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

One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are synthesized. In this Roadmap, we describe the launch of Critical Assessment of Computational Hit-finding Experiments (CACHE), a public benchmarking project...

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Published in:	Nature reviews. Chemistry Vol. 6; no. 4; pp. 287 - 295
Main Authors:	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.
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 01.04.2022 Nature Publishing Group Springer Nature
Subjects:	631/154 639/638 Algorithms Analytical Chemistry Benchmarks Biochemistry Chemistry Chemistry and Materials Science Chemistry/Food Science Computational chemistry Experiments Inorganic Chemistry Organic Chemistry Physical Chemistry Predictions Proteins Roadmap
ISSN:	2397-3358, 2397-3358
Online Access:	Get full text
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Abstract	One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are synthesized. In this Roadmap, we describe the launch of Critical Assessment of Computational Hit-finding Experiments (CACHE), a public benchmarking project to compare and improve small-molecule hit-finding algorithms through cycles of prediction and experimental testing. Participants will predict small-molecule binders for new and biologically relevant protein targets representing different prediction scenarios. Predicted compounds will be tested rigorously in an experimental hub, and all predicted binders as well as all experimental screening data, including the chemical structures of experimentally tested compounds, will be made publicly available and not subject to any intellectual property restrictions. The ability of a range of computational approaches to find novel binders will be evaluated, compared and openly published. CACHE will launch three new benchmarking exercises every year. The outcomes will be better prediction methods, new small-molecule binders for target proteins of importance for fundamental biology or drug discovery and a major technological step towards achieving the goal of Target 2035, a global initiative to identify pharmacological probes for all human proteins. Critical Assessment of Computational Hit-finding Experiments (CACHE) is a public benchmarking project to compare and improve computational small-molecule hit-finding approaches through cycles of prediction, compound synthesis and experimental testing. By that, CACHE will enable a more efficient and effective approach to hit identification and drug discovery.
AbstractList	One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are synthesized. In this Roadmap, we describe the launch of Critical Assessment of Computational Hit-finding Experiments (CACHE), a public benchmarking project to compare and improve small molecule hit-finding algorithms through cycles of prediction and experimental testing. Participants will predict small molecule binders for new and biologically relevant protein targets representing different prediction scenarios. Predicted compounds will be tested rigorously in an experimental hub, and all predicted binders as well as all experimental screening data, including the chemical structures of experimentally tested compounds, will be made publicly available, and not subject to any intellectual property restrictions. The ability of a range of computational approaches to find novel binders will be evaluated, compared, and openly published. CACHE will launch 3 new benchmarking exercises every year. The outcomes will be better prediction methods, new small molecule binders for target proteins of importance for fundamental biology or drug discovery, and a major technological step towards achieving the goal of Target 2035, a global initiative to identify pharmacological probes for all human proteins.One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are synthesized. In this Roadmap, we describe the launch of Critical Assessment of Computational Hit-finding Experiments (CACHE), a public benchmarking project to compare and improve small molecule hit-finding algorithms through cycles of prediction and experimental testing. Participants will predict small molecule binders for new and biologically relevant protein targets representing different prediction scenarios. Predicted compounds will be tested rigorously in an experimental hub, and all predicted binders as well as all experimental screening data, including the chemical structures of experimentally tested compounds, will be made publicly available, and not subject to any intellectual property restrictions. The ability of a range of computational approaches to find novel binders will be evaluated, compared, and openly published. CACHE will launch 3 new benchmarking exercises every year. The outcomes will be better prediction methods, new small molecule binders for target proteins of importance for fundamental biology or drug discovery, and a major technological step towards achieving the goal of Target 2035, a global initiative to identify pharmacological probes for all human proteins. One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are synthesized. In this Roadmap, we describe the launch of Critical Assessment of Computational Hit-finding Experiments (CACHE), a public benchmarking project to compare and improve small molecule hit-finding algorithms through cycles of prediction and experimental testing. Participants will predict small molecule binders for new and biologically relevant protein targets representing different prediction scenarios. Predicted compounds will be tested rigorously in an experimental hub, and all predicted binders as well as all experimental screening data, including the chemical structures of experimentally tested compounds, will be made publicly available, and not subject to any intellectual property restrictions. The ability of a range of computational approaches to find novel binders will be evaluated, compared, and openly published. CACHE will launch 3 new benchmarking exercises every year. The outcomes will be better