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Methods Mol Biol. 2016;1425:23-35. doi: 10.1007/978-1-4939-3609-0_2.

In Silico 3D Modeling of Binding Activities.

Author information

  • 1Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Universit√† Padova, via Marzolo 5, 35131, Padova, Italy. stefano.moro@unipd.it.
  • 2Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Universit√† Padova, via Marzolo 5, 35131, Padova, Italy.
  • 3Dipartimento di Scienze Biomediche, Universit√† degli Studi di Sassari, v.le San Pietro 43/C, 07100, Sassari, Italy.

Abstract

In silico three-dimensional (3D) molecular modeling tools based upon the receptor/enzyme-ligand docking simulation in protein crystal structures and/or homology modeling of receptors have been reliably used in pharmacological research and development for decades. Molecular docking methodologies are helpful for revealing facets of activation and inactivation, thus improving mechanistic understanding and predicting molecular ligand binding activity, and they can have a high level of accuracy, and have also been explored and applied in chemical risk assessment. This computational approach is, however, only applicable for chemical hazard identification situations where the specific target receptor for a given chemical is known and the crystal structure/homology model of the receptor is available.

KEYWORDS:

Binding affinity prediction; Chemical risk assessment; Molecular docking; Molecular modeling; Scoring function

PMID:
27311460
DOI:
10.1007/978-1-4939-3609-0_2
[PubMed - in process]
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