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The binding complexes formed by proteins and small molecule ligands are ubiquitous and critical to life.
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Risi Kondor and John Lafferty · 2002
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“The PDBbind database: methodologies and updates”
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“TM-align: a protein structure alignment algorithm based on the TM-score”
Yang Zhang and Jeffrey Skolnick · 2005
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John Irwin and Brian Shoichet · 2005
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“TM-align: a protein structure alignment algorithm based on the TM-score”
Yang Zhang and Jeffrey Skolnick · 2005
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“TM-align: a protein structure alignment algorithm based on the TM-score”
Yang Zhang and Jeffrey Skolnick · 2005
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“The PDBbind database: methodologies and updates”
Renxiao Wang et al · 2005
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“TM-align: a protein structure alignment algorithm based on the TM-score”
Yang Zhang and Jeffrey Skolnick · 2005
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“ZINC- a free database of commercially available compounds for virtual screening”
John Irwin and Brian Shoichet · 2005
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“TM-align: a protein structure alignment algorithm based on the TM-score”
Yang Zhang and Jeffrey Skolnick · 2005
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“TM-align: a protein structure alignment algorithm based on the TM-score”
Yang Zhang and Jeffrey Skolnick · 2005
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“Dynamically driven protein allostery”
Nataliya Popovych, Shangjin Sun, Richard Ebright and Charalampos Kalodimos · 2006
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“Dynamically driven protein allostery”
Nataliya Popovych, Shangjin Sun, Richard Ebright and Charalampos Kalodimos · 2006
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“Dynamic personalities of proteins”
Katherine Henzler-Wildman and Dorothee Kern · 2007
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“BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities”
Tiqing Liu et al · 2007
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“Dynamic personalities of proteins”
Katherine Henzler-Wildman and Dorothee Kern · 2007
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“BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities”
Tiqing Liu et al · 2007
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“RosettaLigand docking with full ligand and receptor flexibility”
Ian Davis and David Baker · 2009
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“Review of statistical arbitrage, cointegration, and multivariate Ornstein-Uhlenbeck”
Attilio Meucci · 2009
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“RosettaLigand docking with full ligand and receptor flexibility”
Ian Davis and David Baker · 2009
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“RosettaLigand docking with full ligand and receptor flexibility”
Ian Davis and David Baker · 2009
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“RosettaLigand docking with full ligand and receptor flexibility”
Ian Davis and David Baker · 2009
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“Review of statistical arbitrage, cointegration, and multivariate Ornstein-Uhlenbeck”
Attilio Meucci · 2009
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“RosettaLigand docking with full ligand and receptor flexibility”
Ian Davis and David Baker · 2009
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“RosettaLigand docking with full ligand and receptor flexibility”
Ian Davis and David Baker · 2009
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“Atomic-level characterization of the structural dynamics of proteins”
David Shaw et al · 2010
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“Atomic-level characterization of the structural dynamics of proteins”
David Shaw et al · 2010
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“Open Babel: An open chemical toolbox”
Noel O’Boyle et al · 2011
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“Open Babel: An open chemical toolbox”
Noel O’Boyle et al · 2011
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“Open Babel: An open chemical toolbox”
Noel O’Boyle et al · 2011
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“Open Babel: An open chemical toolbox”
Noel O’Boyle et al · 2011
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“Antibody-enabled small-molecule drug discovery”
Alastair Lawson · 2012
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“BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions”
Jianyi Yang, Ambrish Roy and Yang Zhang · 2012
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“BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions”
Jianyi Yang, Ambrish Roy and Yang Zhang · 2012
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“BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions”
Jianyi Yang, Ambrish Roy and Yang Zhang · 2012
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“Antibody-enabled small-molecule drug discovery”
Alastair Lawson · 2012
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“BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions”
Jianyi Yang, Ambrish Roy and Yang Zhang · 2012
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“BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions”
Jianyi Yang, Ambrish Roy and Yang Zhang · 2012
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“BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions”
Jianyi Yang, Ambrish Roy and Yang Zhang · 2012
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“Allostery in disease and in drug discovery”
Ruth Nussinov and Chung-Jung Tsai · 2013
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“Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design”
William Sinko, Steffen Lindert and J McCammon · 2013
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“lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests”
Valerio Mariani, Marco Biasini, Alessandro Barbato and Torsten Schwede · 2013
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“Native contacts determine protein folding mechanisms in atomistic simulations”
Robert Best, Gerhard Hummer and William Eaton · 2013
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“Loss of constitutive activity is correlated with increased thermostability of the human adenosine A2A receptor”
Nicolas Bertheleme et al · 2013
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“RDKit: A software suite for cheminformatics, computational chemistry, and predictive modeling”
