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Advances in Computational Medicinal Chemistry: A Reflection on the Evolution of the Field and Perspective Going Forward

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

Journal of medicinal chemistry, 12 May 2016, Vol.59(9), pp.4033-4 [Peer Reviewed Journal]

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Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics

Lee, Hyelee ; Fischer, Marcus ; Shoichet, Brian K ; Liu, Shih-Yuan

Journal of the American Chemical Society, 21 September 2016, Vol.138(37), pp.12021-4 [Peer Reviewed Journal]

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Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone

Wang, Sheng ; Che, Tao ; Levit, Anat ; Shoichet, Brian K ; Wacker, Daniel ; Roth, Bryan L

Nature, 08 March 2018, Vol.555(7695), pp.269-273 [Peer Reviewed Journal]

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Docking Screens for Novel Ligands Conferring New Biology

Irwin, John J ; Shoichet, Brian K

Journal of medicinal chemistry, 12 May 2016, Vol.59(9), pp.4103-20 [Peer Reviewed Journal]

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The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition

Merski, Matthew ; Shoichet, Brian K

Journal of medicinal chemistry, 11 April 2013, Vol.56(7), pp.2874-84 [Peer Reviewed Journal]

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6
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Enzymatic deamination of the epigenetic base N-6-methyladenine

Kamat, Siddhesh S ; Fan, Hao ; Sauder, J Michael ; Burley, Stephen K ; Shoichet, Brian K ; Sali, Andrej ; Raushel, Frank M

Journal of the American Chemical Society, 23 February 2011, Vol.133(7), pp.2080-3 [Peer Reviewed Journal]

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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 of medicinal chemistry, 26 July 2012, Vol.55(14), pp.6582-94 [Peer Reviewed Journal]

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Computational Methods for Medicinal Chemistry
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Computational Methods for Medicinal Chemistry

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

Journal of Medicinal Chemistry, 02/12/2015, Vol.58(3), pp.1019-1019 [Peer Reviewed Journal]

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Large-scale prediction and testing of drug activity on side-effect targets

Lounkine, Eugen ; Keiser, Michael J ; Whitebread, Steven ; Mikhailov, Dmitri ; Hamon, Jacques ; Jenkins, Jeremy L ; Lavan, Paul ; Weber, Eckhard ; Doak, Allison K ; Côté, Serge ; Shoichet, Brian K ; Urban, Laszlo

Nature, 10 June 2012, Vol.486(7403), pp.361-7 [Peer Reviewed Journal]

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10
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Structure-guided discovery of new deaminase enzymes

Hitchcock, Daniel S ; Fan, Hao ; Kim, Jungwook ; Vetting, Matthew ; Hillerich, Brandan ; Seidel, Ronald D ; Almo, Steven C ; Shoichet, Brian K ; Sali, Andrej ; Raushel, Frank M

Journal of the American Chemical Society, 18 September 2013, Vol.135(37), pp.13927-33 [Peer Reviewed Journal]

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11
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Substrate deconstruction and the nonadditivity of enzyme recognition

Barelier, Sarah ; Cummings, Jennifer A ; Rauwerdink, Alissa M ; Hitchcock, Daniel S ; Farelli, Jeremiah D ; Almo, Steven C ; Raushel, Frank M ; Allen, Karen N ; Shoichet, Brian K

Journal of the American Chemical Society, 21 May 2014, Vol.136(20), pp.7374-82 [Peer Reviewed Journal]

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12
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Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking

Fan, Hao ; Hitchcock, Daniel S ; Seidel, Ronald D ; Hillerich, Brandan ; Lin, Henry ; Almo, Steven C ; Sali, Andrej ; Shoichet, Brian K ; Raushel, Frank M

Journal of the American Chemical Society, 16 January 2013, Vol.135(2), pp.795-803 [Peer Reviewed Journal]

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13
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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 of medicinal chemistry, 26 June 2014, Vol.57(12), pp.5449-58 [Peer Reviewed Journal]

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14
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Colloidal aggregation causes inhibition of G protein-coupled receptors

Sassano, Maria F ; Doak, Allison K ; Roth, Bryan L ; Shoichet, Brian K

Journal of medicinal chemistry, 28 March 2013, Vol.56(6), pp.2406-14 [Peer Reviewed Journal]

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15
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D dopamine receptor high-resolution structures enable the discovery of selective agonists

