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Tavakoli M, Miller RJ, Angel MC, Pfeiffer MA, Gutman ES, Mood AD, Van Vranken D, Baldi P. PMechDB: A Public Database of Elementary Polar Reaction Steps. J Chem Inf Model 2024; 64:1975-1983. [PMID: 38483315 PMCID: PMC10966657 DOI: 10.1021/acs.jcim.3c01810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/26/2024]
Abstract
Most online chemical reaction databases are not publicly accessible or are fully downloadable. These databases tend to contain reactions in noncanonicalized formats and often lack comprehensive information regarding reaction pathways, intermediates, and byproducts. Within the few publicly available databases, reactions are typically stored in the form of unbalanced, overall transformations with minimal interpretability of the underlying chemistry. These limitations present significant obstacles to data-driven applications including the development of machine learning models. As an effort to overcome these challenges, we introduce PMechDB, a publicly accessible platform designed to curate, aggregate, and share polar chemical reaction data in the form of elementary reaction steps. Our initial version of PMechDB consists of over 100,000 such steps. In the PMechDB, all reactions are stored as canonicalized and balanced elementary steps, featuring accurate atom mapping and arrow-pushing mechanisms. As an online interactive database, PMechDB provides multiple interfaces that enable users to search, download, and upload chemical reactions. We anticipate that the public availability of PMechDB and its standardized data representation will prove beneficial for chemoinformatics research and education and the development of data-driven, interpretable models for predicting reactions and pathways. PMechDB platform is accessible online at https://deeprxn.ics.uci.edu/pmechdb.
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Affiliation(s)
- Mohammadamin Tavakoli
- Department
of Computer Science, University of California,
Irvine, Irvine, California 92697, United States
| | - Ryan J. Miller
- Department
of Computer Science, University of California,
Irvine, Irvine, California 92697, United States
| | - Mirana Claire Angel
- Department
of Computer Science, University of California,
Irvine, Irvine, California 92697, United States
| | - Michael A. Pfeiffer
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Eugene S. Gutman
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Aaron D. Mood
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - David Van Vranken
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Pierre Baldi
- Department
of Computer Science, University of California,
Irvine, Irvine, California 92697, United States
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Attri P, Choi EH, Kwon GC, Bhatia R, Gaur J, Arora B, Kim IT. Single-walled Carbon Nanotube-triethylammonium Ionic Liquid as a New Catalytic System for Michael Reaction. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.10.3035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Attri P, Jha I, Choi EH, Venkatesu P. Variation in the structural changes of myoglobin in the presence of several protic ionic liquid. Int J Biol Macromol 2014; 69:114-23. [DOI: 10.1016/j.ijbiomac.2014.05.032] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 11/27/2022]
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