CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Ackloo, Suzanne; Al-awar, Rima; Amaro, Rommie E.; Arrowsmith, Cheryl H.; Azevedo, Hatylas; Batey, Robert A.; Bengio, Yoshua; Betz, Ulrich A.  K.; Bologa, Cristian G.; Chodera, John D.; Cornell, Wendy D.; Dunham, Ian; Ecker, Gerhard F.; Edfeldt, Kristina; Edwards, Aled M.; Gilson, Michael K.; Gordijo, Claudia R.; Hessler, Gerhard; Hillisch, Alexander; Hogner, Anders; Irwin, John J.; Jansen, Johanna M.; Kuhn, Daniel; Leach, Andrew R.; Lee, Alpha A.; Lessel, Uta; Morgan, Maxwell R.; Moult, John; Muegge, Ingo; Oprea, Tudor I.; Perry, Benjamin G.; Riley, Patrick; Rousseaux, Sophie A.  L.; Saikatendu, Kumar Singh; Santhakumar, Vijayaratnam; Schapira, Matthieu; Scholten, Cora; Todd, Matthew H.; Vedadi, Masoud; Volkamer, Andrea; Willson, Timothy M.

doi:10.1038/s41570-022-00363-z

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Journal Article · 15 February 2022 · Nature Reviews Chemistry

DOI:https://doi.org/10.1038/s41570-022-00363-z· OSTI ID:1982142

; Al-awar, Rima; ; Arrowsmith, Cheryl H.; Azevedo, Hatylas; ; ; ; ; ; ; ; ; ; ; ; ; Hessler, Gerhard; ; more »

Not provided.

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC02-05CH11231

OSTI ID:: 1982142

Journal Information:: Nature Reviews Chemistry, Vol. 6, Issue 4; ISSN 2397-3358

Publisher:: Springer Nature

Country of Publication:: United States

Language:: English

References (32)

