Literature DB >> 8177887

A new method for predicting binding affinity in computer-aided drug design.

J Aqvist1, C Medina, J E Samuelsson.   

Abstract

A new semi-empirical method for calculating free energies of binding from molecular dynamics (MD) simulations is presented. It is based on standard thermodynamic cycles and on a linear approximation of polar and non-polar free energy contributions from the corresponding MD averages. The method is tested on a set of endothiapepsin inhibitors and found to give accurate results both for absolute as well as relative free energies.

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Year:  1994        PMID： 8177887     DOI： 10.1093/protein/7.3.385

Source DB:  PubMed          Journal:  Protein Eng        ISSN： 0269-2139


  245 in total

1.  Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7.

Authors:  L T Chong; Y Duan; L Wang; I Massova; P A Kollman
Journal:  Proc Natl Acad Sci U S A       Date:  1999-12-07       Impact factor: 11.205

2.  Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations.

Authors:  L Wang; Y Duan; P Stouten; G V De Lucca; R M Klabe; P A Kollman
Journal:  J Comput Aided Mol Des       Date:  2001-02       Impact factor: 3.686

3.  Automated docking and molecular dynamics simulations of nimesulide in the cyclooxygenase active site of human prostaglandin-endoperoxide synthase-2 (COX-2).

Authors:  R García-Nieto; C Pérez; F Gago
Journal:  J Comput Aided Mol Des       Date:  2000-02       Impact factor: 3.686

4.  A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors.

Authors:  S S So; M Karplus
Journal:  J Comput Aided Mol Des       Date:  1999-05       Impact factor: 3.686

5.  Evaluation of designed ligands by a multiple screening method: application to glycogen phosphorylase inhibitors constructed with a variety of approaches.

Authors:  S S So; M Karplus
Journal:  J Comput Aided Mol Des       Date:  2001-07       Impact factor: 3.686

6.  Calculations of free-energy contributions to protein-RNA complex stabilization.

Authors:  M A Olson
Journal:  Biophys J       Date:  2001-10       Impact factor: 4.033

7.  Protein ligand docking based on empirical method for binding affinity estimation.

Authors:  P Tao; L Lai
Journal:  J Comput Aided Mol Des       Date:  2001-05       Impact factor: 3.686

8.  Steroid binding by antibodies and artificial receptors: exploration of theoretical methods to determine the origins of binding affinities and specificities.

Authors:  S Handschuh; B Goldfuss; J Chen; J Gasteiger; K N Houk
Journal:  J Comput Aided Mol Des       Date:  2000-10       Impact factor: 3.686

9.  The third leg: molecular dynamics simulations of lipid binding proteins.

Authors:  T B Woolf; M Tychko
Journal:  Mol Cell Biochem       Date:  1999-02       Impact factor: 3.396

10.  Differences between apo and three holo forms of the intestinal fatty acid binding protein seen by molecular dynamics computer calculations.

Authors:  T B Woolf; A Grossfield; M Tychko
Journal:  Biophys J       Date:  2000-02       Impact factor: 4.033
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