The 27th annual Nucleic Acids Research database issue and molecular biology database collection
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TLDR
This issue contains three breakthrough articles: AntiBodies Chemically Defined curates antibody sequences and their cognate antigens; SCOP returns with a new schema and breaks away from a purely hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools.Abstract:
The 2020 Nucleic Acids Research Database Issue contains 148 papers spanning molecular biology. They include 59 papers reporting on new databases and 79 covering recent changes to resources previously published in the issue. A further ten papers are updates on databases most recently published elsewhere. This issue contains three breakthrough articles: AntiBodies Chemically Defined (ABCD) curates antibody sequences and their cognate antigens; SCOP returns with a new schema and breaks away from a purely hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools. Major returning nucleic acid databases include miRDB and miRTarBase. Databases for protein sequence analysis include CDD, DisProt and ELM, alongside no fewer than four newcomers covering proteins involved in liquid-liquid phase separation. In metabolism and signaling, Pathway Commons, Reactome and Metabolights all contribute papers. PATRIC and MicroScope update in microbial genomes while human and model organism genomics resources include Ensembl, Ensembl genomes and UCSC Genome Browser. Immune-related proteins are covered by updates from IPD-IMGT/HLA and AFND, as well as newcomers VDJbase and OGRDB. Drug design is catered for by updates from the IUPHAR/BPS Guide to Pharmacology and the Therapeutic Target Database. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been revised, updating 305 entries, adding 65 new resources and eliminating 125 discontinued URLs; so bringing the current total to 1637 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.read more
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Journal ArticleDOI
ResFinder 4.0 for predictions of phenotypes from genotypes.
Valeria Bortolaia,Rolf Sommer Kaas,Etienne Ruppé,Marilyn C. Roberts,Stefan Schwarz,Vincent Cattoir,Alain Philippon,Rosa Lundbye Allesøe,Rosa Lundbye Allesøe,Ana-Rita Rebelo,Alfred Ferrer Florensa,Linda Fagelhauer,Trinad Chakraborty,Bernd Neumann,Guido Werner,Jennifer K. Bender,Kerstin Stingl,Minh Ngoc Nguyen,Jasmine Coppens,Basil Britto Xavier,Surbhi Malhotra-Kumar,Henrik Westh,Henrik Westh,Mette Pinholt,Muna F. Anjum,Nicholas A. Duggett,Isabelle Kempf,Suvi Nykäsenoja,Satu Olkkola,Kinga Wieczorek,Ana Amaro,Lurdes Clemente,Joël Mossong,Serge Losch,Catherine Ragimbeau,Ole Lund,Frank Møller Aarestrup +36 more
TL;DR: WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
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MetaboLights: a resource evolving in response to the needs of its scientific community
Kenneth Haug,Keeva Cochrane,Venkata Chandrasekhar Nainala,Mark Williams,Jiakang Chang,Kalai Vanii Jayaseelan,Claire O'Donovan +6 more
TL;DR: The submission process was completely overhauled to enable MetaboLights to deliver a far more user-friendly submission process and to facilitate the growing demand for reproducibility and integration with other ‘omics.
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Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools.
Faviel F. Gonzalez-Galarza,Antony McCabe,Eduardo José Melo dos Santos,James T. A. Jones,Louise Y. Takeshita,Nestor D. Ortega-Rivera,Glenda M. Del Cid-Pavon,Kerry A Ramsbottom,Gurpreet S. Ghattaoraya,Ana Alfirevic,Derek Middleton,Andrew R. Jones +11 more
TL;DR: AFND has become more popular in terms of clinical and scientific usage, with a recent increase in genotyping data as a necessary component of Short Population Report article submissions to another scientific journal, and a user-friendly desktop application for HLA and KIR genotype/population data submissions.
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Formation of biological condensates via phase separation: Characteristics, analytical methods, and physiological implications.
TL;DR: In this article, the authors summarize commonly used methods to investigate various forms of liquid-liquid phase separation occurring both in 3D aqueous solution and on 2D membrane bilayers, such as LLPS condensates arising from intrinsically disordered proteins or structured modular protein domains.
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MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems.
TL;DR: The updated MiST database provides a comprehensive classification of microbial signal transduction systems, and a novel MiST feature is the integration of unique profile HMMs to link complex chemosensory systems with corresponding chemoreceptors in bacterial and archaeal genomes.
References
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Journal ArticleDOI
SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures
TL;DR: The latest release of SCOPe, 2.03, contains 59 514 Protein Data Bank entries, increasing the number of structures classified in SCOP by 55% and including more than 65% of the protein structures in the PDB.
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Reproducibility crisis: Blame it on the antibodies
TL;DR: Antibodies are the workhorses of biological experiments, but they are littering the field with false findings, according to a few evangelists.
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Earth BioGenome Project: Sequencing life for the future of life.
Harris A. Lewin,Gene E. Robinson,W. John Kress,William J. Baker,Jonathan A. Coddington,Keith A. Crandall,Richard Durbin,Richard Durbin,Scott V. Edwards,Félix Forest,M. Thomas P. Gilbert,M. Thomas P. Gilbert,Melissa M. Goldstein,Igor V. Grigoriev,Igor V. Grigoriev,Kevin J. Hackett,David Haussler,Erich D. Jarvis,Warren E. Johnson,Aristides Patrinos,Stephen Richards,Juan Carlos Castilla-Rubio,Marie-Anne Van Sluys,Pamela S. Soltis,Xun Xu,Huanming Yang,Guojie Zhang,Guojie Zhang +27 more
TL;DR: A perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years, is presented.
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The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.
James J. Davis,James J. Davis,Alice R. Wattam,Alice R. Wattam,Ramy K. Aziz,Thomas Brettin,Thomas Brettin,Ralph Butler,Ralph Butler,Rory Butler,Philippe Chlenski,Neal Conrad,Neal Conrad,Allan Dickerman,Emily M. Dietrich,Emily M. Dietrich,Joseph L. Gabbard,Svetlana Gerdes,Andrew Guard,Ronald W. Kenyon,Dustin Machi,Chunhong Mao,Daniel E. Murphy-Olson,Daniel E. Murphy-Olson,Marcus Nguyen,Marcus Nguyen,Eric K. Nordberg,Gary J. Olsen,Robert Olson,Robert Olson,Jamie C. Overbeek,Jamie C. Overbeek,Ross Overbeek,Bruce Parrello,Bruce Parrello,Gordon D. Pusch,Maulik Shukla,Maulik Shukla,Chris Thomas,Margo VanOeffelen,Veronika Vonstein,Andrew S. Warren,Fangfang Xia,Fangfang Xia,Dawen Xie,Hyunseung Yoo,Hyunseung Yoo,Rick Stevens,Rick Stevens +48 more
TL;DR: The recent updates to the PATRIC resource are reported, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.
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Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics
Yunxia Wang,Song Zhang,Fengcheng Li,Ying Zhou,Ying Zhang,Zhengwen Wang,Runyuan Zhang,Jiang Zhu,Yuxiang Ren,Ying Tan,Chu Qin,Yinghong Li,Xiaoxu Li,Yu Zong Chen,Feng Zhu +14 more
TL;DR: The Therapeutic Target Database (TTD) is constructed with expanded information about target-regulating microRNAs and transcription factors, target-interacting proteins, and patented agents and their targets, which can be conveniently retrieved and is further enriched with regulatory mechanisms or biochemical classes.
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