Absolv: Difference between revisions

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==Overview==
==Overview==


Solvation parameters/hydrogen bonding potential are essential characteristics of solutes that are key determinants of many biological properties. In certain cases a simple model relating the property of interest to solvation descriptors (Abraham type equation) may suffice for a quick estimate of the behavior of new compounds in the relevant system.
The Absolv module is a product of cooperation between Pharma Algorithms and Prof. M. H. Abraham. It is used for calculating various solvation-associated properties from Abraham type equations and predicting Abraham solvation parameters necessary for those calculations. These and various other useful features of this module are all wrapped up in a straightforward ACD/Percepta style interface.<br />
The Absolv module is a product of cooperation between Pharma Algorithms and Prof. M. H. Abraham. It is used for calculating various solvation-associated properties from Abraham type equations and predicting Abraham solvation parameters necessary for those calculations. These and various other useful features of this module are all wrapped up in a straightforward ACD/Percepta style interface.<br />
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===Features===
===Features===


* Calculates the following properties of a solute: A, B, Bo, E, A, L, and V.
* Calculates the following properties of a solute: A, B, Bo, E, S, L, and V.
* Visualizes the contributions of each atom in the structure to the currently selected Abraham parameter in terms of color intensity of highlighted atoms.
* Visualizes the contributions of each atom in the structure to the currently selected Abraham parameter in terms of color intensity of highlighted atoms.
* Lists up to 5 most similar structures from the Absolv database along with their experimental values of Abraham parameters and literature references.<br />
* Lists up to 5 most similar structures from the Absolv database along with their experimental values of Abraham parameters and literature references.<br />
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==Technical information==
==Technical information==
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===Calculated quantitative parameters===
===Calculated quantitative parameters===
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Parameters calculated by Absolv module represent the following properties of a solute:
Absolv module calculates the following list of solute properties, commonly known as Abraham Solvation parameters:
* H-Bonding acidity - α<sub>2</sub><sup>''H''</sup> (A)
* Overall solute H-Bonding acidity - α<sub>2</sub><sup>''H''</sup> (A)
* H-Bonding basicity - β<sub>2</sub><sup>''H''</sup> (B) and β<sub>2</sub><sup>''O''</sup> (Bo)
* Overall solute H-Bonding basicity - β<sub>2</sub><sup>''H''</sup> (B) and β<sub>2</sub><sup>''O''</sup> (Bo)
* Partitioning coefficient between gaseous phase and hexadecane - log ''L''<sup>16</sup> (L)
* Partitioning coefficient between gaseous phase and hexadecane - log ''L''<sup>16</sup> (L)
* Polarity / polarizability - π<sub>2</sub><sup>''H''</sup> (S)
* Polarity / polarizability - π<sub>2</sub><sup>''H''</sup> (S)
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===Reference database===
===Reference database===
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Absolv\Absolv DB module contains a browsable database of human intestinal absorption & bioavailability. The database consists of 5004 compounds with experimental values of solvation parameters determined by Prof. M. H. Abraham and coworkers. The main literature references where the values comprising the Absolv DB were presented include:
Absolv DB contains a browsable dataset consisting of 7885 compounds with experimental values of solvation parameters determined by Prof. M. H. Abraham and coworkers. The main literature references where the values comprising the Absolv DB were presented include:
* Abraham, M. H., Grellier, P. L., Prior, D. V., Duce, P. P., Morris, J. J., and Taylor, P. J., ''J. Chem. Soc. Perkin Trans 2'', '''1989''', 699.
* Abraham, M. H., Grellier, P. L., Prior, D. V., Duce, P. P., Morris, J. J., and Taylor, P. J., ''J. Chem. Soc. Perkin Trans 2'', '''1989''', 699.
* Abraham, M. H., Grellier, P. L., Prior, D. V., Morris, J. J., and Taylor, P. J., ''J. Chem. Soc. Perkin Trans 2'', '''1990''', 521.
* Abraham, M. H., Grellier, P. L., Prior, D. V., Morris, J. J., and Taylor, P. J., ''J. Chem. Soc. Perkin Trans 2'', '''1990''', 521.
* Abraham, M. H., Whiting, G. S., Doherty, R. M., and Shuely, W. J., ''J. Chromatogr.'', '''1991''' (587), 213-228.  
* Abraham, M. H., Whiting, G. S., Doherty, R. M., and Shuely, W. J., ''J. Chromatogr.'', '''1991''' (587), 213-228.  
Absolv DB module provides powerful searching and filtering capabilities, enabling the user to search compounds by name, by structural similarity, as well as limit the output to molecules possessing parameter values in the specified range or described in a particular publication.<br />
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Latest revision as of 09:56, 15 June 2017

Overview

Solvation parameters/hydrogen bonding potential are essential characteristics of solutes that are key determinants of many biological properties. In certain cases a simple model relating the property of interest to solvation descriptors (Abraham type equation) may suffice for a quick estimate of the behavior of new compounds in the relevant system. The Absolv module is a product of cooperation between Pharma Algorithms and Prof. M. H. Abraham. It is used for calculating various solvation-associated properties from Abraham type equations and predicting Abraham solvation parameters necessary for those calculations. These and various other useful features of this module are all wrapped up in a straightforward ACD/Percepta style interface.

Features

  • Calculates the following properties of a solute: A, B, Bo, E, S, L, and V.
  • Visualizes the contributions of each atom in the structure to the currently selected Abraham parameter in terms of color intensity of highlighted atoms.
  • Lists up to 5 most similar structures from the Absolv database along with their experimental values of Abraham parameters and literature references.


Module interface


Absolv Screenshot.png


  1. Contributions of each atom to the currently selected Abraham parameter are color-mapped onto the structure, with intensity of the color indicating the degree of contribution of each atom or substructure to the selected parameter
  2. Calculated Abraham solvation parameters for a solute
  3. Up to 5 most similar structures from the training set with experimental values



Technical information


Calculated quantitative parameters


Absolv module calculates the following list of solute properties, commonly known as Abraham Solvation parameters:

  • Overall solute H-Bonding acidity - α2H (A)
  • Overall solute H-Bonding basicity - β2H (B) and β2O (Bo)
  • Partitioning coefficient between gaseous phase and hexadecane - log L16 (L)
  • Polarity / polarizability - π2H (S)
  • Excessive molar refraction - R2 (E)
  • McGowan characteristic volume - Vx (V)


Reference database


Absolv DB contains a browsable dataset consisting of 7885 compounds with experimental values of solvation parameters determined by Prof. M. H. Abraham and coworkers. The main literature references where the values comprising the Absolv DB were presented include:

  • Abraham, M. H., Grellier, P. L., Prior, D. V., Duce, P. P., Morris, J. J., and Taylor, P. J., J. Chem. Soc. Perkin Trans 2, 1989, 699.
  • Abraham, M. H., Grellier, P. L., Prior, D. V., Morris, J. J., and Taylor, P. J., J. Chem. Soc. Perkin Trans 2, 1990, 521.
  • Abraham, M. H., Whiting, G. S., Doherty, R. M., and Shuely, W. J., J. Chromatogr., 1991 (587), 213-228.


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