ArticleNucleic acids research2011
BriX: a database of protein building blocks for structural analysis, modeling and design.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 60 citations in OpenAlex.
- Cryo-EM structure of a lysozyme-derived amyloid fibril from hereditary amyloidosis.Nature communications · 2024Article
- Insights into the Dissociation Process and Binding Pattern of the BRCT7/8-PHF8 Complex.ACS omega · 2024Article
- A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis.Journal of chemical information and modeling · 2023Article
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- Switching an active site helix in dihydrofolate reductase reveals limits to subdomain modularity.Biophysical journal · 2021Article
- Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure.BMC bioinformatics · 2020Article
- Computational reconstruction of atomistic protein structures from coarse-grained models.Computational and structural biotechnology journal · 2020Review
- Adaption of human antibody λ and κ light chain architectures to CDR repertoires.Protein engineering, design & selection : PEDS · 2019Article
- Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1.Structure (London, England : 1993) · 2019Article
- FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1).Nucleic acids research · 2018Article
- High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock.PLoS computational biology · 2017Article
- Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Protein structural motifs in prediction and design.Current opinion in structural biology · 2017Review
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- Article
- Fragger: a protein fragment picker for structural queries.F1000Research · 2017Article
- Tertiary alphabet for the observable protein structural universe.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- C-Terminal Domain of Integrase Binds between the Two Active Sites.Journal of chemical theory and computation · 2015Article
- Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.Protein science : a publication of the Protein Society · 2014Article
- Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations.Biochimica et biophysica acta · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-resolution structures of proteins remain the most valuable source for understanding their function in the cell and provide leads for drug design. Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches using small, recurrent protein fragments have been employed. Here we present two databases that provide a vast resource for implementing such fragment-based strategies. The BriX database contains fragments from over 7000 non-homologous proteins from the Astral collection, segmented in lengths from 4 to 14 residues and clustered according to structural similarity, summing up to a content of 2 million fragments per length. To overcome the lack of loops classified in BriX, we constructed the Loop BriX database of non-regular structure elements, clustered according to end-to-end distance between the regular residues flanking the loop. Both databases are available online (http://brix.crg.es) and can be accessed through a user-friendly web-interface. For high-throughput queries a web-based API is provided, as well as full database downloads. In addition, two exciting applications are provided as online services: (i) user-submitted structures can be covered on the fly with BriX classes, representing putative structural variation throughout the protein and (ii) gaps or low-confidence regions in these structures can be bridged with matching fragments.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.