UniProt: the Universal Protein Knowledgebase in 2023

Article Biochemistry & Molecular Biology

Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind's AlphaFold2 Program Dramatically Expands the Metalloproteome Zachary J. Wehrspan † Robert T. McDonnell † and Adrian H. Elcock ⇈

Zachary J. Wehrspan et al.

Summary: DeepMind's AlphaFold2 software can accurately predict ligand binding sites in protein structures, providing an important tool for the functional annotation of proteomes.

JOURNAL OF MOLECULAR BIOLOGY (2022)

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Article Biochemistry & Molecular Biology

Rhea, the reaction knowledgebase in 2022

Parit Bansal et al.

Summary: Rhea is an expert-curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI, with recent developments including increased reaction coverage, adoption as the reference vocabulary for enzyme annotation in UniProtKB, and the development of a new Rhea website. These developments aim to enhance the utility of Rhea as a reference resource for studying enzymes and metabolic systems.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Mihaly Varadi et al.

Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

Database resources of the national center for biotechnology information

Eric W. Sayers et al.

Summary: The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including databases for nucleic acid sequences and life science journal citations. It provides search and retrieval operations for most of these data from 35 distinct databases, with E-utilities serving as the programming interface. Several resources received significant updates in the past year.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

The European Bioinformatics Institute (EMBL-EBI) in 2021

Gaia Cantelli et al.

Summary: The European Bioinformatics Institute (EMBL-EBI) offers a wide range of freely available molecular data resources, including new resources like the PGS Catalog and AlphaFold DB. They have also been involved in developing community-driven data standards, such as the Recommended Metadata for Biological Images and the BioModels Reproducibility Scorecard. Training is a core mission of EMBL-EBI, with improvements to their online training offerings being part of this year's update.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

The European Nucleotide Archive in 2021

Carla Cummins et al.

Summary: The European Nucleotide Archive, maintained at EMBL-EBI, offers free services for deposition and access to open nucleotide sequencing data, playing a crucial role in advancing scientific research.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

Ensembl 2022

Fiona Cunningham et al.

Summary: Ensembl is unique in its flexible infrastructure for access to genomic data and annotation. They have focused on expediting annotation of new assemblies via the Ensembl Rapid Release platform, with the greatest annual number of newly annotated genomes released. They also developed a new method for comparative analyses and annotated non-vertebrate eukaryotes for the first time.

NUCLEIC ACIDS RESEARCH (2022)

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Article Multidisciplinary Sciences

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research

Joannella Morales et al.

Summary: Comprehensive genome annotation is crucial for understanding clinically relevant variants, but the lack of standardized reporting and browser display complicates interpretation and reporting. To address this, Ensembl/GENCODE and RefSeq launched the MATCHED Annotation from NCBI and EMBL-EBI (MANE) collaboration to define universal standards for variant reporting and browser display. The MANE transcript sets provide representative transcripts for each human protein-coding gene, improving consistency and facilitating clinical interpretation.

NATURE (2022)

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Article Mathematical & Computational Biology

SwissBioPics - an interactive library of cell images for the visualization of subcellular location data

Philippe Le Mercier et al.

Summary: SwissBioPics is a freely accessible resource that provides interactive, high-resolution cell images for visualizing subcellular location data. The images cover various cell types from different kingdoms of life and are tagged with unique identifiers from the controlled vocabulary of UniProt. Users can search and explore the cell images through the website and embed them in their own websites using the provided web component. SwissBioPics is also used by UniProt to visualize the subcellular locations and organelles where proteins function.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2022)

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Article Biochemistry & Molecular Biology

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Stephen K. Burley et al.

Summary: RCSB PDB, as the US data center for the global PDB archive, provides free access to 3D macromolecular structure data for millions of users worldwide, including educators, students, and the general public, integrating over 40 external biodata resources. The redesigned website now features improved search functionality and easier access to PDB data, showcasing new structures relevant to the understanding and addressing of the COVID-19 pandemic.

NUCLEIC ACIDS RESEARCH (2021)

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Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase in 2021

Alex Bateman et al.

Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.

NUCLEIC ACIDS RESEARCH (2021)

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Article Multidisciplinary Sciences

Protein embeddings and deep learning predict binding residues for various ligand classes

Maria Littmann et al.

Summary: The study introduces a new method called bindEmbed21 for predicting protein residue binding to metal ions, nucleic acids, or small molecules. This AI-based method outperforms traditional multiple sequence alignment methods and shows improved performance when combined with homology-based inference.

SCIENTIFIC REPORTS (2021)

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Editorial Material Biochemistry & Molecular Biology

A crowdsourcing open platform for literature curation in UniProt

Yuqi Wang et al.

Summary: The UniProt knowledgebase is a public database for protein sequence and function, encompassing the tree of life and over 220 million protein entries. The community now has access to a new crowdsourcing annotation system to assist in scaling up UniProt curation and ensuring proper attribution for their biocuration work.

PLOS BIOLOGY (2021)

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Article Medicine, Research & Experimental

A putative long noncoding RNA-encoded micropeptide maintains cellular homeostasis in pancreatic β cells

Mark Li et al.

Summary: Micropeptides encoded by lncRNAs play a critical role in pancreatic β cell functions and have a pathophysiological impact on diabetes. Experimental validation of one such micropeptide, BNLN, showed that it regulates ER calcium levels and insulin secretion in pancreatic β cells. The expression of BNLN is suppressed in islets from mice fed a high-fat diet, suggesting a potential link between diet-induced obesity and pancreatic function.

MOLECULAR THERAPY-NUCLEIC ACIDS (2021)

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Article Biochemistry & Molecular Biology

LitSuggest: a web-based system for literature recommendation and curation using machine learning

Alexis Allot et al.

Summary: Searching and reading relevant literature is a routine practice in biomedical research, but designing optimal search queries can be challenging. LitSuggest is a web server that offers an all-in-one literature recommendation and curation service to help biomedical researchers stay up to date with scientific literature.

NUCLEIC ACIDS RESEARCH (2021)

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Article Biochemistry & Molecular Biology

DDBJ update: streamlining submission and access of human data

Asami Fukuda et al.

Summary: The DDBJ Center provides diverse biological databases and the NIG supercomputer for life sciences research. Collaborating with NCBI, EBI, and NBDC, it manages nucleotide sequences and human genotype-phenotype data.

NUCLEIC ACIDS RESEARCH (2021)

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Article Biochemistry & Molecular Biology

The international nucleotide sequence database collaboration

Masanori Arita et al.

Summary: The International Nucleotide Sequence Database Collaboration (INSDC) has been a core infrastructure for collecting and providing nucleotide sequence data and metadata for over 30 years. Collaboratively maintained by three partner organizations, INSDC benefits science and communities worldwide.

NUCLEIC ACIDS RESEARCH (2021)

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Article Multidisciplinary Sciences