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      • Record: found
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      Is Open Access

      Chemsearch: collaborative compound libraries with structure-aware browsing

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          Abstract

          Summary

          Chemsearch is a cross-platform server application for developing and managing a chemical compound library and associated data files, with an interface for browsing and search that allows for easy navigation to a compound of interest, similar compounds or compounds that have desired structural properties. With provisions for access control and centralized document and data storage, Chemsearch supports collaboration by distributed teams.

          Availability and implementation

          Chemsearch is a free and open-source Flask web application that can be linked to a Google Workspace account. Source code is available at https://github.com/gem-net/chemsearch (GPLv3 license). A Docker image allowing rapid deployment is available at https://hub.docker.com/r/cgemcci/chemsearch.

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          Most cited references14

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          SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

          David Weininger (1988)
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            PubChem Substance and Compound databases

            Sunghwan Kim, Paul Thiessen, Evan Bolton … (2015)
            PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the US National Institutes of Health (NIH). For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database. This paper provides an overview of the PubChem Substance and Compound databases, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. It also gives a brief description of PubChem3D, a resource derived from theoretical three-dimensional structures of compounds in PubChem, as well as PubChemRDF, Resource Description Framework (RDF)-formatted PubChem data for data sharing, analysis and integration with information contained in other databases.
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              DataWarrior: an open-source program for chemistry aware data visualization and analysis.

              Thomas Sander, Joel Freyss, Modest von Korff … (2015)
              Drug discovery projects in the pharmaceutical industry accumulate thousands of chemical structures and ten-thousands of data points from a dozen or more biological and pharmacological assays. A sufficient interpretation of the data requires understanding, which molecular families are present, which structural motifs correlate with measured properties, and which tiny structural changes cause large property changes. Data visualization and analysis software with sufficient chemical intelligence to support chemists in this task is rare. In an attempt to contribute to filling the gap, we released our in-house developed chemistry aware data analysis program DataWarrior for free public use. This paper gives an overview of DataWarrior's functionality and architecture. Exemplarily, a new unsupervised, 2-dimensional scaling algorithm is presented, which employs vector-based or nonvector-based descriptors to visualize the chemical or pharmacophore space of even large data sets. DataWarrior uses this method to interactively explore chemical space, activity landscapes, and activity cliffs.
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                Author and article information

                Contributors
                Ivet Bahar: Role: Associate Editor
                Journal
                Journal ID (nlm-ta): Bioinform Adv
                Journal ID (iso-abbrev): Bioinform Adv
                Journal ID (publisher-id): bioadv
                Title: Bioinformatics Advances
                Publisher: Oxford University Press
                ISSN (Electronic): 2635-0041
                Publication date Collection: 2021
                Publication date (Electronic): 16 July 2021
                Publication date PMC-release: 16 July 2021
                Volume: 1
                Issue: 1
                Electronic Location Identifier: vbab008
                Affiliations
                [1 ] Department of Biostatistics, Yale University School of Public Health , New Haven, CT 06510 USA
                [2 ] Department of Chemistry, University of California Berkeley , Berkeley, CA 94705, USA
                [3 ] Department of Molecular & Cellular Biology, University of California Berkeley , Berkeley, CA 94705, USA
                Author notes
                To whom correspondence should be addressed. stephen.gaffney@ 123456yale.edu
                Author information
                https://orcid.org/0000-0002-5490-2945
                https://orcid.org/0000-0003-3469-2642
                https://orcid.org/0000-0003-2127-3932
                https://orcid.org/0000-0002-9890-3907
                Article
                Publisher ID: vbab008
                DOI: 10.1093/bioadv/vbab008
                PMC ID: 9710581
                PubMed ID: 36700113
                SO-VID: daed2615-d78b-4794-91fa-eb5004c20634
                Copyright © © The Author(s) 2021. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 13 April 2021
                Date revision received : 07 June 2021
                Date: 24 June 2021
                Date accepted : 07 July 2021
                Date: 20 August 2021
                Page count
                Pages: 3
                Funding
                Funded by: Center for Genetically Encoded Materials, an NSF Center for Chemical Innovation;
                Award ID: NSF CHE-2002182
                Categories
                Subject: Applications Note
                Subject: AcademicSubjects/SCI01060

                Data availability:

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