Featured
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Article
| Open Access
Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation
During preclinical drug development, the ability of cancer cell lines to faithfully model human disease is important for identifying potential therapeutic strategies. Here, using transcriptomic datasets of over 1000 cell lines, the authors evaluate how representative each line is of its cancer type and present their cell line selection tool.
- Han Jin
- , Cheng Zhang
- & Adil Mardinoglu
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Article
| Open Access
Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies
Prediction of antibody structures is critical for understanding and designing novel therapeutic and diagnostic molecules. Here, the authors present IgFold: a fast, accurate method for antibody structure prediction using an end-to-end deep learning model.
- Jeffrey A. Ruffolo
- , Lee-Shin Chu
- & Jeffrey J. Gray
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Article
| 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
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Perspective
| Open Access
Towards a unified open access dataset of molecular interactions
The IMEx consortium provides one of the largest resources of curated, experimentally verified molecular interaction data. Here, the authors review how IMEx evolved into a fundamental resource for life scientists and describe how IMEx data can support biomedical research.
- Pablo Porras
- , Elisabet Barrera
- & Sandra Orchard
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Article
| Open Access
ProtCID: a data resource for structural information on protein interactions
The authors previously developed the Protein Common Interface Database (ProtCID), which compares and clusters the interfaces of pairs of full-length protein chains with defined Pfam domain architectures in different PDB entries to identify biological assemblies. Here the authors extend ProtCID to the clustering of domain-domain interactions that also allows analyzing domain interactions with peptides, nucleic acids, and ligands.
- Qifang Xu
- & Roland L. Dunbrack Jr.
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Article
| Open Access
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set
Genetic variants might exert their functional effects via influencing molecular interaction. Here, the authors present a resource featuring almost 28,000 annotations describing the effect of small sequence changes on physical protein interactions, curated by IMEx Consortium curators.
- J. Khadake
- , B. Meldal
- & P. Porras
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Article
| Open Access
Haplosaurus computes protein haplotypes for use in precision drug design
Proteoforms arise as protein isoforms or as protein haplotypes, which are the result of genetic variation. Here, the authors develop Haplosaurus, a database that computes protein haplotypes genome-wide from existing genotype data and analyse protein haplotype variability in the 1000 Genomes dataset.
- William Spooner
- , William McLaren
- & Catherine Chaillan Huntington
lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation