Compute the Interaction Matrix
Calculation of the interaction strength between all amino acids of a protein.
build.interact(cseq, mj1, mj2 = mj1, d, alpha = 82)
(coded) amino acid sequence
matrix for intrachain interactions between amino acids
matrix for interchain interactions between amino acids
vector of chain lengths
strength of the peptide bond
Per default only one matrix with interaction strengths between amino acids is used to compute the interaction map. But it is possible to differentiate between intrachain [Miyazawa and Jernigan (1996)] and interchain [Keskin et al. (1998)] interactions by using an additional interaction matrix. Both matrices are included in the package and can be used directly. The value of
d specifies the lengths of the different chains in the sequence.
Per definition there is no interaction between an amino acid and itself, therefore the diagonal is set to zero. All entries that represent peptide bonds between two amino acides are set to
alpha (only entries in the off-diagonals).
The input of
cseq can be a numeric sequences [0,19] as well as a string vector of standard amino acid sequences in one or three-letter code.
Return value is a symmetric matrix specifying the interactions between the amino acids. If n is the length of the sequence, the matrix dimension results in n \times n.
Choosing one's own matrices for inter- and intrachain interactions requires some thought: this funcion only deals with the standard amino acids thus it requires always symmetric, 20 \times 20 matrices.
Miyazawa and Jernigan (1996) Journal of Molecular Biology 256, 623–644.
Hamacher (2006) Journal of Chemical Theory and Computation 2, 873–878.
Keskin, Bahar, Badretdinov, Ptitsyn and Jernigan (1998) Protein Science 7, 2578–2586.
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