An open-source drug discovery platform enables ultra-large virtual screens Gorgulla, Christoph; Boeszoermenyi, Andras; Wang, Zi-Fu Nature, Vol. 580, Issue 7805 https://doi.org/10.1038/s41586-020-2117-z	journal	March 2020
Ultra-large library docking for discovering new chemotypes Lyu, Jiankun; Wang, Sheng; Balius, Trent E. Nature, Vol. 566, Issue 7743 https://doi.org/10.1038/s41586-019-0917-9	journal	February 2019
New Trends in Virtual Screening Walters, W. Patrick; Wang, Renxiao Journal of Chemical Information and Modeling, Vol. 60, Issue 9 https://doi.org/10.1021/acs.jcim.0c01009	journal	September 2020
Virtual Screening in the Cloud: How Big Is Big Enough? Grebner, Christoph; Malmerberg, Erik; Shewmaker, Andrew Journal of Chemical Information and Modeling, Vol. 60, Issue 9 https://doi.org/10.1021/acs.jcim.9b00779	journal	November 2019
A large-scale experiment to assess protein structure prediction methods Moult, John; Pedersen, Jan T.; Judson, Richard Proteins: Structure, Function, and Genetics, Vol. 23, Issue 3 https://doi.org/10.1002/prot.340230303	journal	November 1995
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
Accurate prediction of protein structures and interactions using a three-track neural network Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan Science, Vol. 373, Issue 6557 https://doi.org/10.1126/science.abj8754	journal	July 2021
Protein complex prediction with AlphaFold-Multimer Evans, Richard; O???Neill, Michael; Pritzel, Alexander https://doi.org/10.1101/2021.10.04.463034	preprint	March 2022
Computed structures of core eukaryotic protein complexes Humphreys, Ian R.; Pei, Jimin; Baek, Minkyung Science, Vol. 374, Issue 6573 https://doi.org/10.1126/science.abm4805	journal	December 2021
D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings Gaieb, Zied; Parks, Conor D.; Chiu, Michael Journal of Computer-Aided Molecular Design, Vol. 33, Issue 1 https://doi.org/10.1007/s10822-018-0180-4	journal	January 2019
D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies Parks, Conor D.; Gaieb, Zied; Chiu, Michael Journal of Computer-Aided Molecular Design, Vol. 34, Issue 2 https://doi.org/10.1007/s10822-020-00289-y	journal	January 2020
D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies Gaieb, Zied; Liu, Shuai; Gathiaka, Symon Journal of Computer-Aided Molecular Design, Vol. 32, Issue 1 https://doi.org/10.1007/s10822-017-0088-4	journal	December 2017
Teach–Discover–Treat (TDT): Collaborative computational drug discovery for neglected diseases Jansen, Johanna M.; Cornell, Wendy; Tseng, Y. Jane Journal of Molecular Graphics and Modelling, Vol. 38 https://doi.org/10.1016/j.jmgm.2012.07.007	journal	September 2012
Computational chemistry and drug discovery: a call to action Jansen, Johanna M.; Amaro, Rommie E.; Cornell, Wendy Future Medicinal Chemistry, Vol. 4, Issue 15 https://doi.org/10.4155/fmc.12.137	journal	October 2012
D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions Gathiaka, Symon; Liu, Shuai; Chiu, Michael Journal of Computer-Aided Molecular Design, Vol. 30, Issue 9 https://doi.org/10.1007/s10822-016-9946-8	journal	September 2016
Overview of the SAMPL5 host–guest challenge: Are we doing better? Yin, Jian; Henriksen, Niel M.; Slochower, David R. Journal of Computer-Aided Molecular Design, Vol. 31, Issue 1 https://doi.org/10.1007/s10822-016-9974-4	journal	September 2016
Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge Bannan, Caitlin C.; Burley, Kalistyn H.; Chiu, Michael Journal of Computer-Aided Molecular Design, Vol. 30, Issue 11 https://doi.org/10.1007/s10822-016-9954-8	journal	September 2016
Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge Xiong, Zhaoping; Jeon, Minji; Allaway, Robert J. PLOS Computational Biology, Vol. 17, Issue 9 https://doi.org/10.1371/journal.pcbi.1009302	journal	September 2021
ZINC20—A Free Ultralarge-Scale Chemical Database for Ligand Discovery Irwin, John J.; Tang, Khanh G.; Young, Jennifer Journal of Chemical Information and Modeling, Vol. 60, Issue 12 https://doi.org/10.1021/acs.jcim.0c00675	journal	October 2020
A white-knuckle ride of open COVID drug discovery von Delft, Frank; Calmiano, Mark; Chodera, John Nature, Vol. 594, Issue 7863 https://doi.org/10.1038/d41586-021-01571-1	journal	June 2021
Open access chemical and clinical probes to support drug discovery Edwards, Aled M.; Bountra, Chas; Kerr, David J. Nature Chemical Biology, Vol. 5, Issue 7 https://doi.org/10.1038/nchembio0709-436	journal	July 2009
Target 2035 – update on the quest for a probe for every protein Müller, Susanne; Ackloo, Suzanne; Al Chawaf, Arij RSC Medicinal Chemistry, Vol. 13, Issue 1 https://doi.org/10.1039/D1MD00228G	journal	January 2022
A Specific Mechanism of Nonspecific Inhibition McGovern, Susan L.; Helfand, Brian T.; Feng, Brian Journal of Medicinal Chemistry, Vol. 46, Issue 20 https://doi.org/10.1021/jm030266r	journal	August 2003
Seven Year Itch: Pan-Assay Interference Compounds (PAINS) in 2017—Utility and Limitations Baell, Jonathan B.; Nissink, J. Willem M. ACS Chemical Biology, Vol. 13, Issue 1 https://doi.org/10.1021/acschembio.7b00903	journal	December 2017
Badapple: promiscuity patterns from noisy evidence Yang, Jeremy J.; Ursu, Oleg; Lipinski, Christopher A. Journal of Cheminformatics, Vol. 8, Issue 1 https://doi.org/10.1186/s13321-016-0137-3	journal	May 2016
Central Nervous System Multiparameter Optimization Desirability: Application in Drug Discovery Wager, Travis T.; Hou, Xinjun; Verhoest, Patrick R. ACS Chemical Neuroscience, Vol. 7, Issue 6 https://doi.org/10.1021/acschemneuro.6b00029	journal	March 2016
Integrating Everything: The Molecule Selection Toolkit, a System for Compound Prioritization in Drug Discovery Cummins, David J.; Bell, Michael A. Journal of Medicinal Chemistry, Vol. 59, Issue 15 https://doi.org/10.1021/acs.jmedchem.5b01338	journal	March 2016
In Silico ADMET Traffic Lights as a Tool for the Prioritization of HTS Hits Lobell, Mario; Hendrix, Martin; Hinzen, Berthold ChemMedChem, Vol. 1, Issue 11 https://doi.org/10.1002/cmdc.200600168	journal	November 2006
Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties Ertl, Peter; Rohde, Bernhard; Selzer, Paul Journal of Medicinal Chemistry, Vol. 43, Issue 20 https://doi.org/10.1021/jm000942e	journal	October 2000
Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success Lovering, Frank; Bikker, Jack; Humblet, Christine Journal of Medicinal Chemistry, Vol. 52, Issue 21 https://doi.org/10.1021/jm901241e	journal	November 2009
Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping Muchmore, Steven W.; Debe, Derek A.; Metz, James T. Journal of Chemical Information and Modeling, Vol. 48, Issue 5 https://doi.org/10.1021/ci7004498	journal	April 2008
The FAIR Guiding Principles for scientific data management and stewardship Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan Scientific Data, Vol. 3, Issue 1 https://doi.org/10.1038/sdata.2016.18	journal	March 2016

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