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DNA-Encoded Compound Libraries as Open Source: A Powerful Pathway to New Drugs

Lerner, Richard A ; Brenner, Sydney

Angewandte Chemie (International ed. in English), 24 January 2017, Vol.56(5), pp.1164-1165 [Peer Reviewed Journal]

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Directed Chemical Evolution with an Outsized Genetic Code

Krusemark, Casey J ; Tilmans, Nicolas P ; Brown, Patrick O ; Harbury, Pehr B

PloS one, 2016, Vol.11(8), pp.e0154765 [Peer Reviewed Journal]

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A molecular dynamics-based algorithm for evaluating the glycosaminoglycan mimicking potential of synthetic, homogenous, sulfated small molecules

Nagarajan, Balaji ; Sankaranarayanan, Nehru Viji ; Patel, Bhaumik B ; Desai, Umesh R

PloS one, 2017, Vol.12(2), pp.e0171619 [Peer Reviewed Journal]

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A Novel Class of Small Molecule Agonists with Preference for Human over Mouse TLR4 Activation

Marshall, Jason D ; Heeke, Darren S ; Rao, Eileen ; Maynard, Sean K ; Hornigold, David ; Mccrae, Christopher ; Fraser, Neil ; Tovchigrechko, Andrey ; Yu, Li ; Williams, Nicola ; King, Sarah ; Cooper, Martin E ; Hajjar, Adeline M ; Woo, Jennifer C

PloS one, 2016, Vol.11(10), pp.e0164632 [Peer Reviewed Journal]

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Template CoMFA Generates Single 3D-QSAR Models that, for Twelve of Twelve Biological Targets, Predict All ChEMBL-Tabulated Affinities

Cramer, Richard D

PloS one, 2015, Vol.10(6), pp.e0129307 [Peer Reviewed Journal]

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Discovery of Small-Molecule Modulators of the Human Y4 Receptor

Sliwoski, Gregory ; Schubert, Mario ; Stichel, Jan ; Weaver, David ; Beck-Sickinger, Annette G ; Meiler, Jens

PloS one, 2016, Vol.11(6), pp.e0157146 [Peer Reviewed Journal]

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A High-Content Assay Enables the Automated Screening and Identification of Small Molecules with Specific ALDH1A1-Inhibitory Activity

Yasgar, Adam ; Titus, Steven A ; Wang, Yuhong ; Danchik, Carina ; Yang, Shyh-Ming ; Vasiliou, Vasilis ; Jadhav, Ajit ; Maloney, David J ; Simeonov, Anton ; Martinez, Natalia J

PloS one, 2017, Vol.12(1), pp.e0170937 [Peer Reviewed Journal]

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Fast docking on graphics processing units via Ray-Casting

Khar, Karen R ; Goldschmidt, Lukasz ; Karanicolas, John

PloS one, 2013, Vol.8(8), pp.e70661 [Peer Reviewed Journal]

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HIV-1 and Human PEG10 Frameshift Elements Are Functionally Distinct and Distinguished by Novel Small Molecule Modulators

Cardno, Tony S ; Shimaki, Yosuke ; Sleebs, Brad E ; Lackovic, Kurt ; Parisot, John P ; Moss, Rebecca M ; Crowe-Mcauliffe, Caillan ; Mathew, Suneeth F ; Edgar, Christina D ; Kleffmann, Torsten ; Tate, Warren P

PloS one, 2015, Vol.10(10), pp.e0139036 [Peer Reviewed Journal]

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In silico mechanistic profiling to probe small molecule binding to sulfotransferases

Martiny, Virginie Y ; Carbonell, Pablo ; Lagorce, David ; Villoutreix, Bruno O ; Moroy, Gautier ; Miteva, Maria A

PloS one, 2013, Vol.8(9), pp.e73587 [Peer Reviewed Journal]

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Exploratory analysis of kinetic solubility measurements of a small molecule library

Guha, Rajarshi ; Dexheimer, Thomas S ; Kestranek, Aimee N ; Jadhav, Ajit ; Chervenak, Andrew M ; Ford, Michael G ; Simeonov, Anton ; Roth, Gregory P ; Thomas, Craig J

Bioorganic & medicinal chemistry, 01 July 2011, Vol.19(13), pp.4127-34 [Peer Reviewed Journal]

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Multicomponent Reaction Design in the Quest for Molecular Complexity and Diversity

Ruijter, Eelco ; Scheffelaar, Rachel ; Orru, Romano V A

Angewandte Chemie, Jul 4, 2011, Vol.50(28), pp.6234-46 [Peer Reviewed Journal]

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Chemical probes and drug leads from advances in synthetic planning and methodology

Gerry, Christopher J ; Schreiber, Stuart L

Nature reviews. Drug discovery, May 2018, Vol.17(5), pp.333-352 [Peer Reviewed Journal]

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Streamlining Chemical Probe Discovery: Libraries of "Fully Functionalized" Small Molecules for Phenotypic Screening

