Brian K. Shoichet: search on Z-Library

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1

A Model Binding Site for Testing Scoring Functions in Molecular Docking

Binqing Q. Wei, Walter A. Baase, Larry H. Weaver, Brian W. Matthews, Brian K. Shoichet

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 2.17 MB

english, 2002

2

Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4)

Cameron, Ryan T., Coleman, Ryan G., Day, Jon P., Yalla, Krishna C., Houslay, Miles D., Adams, David R., Shoichet, Brian K., Baillie, George S.

Journal:

Biochemical Pharmacology

Year:

2013

Language:

english

File:

PDF, 1.23 MB

english, 2013

3

Structure-based activity prediction for an enzyme of unknown function

Hermann, Johannes C., Marti-Arbona, Ricardo, Fedorov, Alexander A., Fedorov, Elena, Almo, Steven C., Shoichet, Brian K., Raushel, Frank M.

Journal:

Year:

2007

Language:

english

File:

PDF, 751 KB

english, 2007

4

Molecular docking and ligand specificity in fragment-based inhibitor discovery

Chen, Yu, Shoichet, Brian K

Journal:

Nature Chemical Biology

Year:

2009

Language:

english

File:

PDF, 454 KB

english, 2009

5

Structural identification of a hotspot on CFTR for potentiation

Liu, Fangyu, Zhang, Zhe, Levit, Anat, Levring, Jesper, Touhara, Kouki K., Shoichet, Brian K., Chen, Jue

Journal:

Year:

2019

Language:

english

File:

PDF, 1.97 MB

english, 2019

6

Automated docking with grid-based energy evaluation

Elaine C. Meng, Brian K. Shoichet, Irwin D. Kuntz

Journal:

Journal of Computational Chemistry

Year:

1992

Language:

english

File:

PDF, 1.39 MB

english, 1992

7

Prediction and Evaluation of Protein Farnesyltransferase Inhibition by Commercial Drugs

DeGraw, Amanda J., Keiser, Michael J., Ochocki, Joshua D., Shoichet, Brian K., Distefano, Mark D.

Journal:

Journal of Medicinal Chemistry

Year:

2010

Language:

english

File:

PDF, 3.32 MB

english, 2010

8

Rapid Context-Dependent Ligand Desolvation in Molecular Docking

Mysinger, Michael M., Shoichet, Brian K.

Journal:

Journal of Chemical Information and Modeling

Year:

2010

Language:

english

File:

PDF, 4.85 MB

english, 2010

9

Docking screens for novel ligands conferring new biology

Irwin, John J., Shoichet, Brian K.

Journal:

Journal of Medicinal Chemistry

Year:

2016

Language:

english

File:

PDF, 2.09 MB

english, 2016

10

Crystal Structure of an LSD-Bound Human Serotonin Receptor

Wacker, Daniel, Wang, Sheng, McCorvy, John D., Betz, Robin M., Venkatakrishnan, A.J., Levit, Anat, Lansu, Katherine, Schools, Zachary L., Che, Tao, Nichols, David E., Shoichet, Brian K., Dror, Ron O.,

Journal:

Year:

2017

Language:

english

File:

PDF, 5.17 MB

english, 2017

11

Relating protein pharmacology by ligand chemistry

Keiser, Michael J, Roth, Bryan L, Armbruster, Blaine N, Ernsberger, Paul, Irwin, John J, Shoichet, Brian K

Journal:

Nature Biotechnology

Year:

2007

Language:

english

File:

PDF, 696 KB

english, 2007

12

Small-molecule aggregates inhibit amyloid polymerization

Feng, Brian Y, Toyama, Brandon H, Wille, Holger, Colby, David W, Collins, Sean R, May, Barnaby C H, Prusiner, Stanley B, Weissman, Jonathan, Shoichet, Brian K

Journal:

Nature Chemical Biology

Year:

2008

Language:

english

File:

PDF, 445 KB

english, 2008

13

Benchmarking Sets for Molecular Docking

Huang, Niu, Shoichet, Brian K., Irwin, John J.

