Literature DB >> 12197662

3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling.

Oleg A Raevsky1, Vladlen S Skvortsov.   

Abstract

A new approach is proposed to more accurately estimate the energies of H-bond interactions in three-dimensional (3D) molecular modelling. The approach is based on the use of H-bond acceptor and donor enthalpy factor values calculated by means of program HYBOT, the use of a sigmoid relationship to determine the optimum H-bond distances and established force-field methods to determine distance and angle dependencies. The base-pair interactions in a short A-form RNA double-helix are presented as an example of enthalpy calculations of hydrogen bonding for a model system.

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Year:  2002        PMID： 12197662     DOI： 10.1023/a:1016361910530

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


  10 in total

1.  Molecular lipophilicity calculations of chemically heterogeneous chemicals and drugs on the basis of structural similarity and physicochemical parameters.

Authors:  O A Raevsky
Journal:  SAR QSAR Environ Res       Date:  2001       Impact factor: 3.000

2.  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

3.  Molecular dynamics simulation of MHC-peptide complexes as a tool for predicting potential T cell epitopes.

Authors:  D Rognan; L Scapozza; G Folkers; A Daser
Journal:  Biochemistry       Date:  1994-09-27       Impact factor: 3.162

4.  Three-dimensional hydrogen-bond geometry and probability information from a crystal survey.

Authors:  J E Mills; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1996-12       Impact factor: 3.686

5.  A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.

Authors:  P J Goodford
Journal:  J Med Chem       Date:  1985-07       Impact factor: 7.446

6.  Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds.

Authors:  R C Wade; K J Clark; P J Goodford
Journal:  J Med Chem       Date:  1993-01-08       Impact factor: 7.446

7.  The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands.

Authors:  G Klebe
Journal:  J Mol Biol       Date:  1994-03-25       Impact factor: 5.469

8.  New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure.

Authors:  D N Boobbyer; P J Goodford; P M McWhinnie; R C Wade
Journal:  J Med Chem       Date:  1989-05       Impact factor: 7.446

9.  Molecular modeling studies on ligand binding to sialidase from influenza virus and the mechanism of catalysis.

Authors:  N R Taylor; M von Itzstein
Journal:  J Med Chem       Date:  1994-03-04       Impact factor: 7.446

10.  Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds.

Authors:  R C Wade; P J Goodford
Journal:  J Med Chem       Date:  1993-01-08       Impact factor: 7.446
  10 in total
  2 in total

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Authors:  Lennart Eriksson; Patrik L Andersson; Erik Johansson; Mats Tysklind
Journal:  Mol Divers       Date:  2006-06-13       Impact factor: 2.943

2.  A facile and improved synthesis of sildenafil (Viagra) analogs through solid support microwave irradiation possessing tyrosinase inhibitory potential, their conformational analysis and molecular dynamics simulation studies.

Authors:  Khalid M Khan; Ghulam M Maharvi; Mahmud T H Khan; Shahnaz Perveen; Muhammad I Choudhary
Journal:  Mol Divers       Date:  2005       Impact factor: 2.943
  2 in total

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