Wang, Sheng ; Wacker, Daniel ; Levit, Anat ; Che, Tao ; Betz, Robin M ; Mccorvy, John D ; Venkatakrishnan, A J ; Huang, Xi-Ping ; Dror, Ron O ; Shoichet, Brian K ; Roth, Bryan L

Science (New York, N.Y.), 20 October 2017, Vol.358(6361), pp.381-386 [Peer Reviewed Journal]

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16
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Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction

O’meara, Matthew J ; Ballouz, Sara ; Shoichet, Brian K ; Gillis, Jesse Tang, Haixu (editor)

PLoS ONE, 2016, Vol.11(7) [Peer Reviewed Journal]

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17
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The chemical basis of pharmacology

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

Biochemistry, 07 December 2010, Vol.49(48), pp.10267-76 [Peer Reviewed Journal]

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18
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Functional annotation and three-dimensional structure of an incorrectly annotated dihydroorotase from cog3964 in the amidohydrolase superfamily

Ornelas, Argentina ; Korczynska, Magdalena ; Ragumani, Sugadev ; Kumaran, Desigan ; Narindoshvili, Tamari ; Shoichet, Brian K ; Swaminathan, Subramanyam ; Raushel, Frank M

Biochemistry, 08 January 2013, Vol.52(1), pp.228-38 [Peer Reviewed Journal]

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19
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An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation

Minasov, George ; Wang, Xiaojun ; Shoichet, Brian K

Journal of the American Chemical Society, 15 May 2002, Vol.124(19), pp.5333-40 [Peer Reviewed Journal]

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20
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Covalent Docking of Large Libraries for the Discovery of Chemical Probes

London, Nir ; Miller, Rand M ; Irwin, John J ; Eidam, Oliv ; Gibold, Lucie ; Bonnet, Richard ; Shoichet, Brian K ; Taunton, Jack

Biophysical Journal, 28 January 2014, Vol.106(2), pp.264a-264a [Peer Reviewed Journal]

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21
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Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking

Rettenmaier, T Justin ; Fan, Hao ; Karpiak, Joel ; Doak, Allison ; Sali, Andrej ; Shoichet, Brian K ; Wells, James A

Journal of medicinal chemistry, 22 October 2015, Vol.58(20), pp.8285-8291 [Peer Reviewed Journal]

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22
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Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets

Weiss, Dahlia R ; Karpiak, Joel ; Huang, Xi-Ping ; Sassano, Maria F ; Lyu, Jiankun ; Roth, Bryan L ; Shoichet, Brian K

Journal of medicinal chemistry, 09 August 2018, Vol.61(15), pp.6830-6845 [Peer Reviewed Journal]

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23
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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 of Molecular Biology, 15 November 2013, Vol.425(22), pp.4569-4583 [Peer Reviewed Journal]

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24
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Roles for Ordered and Bulk Solvent in Ligand Recognition and Docking in Two Related Cavities

Barelier, Sarah ; Boyce, Sarah E ; Fish, Inbar ; Fischer, Marcus ; Goodin, David B ; Shoichet, Brian K Najmanovich, Rafael Josef (editor)

PLoS ONE, 2013, Vol.8(7) [Peer Reviewed Journal]

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25
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Identification of Novel Smoothened Ligands Using Structure-Based Docking

Lacroix, Celine ; Fish, Inbar ; Torosyan, Hayarpi ; Parathaman, Pranavan ; Irwin, John J ; Shoichet, Brian K ; Angers, Stephane Xie, Jingwu (editor)

PLoS ONE, 2016, Vol.11(8) [Peer Reviewed Journal]

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26
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Ligand pose and orientational sampling in molecular docking

Coleman, Ryan G ; Carchia, Michael ; Sterling, Teague ; Irwin, John J ; Shoichet, Brian K

PloS one, 2013, Vol.8(10), pp.e75992 [Peer Reviewed Journal]

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27
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Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones

Xiang, Dao Feng ; Kolb, Peter ; Fedorov, Alexander A ; Xu, Chengfu ; Fedorov, Elena V ; Narindoshivili, Tamari ; Williams, Howard J ; Shoichet, Brian K ; Almo, Steven C ; Raushel, Frank M

Biochemistry, 28 February 2012, Vol.51(8), pp.1762-73 [Peer Reviewed Journal]

