PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education

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

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

PDBe-KB: collaboratively defining the biological context of structural data

Mihaly Varadi et al.

Summary: PDBe-KB is an open collaboration platform that aims to integrate functional and biophysical annotations from world-leading specialist data resources, serving the Protein Data Bank. By developing standardized data exchange formats and integrating functional annotations from partner resources, PDBe-KB aims to place macromolecular structure data in a biological context and provide valuable biological insights.

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 Biochemistry & Molecular Biology

AlphaFold illuminates half of the dark human proteins

Jessica L. Binder et al.

Summary: This paper investigates the use of confidence scores to evaluate the accuracy of AlphaFold protein models for drug discovery. It proposes criteria for useful models and residues and presents findings on the effects of disorder and sequence divergence on accuracy.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2022)

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Article Biochemistry & Molecular Biology

Cryo-EM structure of the human CST-Polα/primase complex in a recruitment state

Sarah W. Cai et al.

Summary: This study reports a cryo-EM structure of human CST-Pol alpha/primase and reveals an evolutionarily conserved interaction between POLA1 and CTC1. The binding mode of CST to the N-terminus of POLA1 is revealed by negative-stain EM and cross-linking mass spectrometry. In addition, disease mutations associated with Coats plus syndrome disrupt protein-protein interfaces observed in the recruitment state.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2022)

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Article Biochemistry & Molecular Biology

The structural context of posttranslational modifications at a proteome-wide scale

Isabell Bludau et al.

Summary: The recent revolution in computational protein structure prediction has provided new insights into the study of the entire proteome. In this study, the researchers analyze posttranslational modifications (PTMs) of proteins to determine their structural context and investigate their potential regulatory sites. The analysis reveals global patterns of PTM occurrence and spatial coregulation of different types of PTMs.

PLOS BIOLOGY (2022)

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Article Pharmacology & Pharmacy

A Pharmacoinformatics Analysis of Artemisinin Targets and de novo Design of Hits for Treating Ulcerative Colitis

Rui Tian et al.

Summary: This study used computer-aided drug design technology to investigate the potential mechanism and compounds of artemisinin in the treatment of ulcerative colitis. The constructed networks highlighted the importance of GALNT2, BMP7 and TGFBR2 in the disease treatment, providing guidance for future experiments and case studies.

FRONTIERS IN PHARMACOLOGY (2022)

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Article Immunology

Epitope-Based Vaccines against the Chlamydia trachomatis Major Outer Membrane Protein Variable Domain 4 Elicit Protection in Mice

Amanda L. Collar et al.

Summary: This study used immunogenic bacteriophage VLP technology to design a vaccine against Chlamydia trachomatis (Ct). Two methods were used to identify potential immunogens that could elicit neutralizing antibodies to Ct, and the resulting vaccines provided protection from Chlamydia infection in a mouse model.

VACCINES (2022)

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Article Multidisciplinary Sciences

Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold

Pietro Fontana et al.

Summary: This study determined the near-complete structure of the cytoplasmic ring of the nuclear pore complex (NPC) using cryo-electron microscopy and AlphaFold prediction. Molecular interactions and the binding modes of Nup358, the largest NPC subunit, were also predicted. The findings shed light on the formation and function of the NPC.

SCIENCE (2022)

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Article Multidisciplinary Sciences

AI-based structure prediction empowers integrative structural analysis of human nuclear pores

Shyamal Mosalaganti et al.

Summary: This study combines artificial intelligence-based structure prediction with in situ structural biology to reveal the structure and function of the human nuclear pore complex (NPC) scaffold. The findings demonstrate the importance of linker nucleoporins in establishing the higher-order structure of the scaffold and suggest that it widens the central pore rather than stabilizing the fusion of the inner and outer nuclear membranes.

SCIENCE (2022)

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Article Biochemistry & Molecular Biology

The structural context of posttranslational modifications at a proteome-wide scale

Isabell Bludau et al.

Summary: The recent advancement in computational protein structure prediction allows integration with large-scale experimental data, helping to determine the structural context of posttranslational modifications (PTMs) and identify potential regulatory sites. Global patterns of PTM occurrence across folded and intrinsically disordered regions have been uncovered, with a focus on distinguishing regulatory PTMs from those marking improperly folded proteins in the human proteome.

PLOS BIOLOGY (2022)

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Article Biochemistry & Molecular Biology

canSAR: update to the cancer translational research and drug discovery knowledgebase

Costas Mitsopoulos et al.

Summary: canSAR is a comprehensive knowledgebase for oncology, integrating multidisciplinary data and providing AI-informed target assessment for drug discovery. The new implementation of the system, canSARblack, offers new functionality to assist in translation hypothesis generation and experimental design.

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 Genetics & Heredity

Missense3D-DB web catalogue: an atom-based analysis and repository of 4M human protein-coding genetic variants

Tarun Khanna et al.

Summary: This study conducted a large-scale structural interpretation of human genetic variation from different databases, identifying potentially unknown disease-causing effects of certain variants. The results of the study have been made available online for clinical genetic reports, offering a new approach to genetic variant interpretation.

HUMAN GENETICS (2021)

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Article Biochemistry & Molecular Biology

RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive

Yana Rose et al.

Summary: RCSB PDB serves millions of users worldwide with experimentally determined 3D structures of biomolecules, delivering data efficiently through new APIs and a search system that integrates heterogeneous types of searches. The new architecture adheres to FAIR Principles, empowering users to address a wide array of research problems in fundamental biology and biomedicine.

JOURNAL OF MOLECULAR BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

David Sehnal et al.

Summary: Large biomolecular structures are being determined experimentally using established techniques such as crystallography and electron microscopy, with performance requirements for visualization and analysis tools increasing rapidly. The Mol* Viewer is an advanced online web-native 3D visualization tool that allows visualization of complex structures, and is the primary tool used by PDBe and RCSB PDB.

NUCLEIC ACIDS RESEARCH (2021)

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Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

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Article Multidisciplinary Sciences

Accurate prediction of protein structures and interactions using a three-track neural network

Minkyung Baek et al.

Summary: Through the three-track network, we achieved accuracies approaching those of DeepMind in CASP14, enabling rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and providing insights into the functions of proteins with currently unknown structure.

SCIENCE (2021)

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Article Multidisciplinary Sciences

R2DT is a framework for predicting and visualising RNA secondary structure using templates

Blake A. Sweeney et al.

Summary: The authors introduced a method for predicting and visualizing a wide range of RNA structures, enabling the linking of RNA sequence to function, which helps in better understanding non-coding RNA function.

NATURE COMMUNICATIONS (2021)

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Article Biochemistry & Molecular Biology

The InterPro protein families and domains database: 20 years on

Matthias Blum et al.

Summary: InterPro database offers a comprehensive classification of protein sequences and is a widely used resource for protein family annotation. Its software InterProScan allows users to search protein and nucleic acid sequences against InterPro's signatures.

NUCLEIC ACIDS RESEARCH (2021)

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Article Biochemistry & Molecular Biology

Pfam: The protein families database in 2021

Jaina Mistry et al.

Summary: The Pfam database has recently added a large number of protein families and domains, made revisions for COVID-19 research, and introduced Pfam-B as a supplement. These updates and improvements can help researchers classify protein sequences more effectively and conduct related studies.

NUCLEIC ACIDS RESEARCH (2021)

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Article Biochemistry & Molecular Biology