ArticleNucleic acids research2016
COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
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- Complex interplay between gene deletions and the environment uncovers cellular roles for genes of unknown function inmSystems · 2025Article
- Cross-Species Insights into PR Proteins: A Comprehensive Study ofIndian journal of microbiology · 2024Article
- Assembling bacterial puzzles: piecing together functions into microbial pathways.NAR genomics and bioinformatics · 2024Article
- The Landscape and Perspectives of the Human Gut Metaproteomics.Molecular & cellular proteomics : MCP · 2024Article
- Back to the Future of Metabolism-Advances in the Discovery and Characterization of Unknown Biocatalytic Functions and Pathways.Life (Basel, Switzerland) · 2024Review
- Learning sequence, structure, and function representations of proteins with language models.bioRxiv : the preprint server for biology · 2023Article
- Functional annotation and importance of marine bacterial transporters of plankton exometabolites.ISME communications · 2023Article
- Development of culture methods capable of culturing a wide range of predominant species of intestinal bacteria.Frontiers in cellular and infection microbiology · 2023Article
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- MSALigMap-A Tool for Mapping Active-Site Amino Acids in PDB Structures onto Known and Novel Unannotated Homologous Sequences with Similar Function.Life (Basel, Switzerland) · 2022Article
- Capillary Electrophoresis-Based Functional Genomics Screening to Discover Novel Archaeal DNA Modifying Enzymes.Applied and environmental microbiology · 2022Article
- Navigating and expanding the roadmap of natural product genome mining tools.Beilstein journal of organic chemistry · 2022Article
- Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class.PLoS computational biology · 2021Article
- Simultaneous elucidation of antibiotic mechanism of action and potency with high-throughput Fourier-transform infrared (FTIR) spectroscopy and machine learning.Applied microbiology and biotechnology · 2021Article
- The Power of Universal Contextualized Protein Embeddings in Cross-species Protein Function Prediction.Evolutionary bioinformatics online · 2021Article
- We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data.PLoS biology · 2020Article
- Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning.Briefings in bioinformatics · 2020Article
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7 authors.
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Abstract
The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼ 3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue.
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