e81051f8fb744c5b0138748
http://www.escholarship.org/uc/item/12p556c5
http://www.escholarship.org/uc/item/12p556c5
Publikováno v:
Shoichet, Brian; Owen, SC; Doak, AK; Wassam, P; Shoichet, MS; & Shoichet, BK. (2012). Colloidal aggregation affects the efficacy of anticancer drugs in cell culture. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/5vz3v12t
Many small molecules, including bioactive molecules and approved drugs, spontaneously form colloidal aggregates in aqueous solution at micromolar concentrations. Though it is widely accepted that aggregation leads to artifacts in screens for ligands
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=od_______325::ce32752a0df1b185ab0de9e18a26e0d9
http://www.escholarship.org/uc/item/5vz3v12t
http://www.escholarship.org/uc/item/5vz3v12t
Publikováno v:
Shoichet, Brian; Mysinger, MM; Carchia, M; Irwin, JJ; & Shoichet, BK. (2012). Directory of useful decoys, enhanced (DUD-E): Better ligands and decoys for better benchmarking. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/3j66v5w2
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 emerged. Here we describe an improved benchmarking set
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=od_______325::25ba4ac95d6ae8c60ced62e964d3f796
http://www.escholarship.org/uc/item/3j66v5w2
http://www.escholarship.org/uc/item/3j66v5w2