Journal:

Journal of Medicinal Chemistry

Year:

2006

Language:

english

File:

PDF, 913 KB

english, 2006

14

Interactions of Oral Molecular Excipients with Breast Cancer Resistance Protein, BCRP

Zou, Ling, Pottel, Joshua, Khuri, Natalia, Ngo, Huy X, Ni, Zhanglin, Tsakalozou, Eleftheria, Warren, Mark S, Huang, Yong, Shoichet, Brian K., Giacomini, Kathleen M.

Journal:

Molecular Pharmaceutics

Year:

2020

Language:

english

File:

PDF, 937 KB

english, 2020

15

Computational Methods for Medicinal Chemistry

Bajorath, Jürgen, Jiang, Hualiang, Shoichet, Brian K., Walters, W. Patrick

Journal:

Journal of Medicinal Chemistry

Year:

2015

Language:

english

File:

PDF, 117 KB

english, 2015

16

Far away from the lamppost

Oprea, Tudor I., Jan, Lily, Johnson, Gary L., Roth, Bryan L., Ma’ayan, Avi, Schürer, Stephan, Shoichet, Brian K., Sklar, Larry A., McManus, Michael T.

Journal:

Year:

2018

Language:

english

File:

PDF, 280 KB

english, 2018

17

Increasing Chemical Space Coverage by Combining Empirical and Computational Fragment Screens

Barelier, Sarah, Eidam, Oliv, Fish, Inbar, Hollander, Johan, Figaroa, Francis, Nachane, Ruta, Irwin, John J., Shoichet, Brian K., Siegal, Gregg

Journal:

ACS Chemical Biology

Year:

2014

Language:

english

File:

PDF, 2.15 MB

english, 2014

18

Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps

Leach, Andrew R., Shoichet, Brian K., Peishoff, Catherine E.

Journal:

Journal of Medicinal Chemistry

Year:

2006

Language:

english

File:

PDF, 46 KB

english, 2006

19

Matching chemistry and shape in molecular docking

Shoichet, Brian K., Kuntz, Irwin D.

Journal:

Protein Engineering Design and Selection

Year:

1993

Language:

english

File:

PDF, 5.49 MB

english, 1993

20

Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking

Wan, Xiaobo, Yang, Tangpo, Cuesta, Adolfo, Pang, Xiaming, Balius, Trent E., Irwin, John, Shoichet, Brian K., Taunton, Jack

Journal:

Journal of the American Chemical Society

Year:

2020

Language:

english

File:

PDF, 759 KB

english, 2020

21

Structural Bases of Stability–function Tradeoffs in Enzymes

Beth M Beadle, Brian K Shoichet

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 526 KB

english, 2002

22

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

Mysinger, Michael M., Carchia, Michael, Irwin, John. J., Shoichet, Brian K.

Journal:

Journal of Medicinal Chemistry

Year:

2012

Language:

english

File:

PDF, 4.61 MB

english, 2012

23

Ligand discovery from a dopamine D3 receptor homology model and crystal structure

Carlsson, Jens, Coleman, Ryan G, Setola, Vincent, Irwin, John J, Fan, Hao, Schlessinger, Avner, Sali, Andrej, Roth, Bryan L, Shoichet, Brian K

Journal:

Nature Chemical Biology

Year:

2011

Language:

english

File:

PDF, 2.81 MB

english, 2011

24

Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

Fischer, Marcus, Coleman, Ryan G., Fraser, James S., Shoichet, Brian K.

Journal:

Nature Chemistry

Year:

2014

Language:

english

File:

PDF, 4.84 MB

english, 2014

25

A hydrogel-based stem cell delivery system to treat retinal degenerative diseases

Brian G. Ballios, Michael J. Cooke, Derek van der Kooy, Molly S. Shoichet

Journal:

Year:

2010

Language:

english

File:

PDF, 943 KB

english, 2010

26

Structure-Based Discovery of a Novel, Noncovalent Inhibitor of AmpC β-Lactamase

Rachel A. Powers, Federica Morandi, Brian K. Shoichet

Journal:

Year:

2002

Language:

english

File:

PDF, 314 KB

english, 2002

27

Structure and Dynamics of CTX-M Enzymes Reveal Insights into Substrate Accommodation by Extended-spectrum β-Lactamases

Julien Delmas, Yu Chen, Fabio Prati, Frédéric Robin, Brian K. Shoichet, Richard Bonnet

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 1.57 MB

english, 2008

28

Design, Synthesis, Crystal Structures, and Antimicrobial Activity of Sulfonamide Boronic Acids as β-Lactamase Inhibitors

Eidam, Oliv, Romagnoli, Chiara, Caselli, Emilia, Babaoglu, Kerim, Pohlhaus, Denise Teotico, Karpiak, Joel, Bonnet, Richard, Shoichet, Brian K., Prati, Fabio

Journal:

Journal of Medicinal Chemistry

Year:

2010

Language:

english

File:

PDF, 3.19 MB

english, 2010

29

Targeting Class A and C Serine β-Lactamases with a Broad-Spectrum Boronic Acid Derivative

Tondi, Donatella, Venturelli, Alberto, Bonnet, Richard, Pozzi, Cecilia, Shoichet, Brian K., Costi, Maria Paola

Journal:

Journal of Medicinal Chemistry

Year:

2014

Language:

english

File:

PDF, 12.81 MB

english, 2014

30

Stability for Function Trade-Offs in the Enolase Superfamily “Catalytic Module” †,‡

Nagatani, Ray A., Gonzalez, Ana, Shoichet, Brian K., Brinen, Linda S., Babbitt, Patricia C.

Journal:

Year:

2007

Language:

english

File:

PDF, 290 KB

english, 2007

31

Ligand solvation in molecular docking

Brian K. Shoichet, Andrew R. Leach, Irwin D. Kuntz

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 1.30 MB

english, 1999

32

Structural study of phenyl boronic acid derivatives as AmpC β-lactamase inhibitors

Donatella Tondi, Samuele Calò, Brian K. Shoichet, Maria Paola Costi

Journal:

Bioorganic & Medicinal Chemistry Letters

Year:

2010

Language:

english

File:

PDF, 1.03 MB

english, 2010

33

Erratum

Beth M Beadle, Indi Trehan, Pamela J Focia, Brian K Shoichet

Journal:

Year:

2002

File:

PDF, 15 KB

2002

34

Structure-Based Approach for Binding Site Identification on AmpC β-Lactamase

Powers, Rachel A., Shoichet, Brian K.

Journal:

Journal of Medicinal Chemistry

Year:

2002

Language:

english

File:

PDF, 917 KB

english, 2002

35

Protein docking and complementarity

Brian K. Shoichet, Irwin D. Kuntz

Journal:

Journal of Molecular Biology

Year:

1991

Language:

english

File:

PDF, 10.54 MB

english, 1991

36

The Chemical Basis of Pharmacology

Keiser, Michael J., Irwin, John J., Shoichet, Brian K.

Journal:

Year:

2010

Language:

english

File:

PDF, 4.16 MB

english, 2010

37

Structure-based discovery and in-parallel optimization of novelcompetitive inhibitors of thymidylate synthase

Donatella Tondi, Ursula Slomczynska, M. Paola Costi, D. Martin Watterson, Stefano Ghelli, Brian K. Shoichet

Journal:

Chemistry & Biology

Year:

1999

Language:

english

File:

PDF, 3.77 MB

english, 1999

38

Using Steric Hindrance to Design New Inhibitors of Class C β-Lactamases

Indi Trehan, Federica Morandi, Larry C Blaszczak, Brian K Shoichet

Journal:

