Protein databases

A protein database is one or more datasets about proteins, which could include a protein's amino acid sequence, conformation, structure, and features such as active sites. Protein databases are compiled by the translation of DNA sequences from different gene databases and include structural information. They are an important resource because proteins mediate most biological functions.

Latest Research and Reviews

Research
05 May 2022 | Open Access

A database of calculated solution parameters for the AlphaFold predicted protein structures
- Emre Brookes
- & Mattia Rocco
Scientific Reports 12, 7349
Research
10 January 2022 | Open Access

Helical structure motifs made searchable for functional peptide design

Here, we present TP-DB; a pattern-based search engine based on 1.67 million helices from the Protein Database (PDB). We demonstrate the utility of TP-DB in identifying microbe-specific antigens, as well as the design of antimicrobial peptides and Protein-protein interaction blockers.
- Cheng-Yu Tsai
- , Emmanuel Oluwatobi Salawu
- & Lee-Wei Yang
Nature Communications 13, 102
Research | 29 November 2021

A 3D structural SARS-CoV-2–human interactome to explore genetic and drug perturbations

This three-dimensional structural SARS-CoV-2–human interactome web server allows hypothesis-driven exploration of the mechanisms of SARS-CoV-2 pathology and host response.
- Shayne D. Wierbowski
- , Siqi Liang
- & Haiyuan Yu
Nature Methods 18, 1477-1488
Research | 18 October 2021

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

New tumor epitopes are discovered by ribosome profiling and immunopeptidome mass spectrometry.
- Tamara Ouspenskaia
- , Travis Law
- & Aviv Regev
Nature Biotechnology 40, 209-217
Research
12 July 2021 | Open Access

The 2021 update of the EPA’s adverse outcome pathway database
- Holly M. Mortensen
- , Jonathan Senn
- & Antony J. Williams
Scientific Data 8, 169
Research
11 June 2021 | Open Access

Uncovering of cytochrome P450 anatomy by SecStrAnnotator
- Adam Midlik
- , Veronika Navrátilová
- & Karel Berka
Scientific Reports 11, 12345

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News and Comment

Comments & Opinion | 07 May 2021

50 years of PDB: a catalyst in structural biology

Integrative structural biology, the culmination of experimental and theoretical methods, will provide a holistic view of molecular processes.
- Alexandre M. J. J. Bonvin
Nature Methods 18, 448-449
Comments & Opinion | 07 May 2021

wwPDB biocuration: on the front line of structural biology

Biocurators, the backbone of the wwPDB, manage structural biology data deposition, quality, and integrity, and provide integral support to the research community worldwide.
- Jasmine Y. Young
- , John Berrisford
- & Minyu Chen
Nature Methods 18, 431-432
Editorial | 07 May 2021

A celebration of structural biology

The Protein Data Bank (PDB) is the primary data resource for structural biology. On its 50th anniversary, we celebrate the future of this ever-growing field.

Nature Methods 18, 427
Comments & Opinion | 07 May 2021

Cryo-electron tomography: observing the cell at the atomic level

Interest in cryo-ET is rapidly growing, but many technical challenges still require solutions.
- Xueming Li
Nature Methods 18, 440-441
Comments & Opinion | 07 May 2021

From structure to mechanism: skiing the energy landscape

It is time for structural biologists to embrace the challenge of quantitatively describing functional energy landscapes.
- Dorothee Kern
Nature Methods 18, 435-436
Comments & Opinion | 07 May 2021

Molecular visualization of cellular complexity

Cryo-ET, which yields both structural and spatial information, will help unlock the molecular architecture of cells.
- Michael R. Wozny
- & Wanda Kukulski
Nature Methods 18, 442-443

All News & Comment

Protein databases

Latest Research and Reviews

A database of calculated solution parameters for the AlphaFold predicted protein structures

Helical structure motifs made searchable for functional peptide design

A 3D structural SARS-CoV-2–human interactome to explore genetic and drug perturbations

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

The 2021 update of the EPA’s adverse outcome pathway database

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

News and Comment

50 years of PDB: a catalyst in structural biology

wwPDB biocuration: on the front line of structural biology

A celebration of structural biology

Cryo-electron tomography: observing the cell at the atomic level

From structure to mechanism: skiing the energy landscape

Molecular visualization of cellular complexity

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