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Recipe: ST - Size Compatibility Index (SCI)
Created by Seagat2011 79 1607
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Name: ST - Size Compatibility Index (SCI)
ID: 28692
Created on: Thu, 05/19/2011 - 21:10
Updated on: Fri, 05/20/2011 - 04:11
Description:

run this on Amino Acid (AA) sequences you want evaluated for size compatibility.



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Joined: 08/24/2010
Hi

ST - Size Compatibility Index (SCI) - v1.0.0.0 -

There is considerable variation in the sizes of amino acids (i.e. the length and bulkiness of the side chain residues, R). The molecular weight (MW) of an amino acid is roughly proportional to its size. Suppose that the residue size has some influence on the bending of a peptide chain and on the amino acid co-locations (convex fits to concave) or, to take an extreme situation, there is already size compatibility at a single residue level. Theoretically, there might be size complementarity between amino acids, similar to nucleic acid base pairs, where the sum of purine and pyrimidine bases is always the same. A size compatibility index and matrix (SCI) is constructed to test these hypotheses.

Amino acid MW varies between 57 (Gly) and 186 (Trp) or between 1 and 130 if only the weight of the residue is counted (-56 for the peptide backbone). This gives an average R weight ~61.5 or ~123 for average residue pairs. The deviation of a given amino acid pair from this average residue weight (RW) is calculated using the equation

SCI = 20-|[MW(A)+MW(B)-123] × 19/135|

..This equation gives a maximal score (20) for amino acid pairs with a common RW = 123 and minimal score (1) for the Trp-Trp pair with maximal deviation from average (129 + 129 - 123 = 135).

Recommended for pocket design puzzles, advanced structure prediction puzzles, or puzzles with mutable segments.

run this on Amino Acid (AA) sequences you want evaluated for size compatibility.

REFERENCES
1. "Amino acid size, charge, hydropathy indices and matrices for protein structure analysis" - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450267/

Joined: 08/24/2010
Hi

-- OPTIONS: Enter Amino Acids (AAs) targeted, for comparison
-- abbreviated (1-letter) names of AAs you wish to have examined.
amino_segs_brief = {'a', .. }

-- OPTIONAL
-- Remove abbreviated (1-letter) names of AAs you do not wish to have examined.
amino_segs_brief2 = {'a', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'k', 'l', 'm', 'n', 'p', 'q', 'r', 's', 't', 'v', 'w', 'y'}

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons