ArticleJournal of biomolecular NMR2005
Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements.
Article in Journal of biomolecular NMR, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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67 citing papers in PubMed.
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- Structure and DNA binding analysis of AT-rich interaction domain present in human BAF-B specific subunit BAF250b.Protein science : a publication of the Protein Society · 2022Article
- Predicting chemical shifts with graph neural networks.Chemical science · 2021Article
- CheSPI: chemical shift secondary structure population inference.Journal of biomolecular NMR · 2021Article
- Mapping temperature-dependent conformational change in the voltage-sensing domain of an engineered heat-activated KProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Backbone and sidechain resonance assignments and secondary structure of Scc4 from Chlamydia trachomatis.Biomolecular NMR assignments · 2020Article
- Structure and Role of BCOR PUFD in Noncanonical PRC1 Assembly and Disease.Biochemistry · 2020Article
- Backbone assignments and conformational dynamics in the S. typhimurium tryptophan synthase α-subunit from solution-state NMR.Journal of biomolecular NMR · 2020Article
- The neuronal transcription factor Myt1L interacts via a conserved motif with the PAH1 domain of Sin3 to recruit the Sin3L/Rpd3L histone deacetylase complex.FEBS letters · 2020Article
- Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins.Nucleic acids research · 2020Article
- Backbone resonance assignments and secondary structure of Ebola nucleoprotein 600-739 construct.Biomolecular NMR assignments · 2019Article
- Function and solution structure of the Arabidopsis thaliana RALF8 peptide.Protein science : a publication of the Protein Society · 2019Article
- TGF-β2 uses the concave surface of its extended finger region to bind betaglycan's ZP domain via three residues specific to TGF-β and inhibin-α.The Journal of biological chemistry · 2019Article
- UBC9 Mutant Reveals the Impact of Protein Dynamics on Substrate Selectivity and SUMO Chain Linkages.Biochemistry · 2019Article
- PINE-SPARKY.2 for automated NMR-based protein structure research.Bioinformatics (Oxford, England) · 2018Article
7 more citing papers are in PubMed but not listed here.
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Abstract
We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ("PECAN", Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.
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