Greg Landrum · 2013
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“OpenStructure: an integrated software framework for computational structural biology”
Marco Biasini et al · 2013
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“RDKit: A software suite for cheminformatics, computational chemistry, and predictive modeling”
Greg Landrum · 2013
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“OpenStructure: an integrated software framework for computational structural biology”
Marco Biasini et al · 2013
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“Allostery in disease and in drug discovery”
Ruth Nussinov and Chung-Jung Tsai · 2013
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“Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design”
William Sinko, Steffen Lindert and J McCammon · 2013
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“lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests”
Valerio Mariani, Marco Biasini, Alessandro Barbato and Torsten Schwede · 2013
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“Native contacts determine protein folding mechanisms in atomistic simulations”
Robert Best, Gerhard Hummer and William Eaton · 2013
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“Loss of constitutive activity is correlated with increased thermostability of the human adenosine A2A receptor”
Nicolas Bertheleme et al · 2013
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“RDKit: A software suite for cheminformatics, computational chemistry, and predictive modeling”
Greg Landrum · 2013
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“OpenStructure: an integrated software framework for computational structural biology”
Marco Biasini et al · 2013
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“RDKit: A software suite for cheminformatics, computational chemistry, and predictive modeling”
Greg Landrum · 2013
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“OpenStructure: an integrated software framework for computational structural biology”
Marco Biasini et al · 2013
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“Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery”
Marcus Fischer, Ryan Coleman, James Fraser and Brian Shoichet · 2014
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“Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery”
Marcus Fischer, Ryan Coleman, James Fraser and Brian Shoichet · 2014
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“Coupling protein side-chain and backbone flexibility improves the re-design of protein-ligand specificity”
Noah Ollikainen, René de Jong and Tanja Kortemme · 2015
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“Deep unsupervised learning using nonequilibrium thermodynamics”
Jascha Sohl-Dickstein, Eric Weiss, Niru Maheswaranathan and Surya Ganguli · 2015
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“Coupling protein side-chain and backbone flexibility improves the re-design of protein-ligand specificity”
Noah Ollikainen, René de Jong and Tanja Kortemme · 2015
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“Deep unsupervised learning using nonequilibrium thermodynamics”
Jascha Sohl-Dickstein, Eric Weiss, Niru Maheswaranathan and Surya Ganguli · 2015
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“Structural mechanisms of activation and desensitization in neurotransmitter-gated ion channels”
Andrew Plested · 2016
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“Gaussian error linear units (gelus)”
Dan Hendrycks and Kevin Gimpel · 2016
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Jimmy Ba, Jamie Kiros and Geoffrey Hinton · 2016
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“Gaussian error linear units (gelus)”
Dan Hendrycks and Kevin Gimpel · 2016
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Jimmy Ba, Jamie Kiros and Geoffrey Hinton · 2016
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“Structural mechanisms of activation and desensitization in neurotransmitter-gated ion channels”
Andrew Plested · 2016
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“Gaussian error linear units (gelus)”
Dan Hendrycks and Kevin Gimpel · 2016
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Jimmy Ba, Jamie Kiros and Geoffrey Hinton · 2016
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“Gaussian error linear units (gelus)”
Dan Hendrycks and Kevin Gimpel · 2016
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Jimmy Ba, Jamie Kiros and Geoffrey Hinton · 2016
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“Protein structure determination using metagenome sequence data”
Sergey Ovchinnikov et al · 2017
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“Protein conformational flexibility modulates kinetics and thermodynamics of drug binding”
Marta Amaral et al · 2017
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“Attention is all you need”
Ashish Vaswani et al · 2017
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“PubChemQC project: a large-scale first-principles electronic structure database for data-driven chemistry”
Maho Nakata and Tomomi Shimazaki · 2017
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“PubChemQC project: a large-scale first-principles electronic structure database for data-driven chemistry”
Maho Nakata and Tomomi Shimazaki · 2017
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“Protein structure determination using metagenome sequence data”
Sergey Ovchinnikov et al · 2017
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“Protein conformational flexibility modulates kinetics and thermodynamics of drug binding”
Marta Amaral et al · 2017
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“Attention is all you need”
Ashish Vaswani et al · 2017
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“PubChemQC project: a large-scale first-principles electronic structure database for data-driven chemistry”
Maho Nakata and Tomomi Shimazaki · 2017
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“PubChemQC project: a large-scale first-principles electronic structure database for data-driven chemistry”
Maho Nakata and Tomomi Shimazaki · 2017
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“COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking”
Qi Wu, Zhenling Peng, Yang Zhang and Jianyi Yang · 2018
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“P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure”
Radoslav Krivák and David Hoksza · 2018
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“Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein”
Javier Garcı́a-Nafrı́a et al · 2018
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“A map of protein-metabolite interactions reveals principles of chemical communication”
Ilaria Piazza et al · 2018
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