defaultBaseMatrix: defaultBaseMatrix

In peplib: Peptide Library Analysis Methods

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

Details

See Descriptors for details. The descriptors were calculated using CDK.

Source

Most of these were descriptors were caclulated using the Chemistry Development Kit (CDK). http://sourceforge.net/projects/cdk/

See Also

Descriptors

peplib documentation built on May 29, 2017, 10:52 p.m.