Chemistry & Biology

Year:

2002

Language:

english

File:

PDF, 351 KB

english, 2002

39

Structure-based drug screening for G-protein-coupled receptors

Brian K. Shoichet, Brian K. Kobilka

Journal:

Trends in Pharmacological Sciences

Year:

2012

Language:

english

File:

PDF, 769 KB

english, 2012

40

Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site

Rocklin, Gabriel J., Boyce, Sarah E., Fischer, Marcus, Fish, Inbar, Mobley, David L., Shoichet, Brian K., Dill, Ken A.

Journal:

Journal of Molecular Biology

Year:

2013

Language:

english

File:

PDF, 1.83 MB

english, 2013

41

Structure, Function, and Inhibition along the Reaction Coordinate of CTX-M β-Lactamases

Chen, Yu, Shoichet, Brian, Bonnet, Richard

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 610 KB

english, 2005

42

Resolution of Chiral Phosphate, Phosphonate, and Phosphinate Esters by an Enantioselective Enzyme Library

Nowlan, Charity, Li, Yingchun, Hermann, Johannes C., Evans, Timothy, Carpenter, Joseph, Ghanem, Eman, Shoichet, Brian K., Raushel, Frank M.

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 374 KB

english, 2006

43

[Drug Discovery Series] Virtual Screening in Drug Discovery Volume 1 || Addressing the Virtual Screening Challenge

Alvarez, Juan, Shoichet, Brian

Year:

2005

Language:

english

File:

PDF, 833 KB

english, 2005

44

Ultra-large library docking for discovering new chemotypes

Lyu, Jiankun, Wang, Sheng, Balius, Trent E., Singh, Isha, Levit, Anat, Moroz, Yurii S., O’Meara, Matthew J., Che, Tao, Algaa, Enkhjargal, Tolmachova, Kateryna, Tolmachev, Andrey A., Shoichet, Brian K.

Journal:

Year:

2019

File:

PDF, 14.16 MB

2019

45

Docking and chemoinformatic screens for new ligands and targets

Peter Kolb, Rafaela S Ferreira, John J Irwin, Brian K Shoichet

Journal:

Current Opinion in Biotechnology

Year:

2009

Language:

english

File:

PDF, 532 KB

english, 2009

46

Flexible ligand docking using conformational ensembles

David M. Lorber, Brian K. Shoichet

Journal:

Protein Science

Year:

1998

Language:

english

File:

PDF, 5.69 MB

english, 1998

47

Structural Milestones in the Reaction Pathway of an Amide Hydrolase: Substrate, Acyl, and Product Complexes of Cephalothin with AmpC β-Lactamase

Beth M Beadle, Indi Trehan, Pamela J Focia, Brian K Shoichet

Journal:

Year:

2002

Language:

english

File:

PDF, 438 KB

english, 2002

48

Structure-Based Enhancement of Boronic Acid-Based Inhibitors of AmpC β-Lactamase

Weston, G. Scott, Blázquez, Jesús, Baquero, Fernando, Shoichet, Brian K.

Journal:

Journal of Medicinal Chemistry

Year:

1998

Language:

english

File:

PDF, 390 KB

english, 1998

49

Atomic Resolution Structures of CTX-M β-Lactamases: Extended Spectrum Activities from Increased Mobility and Decreased Stability

Yu Chen, Julien Delmas, Jacques Sirot, Brian Shoichet, Richard Bonnet

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 800 KB

english, 2005

50

Structural Consequences of the Inhibitor-Resistant Ser130Gly Substitution in TEM β-Lactamase †,‡

Thomas, Veena L., Golemi-Kotra, Dasantila, Kim, Choonkeun, Vakulenko, Sergei B., Mobashery, Shahriar, Shoichet, Brian K.

Journal:

Year:

2005

Language:

english

File:

PDF, 443 KB

english, 2005

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