Oeljeklaus, Julian ; Kaschani, Farnusch ; Kaiser, Markus

Angewandte Chemie, Jan 28, 2013, Vol.52(5), pp.1368-70 [Peer Reviewed Journal]

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Library enhancement through the wisdom of crowds

Hack, Michael D ; Rassokhin, Dmitrii N ; Buyck, Christophe ; Seierstad, Mark ; Skalkin, Andrew ; Ten Holte, Peter ; Jones, Todd K ; Mirzadegan, Taraneh ; Agrafiotis, Dimitris K

Journal of chemical information and modeling, 27 December 2011, Vol.51(12), pp.3275-86 [Peer Reviewed Journal]

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Aliphatic C-H Oxidations for Late-Stage Functionalization

White, M Christina ; Zhao, Jinpeng

Journal of the American Chemical Society, 31 October 2018, Vol.140(43), pp.13988-14009 [Peer Reviewed Journal]

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Checking the STEP-Associated Trafficking and Internalization of Glutamate Receptors for Reduced Cognitive Deficits: A Machine Learning Approach-Based Cheminformatics Study and Its Application for Drug Repurposing

Jamal, Salma ; Goyal, Sukriti ; Shanker, Asheesh ; Grover, Abhinav

PloS one, 2015, Vol.10(6), pp.e0129370 [Peer Reviewed Journal]

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Global analysis reveals families of chemical motifs enriched for HERG inhibitors

Du, Fang ; Babcock, Joseph J ; Yu, Haibo ; Zou, Beiyan ; Li, Min

PloS one, 2015, Vol.10(2), pp.e0118324 [Peer Reviewed Journal]

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19
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Increasing the Endoplasmic Reticulum Pool of the F508del Allele of the Cystic Fibrosis Transmembrane Conductance Regulator Leads to Greater Folding Correction by Small Molecule Therapeutics

Chung, W Joon ; Goeckeler-Fried, Jennifer L ; Havasi, Viktoria ; Chiang, Annette ; Rowe, Steven M ; Plyler, Zackery E ; Hong, Jeong S ; Mazur, Marina ; Piazza, Gary A ; Keeton, Adam B ; White, E Lucile ; Rasmussen, Lynn ; Weissman, Allan M ; Denny, R Aldrin ; Brodsky, Jeffrey L ; Sorscher, Eric J

PloS one, 2016, Vol.11(10), pp.e0163615 [Peer Reviewed Journal]

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20
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Chemical Library Screening and Structure-Function Relationship Studies Identify Bisacodyl as a Potent and Selective Cytotoxic Agent Towards Quiescent Human Glioblastoma Tumor Stem-Like Cells

Zeniou, Maria ; Fève, Marie ; Mameri, Samir ; Dong, Jihu ; Salomé, Christophe ; Chen, Wanyin ; El-Habr, Elias A ; Bousson, Fanny ; Sy, Mohamadou ; Obszynski, Julie ; Boh, Alexandre ; Villa, Pascal ; Assad Kahn, Suzana ; Didier, Bruno ; Bagnard, Dominique ; Junier, Marie-Pierre ; Chneiweiss, Hervé ; Haiech, Jacques ; Hibert, Marcel ; Kilhoffer, Marie-Claude

PloS one, 2015, Vol.10(8), pp.e0134793 [Peer Reviewed Journal]

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21
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Novel small-molecule inhibitors of hepatitis C virus entry block viral spread and promote viral clearance in cell culture

Coburn, Glen A ; Fisch, Danielle N ; Moorji, Sameer M ; De Muys, Jean-Marc ; Murga, Jose D ; Paul, Dorothy ; Provoncha, Kathleen P ; Rotshteyn, Yakov ; Han, Amy Q ; Qian, Dapeng ; Maddon, Paul J ; Olson, William C

PloS one, 2012, Vol.7(4), pp.e35351 [Peer Reviewed Journal]

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22
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Discovery of diverse small molecule chemotypes with cell-based PKD1 inhibitory activity

Sharlow, Elizabeth R ; Mustata Wilson, Gabriela ; Close, David ; Leimgruber, Stephanie ; Tandon, Manuj ; Reed, Robyn B ; Shun, Tong Ying ; Wang, Q Jane ; Wipf, Peter ; Lazo, John S

PloS one, 2011, Vol.6(10), pp.e25134 [Peer Reviewed Journal]

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23
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An in silico analysis of the binding modes and binding affinities of small molecule modulators of PDZ-peptide interactions

Tiwari, Garima ; Mohanty, Debasisa

PloS one, 2013, Vol.8(8), pp.e71340 [Peer Reviewed Journal]

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24
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Highly Promiscuous Small Molecules from Biological Screening Assays Include Many Pan-Assay Interference Compounds but Also Candidates for Polypharmacology

Gilberg, Erik ; Jasial, Swarit ; Stumpfe, Dagmar ; Dimova, Dilyana ; Bajorath, Jürgen

Journal of medicinal chemistry, 23 November 2016, Vol.59(22), pp.10285-10290 [Peer Reviewed Journal]

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25
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SSC: a tool for constructing libraries for systematic screening of conformers

Ling, Sanliang ; Gutowski, Maciej

Journal of computational chemistry, 15 July 2011, Vol.32(9), pp.2047-54 [Peer Reviewed Journal]

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26
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Optimized Lennard-Jones Parameters for Druglike Small Molecules

Boulanger, Eliot ; Huang, Lei ; Rupakheti, Chetan ; Mackerell, Alexander D ; Roux, Benoît

Journal of chemical theory and computation, 12 June 2018, Vol.14(6), pp.3121-3131 [Peer Reviewed Journal]

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27
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Investigating the dynamic aspects of drug-protein recognition through a combination of MD and NMR analyses: implications for the development of protein-protein interaction inhibitors

Meli, Massimiliano ; Pagano, Katiuscia ; Ragona, Laura ; Colombo, Giorgio

PloS one, 2014, Vol.9(5), pp.e97153 [Peer Reviewed Journal]

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28
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Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function

Grover, Prerna ; Shi, Haibin ; Baumgartner, Matthew ; Camacho, Carlos J ; Smithgall, Thomas E

PloS one, 2015, Vol.10(7), pp.e0133590 [Peer Reviewed Journal]

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29
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Hit-to-lead development of the chamigrane endoperoxide merulin A for the treatment of African sleeping sickness

Navarro, Gabriel ; Chokpaiboon, Supchar ; De Muylder, Geraldine ; Bray, Walter M ; Nisam, Sean C ; Mckerrow, James H ; Pudhom, Khanitha ; Linington, Roger G

PloS one, 2012, Vol.7(9), pp.e46172 [Peer Reviewed Journal]

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30
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Identification of small molecule inhibitors of PTPσ through an integrative virtual and biochemical approach

Martin, Katie R ; Narang, Pooja ; Xu, Yong ; Kauffman, Audra L ; Petit, Joachim ; Xu, H Eric ; Meurice, Nathalie ; Mackeigan, Jeffrey P

PloS one, 2012, Vol.7(11), pp.e50217 [Peer Reviewed Journal]

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31
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Computational screening of the human TF-glycome provides a structural definition for the specificity of anti-tumor antibody JAA-F11

Tessier, Matthew B ; Grant, Oliver C ; Heimburg-Molinaro, Jamie ; Smith, David ; Jadey, Snehal ; Gulick, Andrew M ; Glushka, John ; Deutscher, Susan L ; Rittenhouse-Olson, Kate ; Woods, Robert J

PloS one, 2013, Vol.8(1), pp.e54874 [Peer Reviewed Journal]

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32
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Design, Synthesis and Structure-Activity Relationship Studies of Novel Survivin Inhibitors with Potent Anti-Proliferative Properties

Xiao, Min ; Wang, Jin ; Lin, Zongtao ; Lu, Yan ; Li, Zhenmei ; White, Stephen W ; Miller, Duane D ; Li, Wei

PloS one, 2015, Vol.10(6), pp.e0129807 [Peer Reviewed Journal]

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Novel virtual screening approach for the discovery of human tyrosinase inhibitors

Ai, Ni ; Welsh, William J ; Santhanam, Uma ; Hu, Hong ; Lyga, John

PloS one, 2014, Vol.9(11), pp.e112788 [Peer Reviewed Journal]

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Identification of Novel Small Molecule Inhibitors of Oncogenic RET Kinase

Moccia, Marialuisa ; Liu, Qingsong ; Guida, Teresa ; Federico, Giorgia ; Brescia, Annalisa ; Zhao, Zheng ; Choi, Hwan Geun ; Deng, Xianming ; Tan, Li ; Wang, Jinhua ; Billaud, Marc ; Gray, Nathanael S ; Carlomagno, Francesca ; Santoro, Massimo

PloS one, 2015, Vol.10(6), pp.e0128364 [Peer Reviewed Journal]

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35
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A general approach to differential sensing using synthetic molecular receptors

Umali, Alona P ; Anslyn, Eric V

Current opinion in chemical biology, December 2010, Vol.14(6), pp.685-92 [Peer Reviewed Journal]

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Selective killing of cancer cells by a small molecule targeting the stress response to ROS

Raj, Lakshmi ; Ide, Takao ; Gurkar, Aditi ; Foley, Michael ; Schenone, Monica ; Li, Xiaoyu ; Tolliday, Nicola ; Golub, Todd ; Carr, Steven ; Shamji, Alykhan ; Stern, Andrew ; Mandinova, Anna ; Schreiber, Stuart ; Lee, Sam

Nature, Jul 14, 2011, Vol.475(7355), pp.231-4 [Peer Reviewed Journal]

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37