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28
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Colloid formation by drugs in simulated intestinal fluid

Doak, Allison K ; Wille, Holger ; Prusiner, Stanley B ; Shoichet, Brian K

Journal of medicinal chemistry, 27 May 2010, Vol.53(10), pp.4259-65 [Peer Reviewed Journal]

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29
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Structural Bases for Stability–Function Tradeoffs in Antibiotic Resistance

Thomas, Veena L ; Mcreynolds, Andrea C ; Shoichet, Brian K

Journal of Molecular Biology, 12 February 2010, Vol.396(1), pp.47-59 [Peer Reviewed Journal]

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30
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Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors

Coan, Kristin E D ; Shoichet, Brian K

Journal of the American Chemical Society, 23 July 2008, Vol.130(29), pp.9606-12 [Peer Reviewed Journal]

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31
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Structure-based discovery of selective positive allosteric modulators of antagonists for the M2 muscarinic acetylcholine receptor

Korczynska, Magdalena ; Clark, Mary J. ; Valant, Celine ; Xu, Jun ; Moo, Ee Von ; Albold, Sabine ; Weiss, Dahlia R. ; Torosyan, Hayarpi ; Huang, Weijiao ; Kruse, Andrew C. ; Lyda, Brent R. ; May, Lauren T. ; Baltos, Jo-Anne ; Sexton, Patrick M. ; Kobilka, Brian K. ; Christopoulos, Arthur ; Shoichet, Brian K. ; Sunahara, Roger K.

Korczynska, M., M. J. Clark, C. Valant, J. Xu, E. V. Moo, S. Albold, D. R. Weiss, et al. 2018. “Structure-based discovery of selective positive allosteric modulators of antagonists for the M2 muscarinic acetylcholine receptor.” Proceedings of the National Academy of Sciences of the United States of America 115 (10): E2419-E2428. doi:10.1073/pnas.1718037115. http://dx.doi.org/10.1073/pnas.1718037115. [Peer Reviewed Journal]

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32
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Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists

Liu, Hongtao ; Hofmann, Josefa ; Fish, Inbar ; Schaake, Benjamin ; Eitel, Katrin ; Bartuschat, Amelie ; Kaindl, Jonas ; Rampp, Hannelore ; Banerjee, Ashutosh ; Hübner, Harald ; Clark, Mary J ; Vincent, Sandra G ; Fisher, John T ; Heinrich, Markus R ; Hirata, Kunio ; Liu, Xiangyu ; Sunahara, Roger K ; Shoichet, Brian K ; Kobilka, Brian K ; Gmeiner, Peter

Proceedings of the National Academy of Sciences of the United States of America, 20 November 2018, Vol.115(47), pp.12046-12050 [Peer Reviewed Journal]

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33
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The acylation mechanism of CTX-M beta-lactamase at 0.88 a resolution

Chen, Yu ; Bonnet, Richard ; Shoichet, Brian K

Journal of the American Chemical Society, 02 May 2007, Vol.129(17), pp.5378-80 [Peer Reviewed Journal]

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34
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An Aggregation Advisor for Ligand Discovery

Irwin, John J ; Duan, Da ; Torosyan, Hayarpi ; Doak, Allison K ; Ziebart, Kristin T ; Sterling, Teague ; Tumanian, Gurgen ; Shoichet, Brian K

Journal of medicinal chemistry, 10 September 2015, Vol.58(17), pp.7076-87 [Peer Reviewed Journal]

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35
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Interpreting steep dose-response curves in early inhibitor discovery

Shoichet, Brian K

Journal of medicinal chemistry, 14 December 2006, Vol.49(25), pp.7274-7 [Peer Reviewed Journal]

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36
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No free energy lunch

Shoichet, Brian K

Nature biotechnology, October 2007, Vol.25(10), pp.1109-10 [Peer Reviewed Journal]

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The hunt for 8-oxoguanine deaminase

Hall, Richard S ; Fedorov, Alexander A ; Marti-Arbona, Ricardo ; Fedorov, Elena V ; Kolb, Peter ; Sauder, J Michael ; Burley, Stephen K ; Shoichet, Brian K ; Almo, Steven C ; Raushel, Frank M

Journal of the American Chemical Society, 17 February 2010, Vol.132(6), pp.1762-3 [Peer Reviewed Journal]

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