prediction methods, new small molecule binders for target proteins of importance for fundamental biology or drug discovery, and a major technological step towards achieving the goal of Target 2035, a global initiative to identify pharmacological probes for all human proteins. One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are synthesized. In this Roadmap, we describe the launch of Critical Assessment of Computational Hit-finding Experiments (CACHE), a public benchmarking project to compare and improve small-molecule hit-finding algorithms through cycles of prediction and experimental testing. Participants will predict small-molecule binders for new and biologically relevant protein targets representing different prediction scenarios. Predicted compounds will be tested rigorously in an experimental hub, and all predicted binders as well as all experimental screening data, including the chemical structures of experimentally tested compounds, will be made publicly available and not subject to any intellectual property restrictions. The ability of a range of computational approaches to find novel binders will be evaluated, compared and openly published. CACHE will launch three new benchmarking exercises every year. The outcomes will be better prediction methods, new small-molecule binders for target proteins of importance for fundamental biology or drug discovery and a major technological step towards achieving the goal of Target 2035, a global initiative to identify pharmacological probes for all human proteins.Critical Assessment of Computational Hit-finding Experiments (CACHE) is a public benchmarking project to compare and improve computational small-molecule hit-finding approaches through cycles of prediction, compound synthesis and experimental testing. By that, CACHE will enable a more efficient and effective approach to hit identification and drug discovery. One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are synthesized. In this Roadmap, we describe the launch of Critical Assessment of Computational Hit-finding Experiments (CACHE), a public benchmarking project to compare and improve small-molecule hit-finding algorithms through cycles of prediction and experimental testing. Participants will predict small-molecule binders for new and biologically relevant protein targets representing different prediction scenarios. Predicted compounds will be tested rigorously in an experimental hub, and all predicted binders as well as all experimental screening data, including the chemical structures of experimentally tested compounds, will be made publicly available and not subject to any intellectual property restrictions. The ability of a range of computational approaches to find novel binders will be evaluated, compared and openly published. CACHE will launch three new benchmarking exercises every year. The outcomes will be better prediction methods, new small-molecule binders for target proteins of importance for fundamental biology or drug discovery and a major technological step towards achieving the goal of Target 2035, a global initiative to identify pharmacological probes for all human proteins. Critical Assessment of Computational Hit-finding Experiments (CACHE) is a public benchmarking project to compare and improve computational small-molecule hit-finding approaches through cycles of prediction, compound synthesis and experimental testing. By that, CACHE will enable a more efficient and effective approach to hit identification and drug discovery. Not provided.
Author	Riley, Patrick Gilson, Michael K. Jansen, Johanna M. Saikatendu, Kumar Singh Muegge, Ingo Rousseaux, Sophie A. L. Vedadi, Masoud Amaro, Rommie E. Morgan, Maxwell R. Ackloo, Suzanne Hillisch, Alexander Lessel, Uta Ecker, Gerhard F. Oprea, Tudor I. Bologa, Cristian G. Kuhn, Daniel Willson, Timothy M. Irwin, John J. Betz, Ulrich A. K. Dunham, Ian Perry, Benjamin G. Todd, Matthew H. Volkamer, Andrea Santhakumar, Vijayaratnam Hessler, Gerhard Batey, Robert A. Chodera, John D. Azevedo, Hatylas Edfeldt, Kristina Al-awar, Rima Cornell, Wendy D. Moult, John Edwards, Aled M. Leach, Andrew R. Scholten, Cora Arrowsmith, Cheryl H. Lee, Alpha A. Gordijo, Claudia R. Hogner, Anders Bengio, Yoshua Schapira, Matthieu
AuthorAffiliation	13 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK 6 Aché Laboratórios Farmacêuticos, Guarulhos, São Paulo, Brazil 10 Department of Internal Medicine, University of New Mexico School of Medicine, University of New Mexico Albuquerque, Albuquerque, NM, USA 15 Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria 11 Computational and Systems Biology Program Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA 27 Institute for Bioscience and Biotechnology Research, Rockville, MD, USA 25 Department of Physics, University of Cambridge, Cambridge, UK 8 Mila, University of Montreal, Québec, Canada 1 Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada 21 Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA 37 Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina
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BackLink	https://www.ncbi.nlm.nih.gov/pubmed/35783295$$D View this record in MEDLINE/PubMed https://www.osti.gov/biblio/1982142$$D View this record in Osti.gov
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Copyright	Springer Nature Limited 2022 Springer Nature Limited 2022.
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CorporateAuthor	Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
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Snippet	One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are synthesized. In... Not provided.
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SubjectTerms	631/154 639/638 Algorithms Analytical Chemistry Benchmarks Biochemistry Chemistry Chemistry and Materials Science Chemistry/Food Science Computational chemistry Experiments Inorganic Chemistry Organic Chemistry Physical Chemistry Predictions Proteins Roadmap
Title	CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding
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