scholarly journals The 2022 Nucleic Acids Research database issue and the online molecular biology database collection

2021 ◽  
Vol 50 (D1) ◽  
pp. D1-D10
Author(s):  
Daniel J Rigden ◽  
Xosé M Fernández
Keyword(s):  
Nucleic Acid ◽  
Molecular Biology ◽  
Nucleic Acids ◽  
Ucsc Genome Browser ◽  
Disordered Proteins ◽  
Research Database ◽  
Post Translational Modifications ◽  
Viral Genomes ◽  
Structure Database ◽  
Target Database

Abstract The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

scholarly journals The 27th annual Nucleic Acids Research database issue and molecular biology database collection

2019 ◽  
Vol 48 (D1) ◽  
pp. D1-D8 ◽  
Author(s):  
Daniel J Rigden ◽  
Xosé M Fernández
Keyword(s):  
Molecular Biology ◽  
Nucleic Acids ◽  
Model Organism ◽  
Research Database ◽  
Protein Sequence Analysis ◽  
Microbial Genomes ◽  
Related Proteins ◽  
Model Organism Databases ◽  
Target Database ◽  
Liquid Liquid Phase Separation

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/.

scholarly journals The 2021 Nucleic Acids Research database issue and the online molecular biology database collection

2020 ◽  
Vol 49 (D1) ◽  
pp. D1-D9
Author(s):  
Daniel J Rigden ◽  
Xosé M Fernández
Keyword(s):  
Molecular Biology ◽  
Nucleic Acids ◽  
Viral Genome ◽  
Ucsc Genome Browser ◽  
Protein Structures ◽  
Model Organism ◽  
Research Database ◽  
Wide Range ◽  
Cancer Drivers ◽  
Cancer Studies

Abstract The 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new databases and 90 covering recent changes to resources previously published in the Issue. A further ten are updates on databases most recently published elsewhere. Seven new databases focus on COVID-19 and SARS-CoV-2 and many others offer resources for studying the virus. Major returning nucleic acid databases include NONCODE, Rfam and RNAcentral. Protein family and domain databases include COG, Pfam, SMART and Panther. Protein structures are covered by RCSB PDB and dispersed proteins by PED and MobiDB. In metabolism and signalling, STRING, KEGG and WikiPathways are featured, along with returning KLIFS and new DKK and KinaseMD, all focused on kinases. IMG/M and IMG/VR update in the microbial and viral genome resources section, while human and model organism genomics resources include Flybase, Ensembl and UCSC Genome Browser. Cancer studies are covered by updates from canSAR and PINA, as well as newcomers CNCdatabase and Oncovar for cancer drivers. Plant comparative genomics is catered for by updates from Gramene and GreenPhylDB. 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 substantially updated, revisiting nearly 1000 entries, adding 90 new resources and eliminating 86 obsolete databases, bringing the current total to 1641 databases. It is available at https://www.oxfordjournals.org/nar/database/c/.

Recent advances in fluorescence resonance energy transfer-based probes in nucleic acid diagnosis

2020 ◽  
Vol 12 (7) ◽  
pp. 884-893
Author(s):  
Jiaxin Chen ◽  
Cheng Shi ◽  
Xin yue Kang ◽  
Xu tong Shen ◽  
Xingzhen Lao ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Nucleic Acid ◽  
Molecular Biology ◽  
Nucleic Acids ◽  
Fluorescence Resonance Energy Transfer ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Recent Advances ◽  
Fluorescence Resonance

Nucleic acid diagnosis is a method that diagnoses human conditions and diseases by directly exploring the existing states or defects of nucleic acids using theoretical and technical approaches from molecular biology.

scholarly journals The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

2012 ◽  
Vol 41 (D1) ◽  
pp. D1-D7 ◽  
Author(s):  
Xosé M. Fernández-Suárez ◽  
Michael Y. Galperin
Keyword(s):  
Molecular Biology ◽  
Nucleic Acids ◽  
Research Database

Above and Beyond Watson and Crick: Guanine Quadruplex Structures and Microbes

2018 ◽  
Vol 72 (1) ◽  
pp. 49-69 ◽  
Author(s):  
H Steven Seifert
Keyword(s):  
Nucleic Acid ◽  
Molecular Biology ◽  
Nucleic Acids ◽  
Human Disease ◽  
State Of The Art ◽  
Dna Structure ◽  
Biological Functions ◽  
Molecular Processes ◽  
Guanine Quadruplex ◽  
The 1960S

Advances in understanding mechanisms of nucleic acids have revolutionized molecular biology and medicine, but understanding of nontraditional nucleic acid conformations is less developed. The guanine quadruplex (G4) alternative DNA structure was first described in the 1960s, but the existence of G4 structures (G4-S) and their participation in myriads of biological functions are still underappreciated. Despite many tools to study G4s and many examples of roles for G4s in eukaryotic molecular processes and issues with uncontrolled G4-S formation, there is relatively little knowledge about the roles of G4-S in viral or prokaryotic systems. This review summarizes the state of the art with regard to G4-S in eukaryotes and their potential roles in human disease before discussing the evidence that G4-S have equivalent importance in affecting viral and bacterial life.

scholarly journals The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection

2015 ◽  
Vol 43 (D1) ◽  
pp. D1-D5 ◽  
Author(s):  
Michael Y. Galperin ◽  
Daniel J. Rigden ◽  
Xosé M. Fernández-Suárez
Keyword(s):  
Molecular Biology ◽  
Nucleic Acids ◽  
Research Database
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