SureChEMBL: a large-scale, chemically annotated patent document database

Papadatos, George; Davies, Mark; Dedman, Nathan; Chambers, Jon; Gaulton, Anna; Siddle, James; Koks, Richard; Irvine, Sean A.; Pettersson, Joe; Goncharoff, Nicholas T.; Hersey, Anne; Overington, John P.

doi:10.1093/nar/gkv1253

Cited by 185 publications

(176 citation statements)

References 26 publications

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“…PubChem currently offers links between about 6 million patent documents and more than 16 million unique chemical structures, with over 336 million chemical substance-patent links covering U.S., European, and World Intellectual Property Organization (WIPO) patent documents published since 1800. This information is contributed by various organizations, including IBM, 67 SureChEMBL (formerly known as SureChem), 68,69 NextMove Software, 70 SCRIPDB, 71 and BindingDB. 57 …”

Section: An Overview Of Pubchem As a Resource For Virtual Screeningmentioning

confidence: 99%

Getting the most out of PubChem for virtual screening

Kim

2016

Expert Opinion on Drug Discovery

135

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Introduction With the emergence of the “big data” era, the biomedical research community has great interest in exploiting publicly available chemical information for drug discovery. PubChem is an example of public databases that provide a large amount of chemical information free of charge. Areas covered This article provides an overview of how PubChem’s data, tools, and services can be used for virtual screening and reviews recent publications that discuss important aspects of exploiting PubChem for drug discovery. Expert opinion PubChem offers comprehensive chemical information useful for drug discovery. It also provides multiple programmatic access routes, which are essential to build automated virtual screening pipelines that exploit PubChem data. In addition, PubChemRDF allows users to download PubChem data and load them into a local computing facility, facilitating data integration between PubChem and other resources. PubChem resources have been used in many studies for developing bioactivity and toxicity prediction models, discovering polypharmacologic (multi-target) ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). These studies demonstrate the usefulness of PubChem as a key resource for computer-aided drug discovery and related area.

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Section: An Overview Of Pubchem As a Resource For Virtual Screeningmentioning

confidence: 99%

Getting the most out of PubChem for virtual screening

Kim

2016

Expert Opinion on Drug Discovery

135

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“…Their characteristics, including number of rows (n), columns (m), nonzeros (nnz), and mean row/column length (μ r /μ c ), are detailed in [40] database, which includes a large set of chemical compounds automatically extracted from text, images, and attachments of patent documents. SC-5M, SC-1M, SC-500K, and SC-100K are random subsets of 5E+6, 1E+6, 5E+5, and 1E+5 compounds, respectively, from the SC-11.5M dataset.…”

Section: Datasetsmentioning

confidence: 99%

Efficient identification of Tanimoto nearest neighbors

Anastasiu

Karypis

2017

Int J Data Sci Anal

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Tanimoto, or extended Jaccard, is an important similarity measure which has seen prominent use in fields such as data mining and chemoinformatics. Many of the existing state-of-the-art methods for market basket analysis, plagiarism and anomaly detection, compound database search, and ligand-based virtual screening rely heavily on identifying Tanimoto nearest neighbors. Given the rapidly increasing size of data that must be analyzed, new algorithms are needed that can speed up nearest neighbor search, while at the same time providing reliable results. While many search algorithms address the complexity of the task by retrieving only some of the nearest neighbors, we propose a method that finds all of the exact nearest neighbors efficiently by leveraging recent advances in similarity search filtering. We provide tighter filtering bounds for the Tanimoto coefficient and show that our method, TAPNN, greatly outperforms existing base-

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“…[1][2][3][4][5][6] application providing an adequate user interface. In previous work, we have shown the viability of this approach by making the generated mappings of a variety of databases available through desktop and web applications.…”

Section: Introductionmentioning

confidence: 99%

Exploring Drugbank in Virtual Reality Chemical Space

Probst¹,

Reymond²

2018

Preprint

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The recent general availability of low-cost virtual reality headsets, and accompanying 3D engine support, presents an opportunity to bring the concept of chemical space into virtual environments. While virtual reality applications represent a category of widespread tools in other fields, their use in the visualization and exploration of abstract data such as chemical spaces has been experimental. In our previous work we established the concept of interactive 2D maps of chemical spaces, followed by interactive web-based 3D visualizations, culminating in the interactive web-based 3D visualization of extremely large chemical spaces. Virtual reality chemical spaces are a natural extension of these concepts. As 2D and 3D embeddings, and projections of high-dimensional chemical fingerprint spaces were shown to be valuable tools in chemical space visualization and exploration, existing pipelines of data mining and preparation can be extended to be used in virtual reality applications. Here we present an application based on the Unity engine and the virtual reality toolkit (VRTK), allowing for the interactive exploration of chemical space populated by Drugbank compounds in virtual reality. The source code of the application as well as the most recent build are available on GitHub (https://github.com/reymond-group/virtual-reality-chemical-space).2

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SureChEMBL: a large-scale, chemically annotated patent document database

Cited by 185 publications

References 26 publications

Getting the most out of PubChem for virtual screening

Getting the most out of PubChem for virtual screening

Efficient identification of Tanimoto nearest neighbors

Exploring Drugbank in Virtual Reality Chemical Space

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