defaultBaseMatrix:
defaultBaseMatrix
Description
This dataset is a matrix of decsriptors for each amino acid. It is used
for creating the desrciptors of peptide sequences.
Format
A data frame with 24 observations on the following 53 variables.
naAromAtom- Number of aromatic atoms
nAromBond- Number of aromatic bonds
MW- molecular weight
nRotB- number of rotatable bonds
apol- polarizability
bpol- the sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens).
PPSA.1- combination of surface area and partial charge
PPSA.2- a combination of surface area and partial charge
PPSA.3- a combination of surface area and partial charge
PNSA.1- a combination of surface area and partial charge
PNSA.2- a combination of surface area and partial charge
PNSA.3- a combination of surface area and partial charge
DPSA.1- a combination of surface area and partial charge
DPSA.2- a combination of surface area and partial charge
DPSA.3- a combination of surface area and partial charge
FPSA.1- a combination of surface area and partial charge
FPSA.2- a combination of surface area and partial charge
FPSA.3- a combination of surface area and partial charge
FNSA.1- a combination of surface area and partial charge
FNSA.2- a combination of surface area and partial charge
FNSA.3- a combination of surface area and partial charge
WPSA.1- a combination of surface area and partial charge
WPSA.2- a combination of surface area and partial charge
WPSA.3- a combination of surface area and partial charge
WNSA.1- a combination of surface area and partial charge
WNSA.2- a combination of surface area and partial charge
WNSA.3- a combination of surface area and partial charge
RPCG- a combination of surface area and partial charge
RNCG- a combination of surface area and partial charge
RPCS- a combination of surface area and partial charge
RNCS- a combination of surface area and partial charge
THSA- a combination of surface area and partial charge
TPSA- a combination of surface area and partial charge
RHSA- a combination of surface area and partial charge
RPSA- a combination of surface area and partial charge
nHBDon- number of hydrogen bond donors
nHBAcc- number of hydrogen bond acceptors
TopoPSA- Topological polar surface area based on fragment contributions
XLogP- An estimate of the
logP partition coefficient fragC- a numeric vector
count.AcidicGroups- number of acidic groups: E, D
count.AromaticGroups- number of aromatic groups: Y, W, F
count.BasicGroups- number of basic groups: H, K R
count.ChargedGroups- number of charged groups: E, D, R,
K, H
count.NonPolarGroups- number of nonpolar groups: A, G,
I, L, M, F, W, Y, V
count.PolarGroups- number of polar groups: S, T, C,
P, N, Q, K, R, H, E, D
ALogP- atom additive logP and molar refractivity values as described by Ghose and Crippen
ALogp2- atom additive logP and molar refractivity values as described by Ghose and Crippen
AMR- atom additive logP and molar refractivity values as described by Ghose and Crippen
WPATH- Wiener path number and Wiener polarity number
WPOL- Wiener path number and Wiener polarity number
PetitjeanNumber- Petitjean Number
helix- how helical the amino acid is.
pdbhelix- how helical a amino acid is using data derived
from the protein databank
CaSD- The solvation density near the C-alpha carbon on
the amino acid
Source
Most of these were descriptors were caclulated using the Chemistry
Development Kit (CDK). http://sourceforge.net/projects/cdk/Details
See Descriptors for details. The descriptors
were calculated using CDK.