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Recipe: ST - Hydropathy Compatibility Index (HCI)
Created by Seagat2011 79 1590
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Name: ST - Hydropathy Compatibility Index (HCI)
ID: 28691
Created on: Thu, 05/19/2011 - 20:50
Updated on: Fri, 05/20/2011 - 03:57
Description:

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



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Joined: 08/24/2010
Hi

ST - Hydropathy Compatibility Index (HCI) - v1.0.0.0 -

Hydropathy (hydrophobicity vs. hydrophilicity or lipophobicity vs. lipophilicity) is usually characterized by numbers (hydrophobic moments, HM) from -7.5 (Arg) to 3.1 (Ile), whereas hydrophobicity is a measure of how strongly the side chains are pushed out of water. The more positive a number, the more the amino acid residue will tend not to be in an aqueous environment. Negative numbers indicate hydrophilic side chains, with more negative numbers indicating greater affinity for water.

Molecules with similar hydropathy have affinity to each other, they are compatible; molecules with different hydropathy repel each other, and they are not compatible. To express this numerically, we use the hydropathy compatibility index (HCI) and collect these indices (20 × 20) in the matrix. HCIs were calculated using the formula

HCI = 20 - | [HM(A) - HM(B)] × 19/10.6] |

..where HM(A) and HM(B) are the hydrophobic moments of the amino acids A and B and HM(Arg)-HM (Ile) = 10.6. This formula gives the maximal index (20) for identical amino acids (closest hydrophobicity) and the minimal value (1) for the two hydrophobically most distant amino acids (Arg and Ile). [1]

run this on Amino Acid (AA) sequences you want evaluated for hydropathy 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