PCModels-X-Windows interface to the Biobyte CLOGP/CMR software

PCFilters-Command line inteface to the Biobyte CLOGP/CMR software

PCModels program includes the PCFilters and is available as a Daylight program. PCFilters is also available as a Daylight program.

Theoretical Background

CLOGP-Calculated Log of the Octanol/Water Partition Coefficeint

Measure of the hydrophobicity/lipophilicity of a compound

Low values (close to 0) classify a compound as hydrophobic/lipophillic, high values classify compound as hydrophilic/lipophobic

Drug Discovery, QSAR, e.g. Central Nervous Systems Drugs need to cross the blood/brain barrier, want CLOGP's near 3.
Environmental Studies use CLOGP's to determine the transport properties of compounds.
Many citations see: http:://www.daylight.com/papers

Fragment based approach

Structure is divided into fragments determined by "Isolating Carbons"

Isolating Carbon-Carbon which is not bounded to a doubly or triply-bonded to a hetero atom.,e.g. coumarin has 8

Polar Fragments-atoms or groups of atoms bounded by isolating carbons

Halogens
H-Polar
Ions
Unsaturations

Correction Factors are made for

Bonds

Chain Bonds
Ring Bonds
Branch Bonds

Interaction Factors

Halogen vs Halogen
H-Polar vs H-Polar
Halogen vs H-polar

Electronic Factors

Fragment valence type
Extension of Aromaticity
Sigma/Rho Fragment interaction

sigma-electronic strength
rho-susceptibility

Crowding
Intr-molecular Hydrogen Bonding

LogP is calculated from the summation of these factors. For unknown fragments, some are estimated some are not

Pomona College's "Star List"
Error codes are generated to explain the calculation details, values for which there were unknown fragments should be considered as "unknown"

CMR-Calculated Molecular Refractivity

QSAR found that minimizing the covariance between CMR and hydrophobicity, CMR could be used as measure of the binding force in an enzyme/substrate complex
Primarily a atom based approach with a few corrections for single bond types, double bound types and degrees of conjugation
Uses measured values

PCFILTERS-Command line interface

CLOGP

to add clogp vaules to a TDT file

clogp < infile.tdt >outfile.tdt

for a list of error codes

clogp +PCMODELS_ERRORTEXT

CMR

to add cmr values to a TDT file

cmr < infile.tdt >outfile.tdt

for "Help"

cmr + HELP

PCMODELS-X-Windows interface

To start X-Windows interface to CLOGP/CMR

xvpcmodels (xvpcmodels4d-Silicon Graphics)

Example:

Main Window

GRINS Window

CLOGP Calculation with fragments highlighted

Daylight Chemical Information Systems Inc.