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      CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides

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          Abstract

          Cyclic peptides offer a range of notable advantages, including potent antibacterial properties, high binding affinity and specificity to target molecules, and minimal toxicity, making them highly promising candidates for drug development. However, a comprehensive database that consolidates both synthetically derived and naturally occurring cyclic peptides is conspicuously absent. To address this void, we introduce CyclicPepedia ( https://www.biosino.org/iMAC/cyclicpepedia/), a pioneering database that encompasses 8744 known cyclic peptides. This repository, structured as a composite knowledge network, offers a wealth of information encompassing various aspects of cyclic peptides, such as cyclic peptides’ sources, categorizations, structural characteristics, pharmacokinetic profiles, physicochemical properties, patented drug applications, and a collection of crucial publications. Supported by a user-friendly knowledge retrieval system and calculation tools specifically designed for cyclic peptides, CyclicPepedia will be able to facilitate advancements in cyclic peptide drug development.

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          DrugBank 5.0: a major update to the DrugBank database for 2018

          David S Wishart, Yannick D Feunang, An C Guo … (2017)
          Abstract DrugBank (www.drugbank.ca) is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. First described in 2006, DrugBank has continued to evolve over the past 12 years in response to marked improvements to web standards and changing needs for drug research and development. This year’s update, DrugBank 5.0, represents the most significant upgrade to the database in more than 10 years. In many cases, existing data content has grown by 100% or more over the last update. For instance, the total number of investigational drugs in the database has grown by almost 300%, the number of drug-drug interactions has grown by nearly 600% and the number of SNP-associated drug effects has grown more than 3000%. Significant improvements have been made to the quantity, quality and consistency of drug indications, drug binding data as well as drug-drug and drug-food interactions. A great deal of brand new data have also been added to DrugBank 5.0. This includes information on the influence of hundreds of drugs on metabolite levels (pharmacometabolomics), gene expression levels (pharmacotranscriptomics) and protein expression levels (pharmacoprotoemics). New data have also been added on the status of hundreds of new drug clinical trials and existing drug repurposing trials. Many other important improvements in the content, interface and performance of the DrugBank website have been made and these should greatly enhance its ease of use, utility and potential applications in many areas of pharmacological research, pharmaceutical science and drug education.
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            KEGG for taxonomy-based analysis of pathways and genomes

            Minoru Kanehisa, Miho Furumichi, Yoko Sato … (2022)
            KEGG ( https://www.kegg.jp ) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.
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              PubChem in 2021: new data content and improved web interfaces

              Sunghwan Kim, Jie Chen, Tiejun Cheng … (2020)
              Abstract PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem, including chemical-literature links from Thieme Chemistry, chemical and physical property links from SpringerMaterials, and patent links from the World Intellectual Properties Organization (WIPO). PubChem's homepage and individual record pages were updated to help users find desired information faster. This update involved a data model change for the data objects used by these pages as well as by programmatic users. Several new services were introduced, including the PubChem Periodic Table and Element pages, Pathway pages, and Knowledge panels. Additionally, in response to the coronavirus disease 2019 (COVID-19) outbreak, PubChem created a special data collection that contains PubChem data related to COVID-19 and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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                Author and article information

                Contributors
                Lei Liu
                Liu Yang
                Suqi Cao
                Zhigang Gao
                Bin Yang
                Guoqing Zhang
                Ruixin Zhu
                Dingfeng Wu:
                ORCID: https://orcid.org/0000-0002-9287-122X
                Journal
                Journal ID (nlm-ta): Brief Bioinform
                Journal ID (iso-abbrev): Brief Bioinform
                Journal ID (publisher-id): bib
                Title: Briefings in Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1467-5463
                ISSN (Electronic): 1477-4054
                Publication date Collection: May 2024
                Publication date (Electronic): 27 April 2024
                Publication date PMC-release: 27 April 2024
                Volume: 25
                Issue: 3
                Electronic Location Identifier: bbae190
                Affiliations
                Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai 200072, P. R. China
                National Center, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , Hangzhou 310052, P. R. China
                National Center, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , Hangzhou 310052, P. R. China
                Department of General Surgery, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , Hangzhou 310052, P. R. China
                Shanghai Southgene Technology Co., Ltd. , Shanghai 201203, China
                National Genomics Data Center & Bio-Med Big Data Center, Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, P. R. China
                Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai 200072, P. R. China
                National Center, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , Hangzhou 310052, P. R. China
                Author notes
                Corresponding authors: Dingfeng Wu, National Center, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, P.R. China. Tel: 86-571-8173-2391; E-mail: dfw_bioinfo@ 123456126.com ; Ruixin Zhu, Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P. R. China. Tel: 86-21-6598-1041; E-mail: rxzhu@ 123456tongji.edu.cn ; Guoqing Zhang, National Genomics Data Center & Bio-Med Big Data Center, Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, P. R. China. Tel: 86-21-5492-0465; E-mail: gqzhang@ 123456sinh.ac.cn

                Lei Liu and Liu Yang contributed equally.

                Author information
                https://orcid.org/0000-0002-9287-122X
                Article
                Publisher ID: bbae190
                DOI: 10.1093/bib/bbae190
                PMC ID: 11056021
                PubMed ID: 38678388
                SO-VID: afd73498-2d77-4a90-aadf-ca8f488707c1
                Copyright © © The Author(s) 2024. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                Date received : 27 November 2023
                Date revision received : 28 February 2024
                Date accepted : 09 April 2024
                Page count
                Pages: 11
                Funding
                Funded by: National Natural Science Foundation of China, DOI 10.13039/501100001809;
                Award ID: 32200529
                Award ID: 92251307
                Award ID: 82170542
                Award ID: 92051116
                Funded by: National Key Research and Development Program of China, DOI 10.13039/501100012166;
                Award ID: 2021YFF0703702
                Funded by: Key Research and Development Program of Zhejiang Province, DOI 10.13039/100022963;
                Award ID: 2023C03029
                Categories
                Subject: Problem Solving Protocol
                Subject: AcademicSubjects/SCI01060

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Keywords: cyclic peptide,drug development,knowledge network,database
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology
                Keywords: cyclic peptide, drug development, knowledge network, database

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