Literature DB >> 1818090

HINT: a new method of empirical hydrophobic field calculation for CoMFA.

G E Kellogg1, S F Semus, D J Abraham.   

Abstract

An empirical hydrophobic field-like 3D function has been calculated with the program HINT (hydrophobic interactions) and imported into the SYBYL implementation of CoMFA (Comparative Molecular Field Analysis). The addition of hydrophobicity appears to offer increased chemical interpretability of CoMFA models. An example is given using the steroid model reported by Cramer et al. (J. Am. Chem. Soc., 110 (1988) 5959). While addition of the HINT field did not improve statistical parameters in this model, the CoMFA coefficient contours from the hydrophobic field unambiguously define the most active steroid molecules in the chemical terms of hydrophobic and polar substituents.

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Year:  1991        PMID: 1818090     DOI: 10.1007/BF00135313

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  5 in total

1.  Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins.

Authors:  R D Cramer; D E Patterson; J D Bunce
Journal:  J Am Chem Soc       Date:  1988-08-01       Impact factor: 15.419

2.  Experimental design based 3-D QSAR analysis of steroid-protein interactions: application to human CBG complexes.

Authors:  U Norinder
Journal:  J Comput Aided Mol Des       Date:  1990-12       Impact factor: 3.686

3.  Allosteric modifiers of hemoglobin. 2. Crystallographically determined binding sites and hydrophobic binding/interaction analysis of novel hemoglobin oxygen effectors.

Authors:  F C Wireko; G E Kellogg; D J Abraham
Journal:  J Med Chem       Date:  1991-02       Impact factor: 7.446

4.  Extension of the fragment method to calculate amino acid zwitterion and side chain partition coefficients.

Authors:  D J Abraham; A J Leo
Journal:  Proteins       Date:  1987

5.  Synthetic and computer-assisted analyses of the pharmacophore for the benzodiazepine receptor inverse agonist site.

Authors:  M S Allen; Y C Tan; M L Trudell; K Narayanan; L R Schindler; M J Martin; C Schultz; T J Hagen; K F Koehler; P W Codding
Journal:  J Med Chem       Date:  1990-09       Impact factor: 7.446

  5 in total
  48 in total

1.  A CoMFA analysis with conformational propensity: an attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method.

Authors:  K Gohda; I Mori; D Ohta; T Kikuchi
Journal:  J Comput Aided Mol Des       Date:  2000-03       Impact factor: 3.686

2.  Substructure and whole molecule approaches for calculating log P.

Authors:  R Mannhold; H van de Waterbeemd
Journal:  J Comput Aided Mol Des       Date:  2001-04       Impact factor: 3.686

3.  Localization and quantification of hydrophobicity: the molecular free energy density (MolFESD) concept and its application to sweetness recognition.

Authors:  R Jäger; F Schmidt; B Schilling; J Brickmann
Journal:  J Comput Aided Mol Des       Date:  2000-10       Impact factor: 3.686

4.  A Bayesian molecular interaction library.

Authors:  Ville-Veikko Rantanen; Mats Gyllenberg; Timo Koski; Mark S Johnson
Journal:  J Comput Aided Mol Des       Date:  2003-07       Impact factor: 3.686

5.  QSAR of conformationally flexible molecules: comparative molecular field analysis of protein-tyrosine kinase inhibitors.

Authors:  M C Nicklaus; G W Milne; T R Burke
Journal:  J Comput Aided Mol Des       Date:  1992-10       Impact factor: 3.686

Review 6.  Pushing the boundaries of 3D-QSAR.

Authors:  Richard D Cramer; Bernd Wendt
Journal:  J Comput Aided Mol Des       Date:  2007-01-26       Impact factor: 3.686

7.  A hydrophobic similarity analysis of solvation effects on nucleic acid bases.

Authors:  Jordi Muñoz-Muriedas; Xavier Barril; José María López; Modesto Orozco; Francisco Javier Luque
Journal:  J Mol Model       Date:  2006-09-21       Impact factor: 1.810

8.  Quantitative Series Enrichment Analysis (QSEA): a novel procedure for 3D-QSAR analysis.

Authors:  Bernd Wendt; Richard D Cramer
Journal:  J Comput Aided Mol Des       Date:  2008-02-27       Impact factor: 3.686

9.  A comprehensive analysis of the thermodynamic events involved in ligand-receptor binding using CoRIA and its variants.

Authors:  Jitender Verma; Vijay M Khedkar; Arati S Prabhu; Santosh A Khedkar; Alpeshkumar K Malde; Evans C Coutinho
Journal:  J Comput Aided Mol Des       Date:  2008-01-25       Impact factor: 3.686

Review 10.  Computational methods in drug discovery.

Authors:  Gregory Sliwoski; Sandeepkumar Kothiwale; Jens Meiler; Edward W Lowe
Journal:  Pharmacol Rev       Date:  2013-12-31       Impact factor: 25.468

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