PECAN is an algorithm for probabilistic prediction of Protein secondary structure from NMR chemical shifts.
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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.
PECAN requires chemical shift assignments input as an NMR-STAR formatted text file, as shown below. The input format is the portion of the NMR-STAR file format that describes the chemical shift information.
Please do not remove the words:
The example below illustrates the format:
4 2 LYS HG2 H 1.61 . 2
5 2 LYS HD2 H 1.40 . 2
6 2 LYS HE2 H 2.91 . 2
Please make sure you have the:
atom type column
and that residue 3-letter codes are ALL CAPS.
Hamid R. Eghbalnia, Liya Wang, Arash Bahrami, Amir Assadi, John L. Markley, “Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements”, Journal of Biomolecular NMR,2005 May;32(1):71-81.