ArticleBioinformatics (Oxford, England)2011
Generation of a consensus protein domain dictionary.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Using evolutionary context to classify difficult protein folds.PLoS computational biology · 2025Article
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- Tumorigenic p53 mutants undergo common structural disruptions including conversion to α-sheet structure.Protein science : a publication of the Protein Society · 2020Article
- Shared unfolding pathways of unrelated immunoglobulin-like β-sandwich proteins.Protein engineering, design & selection : PEDS · 2019Article
- Molecular dynamics-derived rotamer libraries for d-amino acids within homochiral and heterochiral polypeptides.Protein engineering, design & selection : PEDS · 2018Article
- An in silico algorithm for identifying stabilizing pockets in proteins: test case, the Y220C mutant of the p53 tumor suppressor protein.Protein engineering, design & selection : PEDS · 2016Article
- New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities.Structure (London, England : 1993) · 2016Article
- A hybrid method for identification of structural domains.Scientific reports · 2014Article
- 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
- Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances.Protein science : a publication of the Protein Society · 2014Article
- Structural consequences of mutations to the α-tocopherol transfer protein associated with the neurodegenerative disease ataxia with vitamin E deficiency.Biochemistry · 2013Article
- When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative.BioEssays : news and reviews in molecular, cellular and developmental biology · 2012Article
- Protein Simulation Data in the Relational Model.The Journal of supercomputing · 2012Article
- A chemical group graph representation for efficient high-throughput analysis of atomistic protein simulations.Journal of bioinformatics and computational biology · 2012Article
- Wavelet Analysis of Protein Motion.International journal of wavelets, multiresolution and information processing · 2012Article
- The effect of context on the folding of β-hairpins.Journal of structural biology · 2011Article
- Design of native-like proteins through an exposure-dependent environment potential.Biochemistry · 2011Article
- Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.BMC bioinformatics · 2011Article
- The Dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water.Protein science : a publication of the Protein Society · 2011Article
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4 authors.
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Abstract
motivationThe discovery of new protein folds is a relatively rare occurrence even as the rate of protein structure determination increases. This rarity reinforces the concept of folds as reusable units of structure and function shared by diverse proteins. If the folding mechanism of proteins is largely determined by their topology, then the folding pathways of members of existing folds could encompass the full set used by globular protein domains.
resultsWe have used recent versions of three common protein domain dictionaries (SCOP, CATH and Dali) to generate a consensus domain dictionary (CDD). Surprisingly, 40% of the metafolds in the CDD are not composed of autonomous structural domains, i.e. they are not plausible independent folding units. This finding has serious ramifications for bioinformatics studies mining these domain dictionaries for globular protein properties. However, our main purpose in deriving this CDD was to generate an updated CDD to choose targets for MD simulation as part of our dynameomics effort, which aims to simulate the native and unfolding pathways of representatives of all globular protein consensus folds (metafolds). Consequently, we also compiled a list of representative protein targets of each metafold in the CDD. AVAILABILITY AND IMPLEMENTATION: This domain dictionary is available at www.dynameomics.org.
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