ArticleMonatshefte fur chemie
Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations.
Article in Monatshefte fur chemie. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Structure-based molecular modeling in SAR analysis and lead optimization.Computational and structural biotechnology journal · 2021Review
- Exploring NovelACS omega · 2019Article
- An overview of recent molecular dynamics applications as medicinal chemistry tools for the undruggable site challenge.MedChemComm · 2018Review
- All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.The journal of physical chemistry letters · 2017Article
- Structure-based discovery of potentially active semiochemicals for Cydia pomonella (L.).Scientific reports · 2016Article
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5 authors.
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Abstract
abstractPharmacophore modeling is a widely used technique in computer-aided drug discovery. Structure-based pharmacophore models of a ligand in complex with a protein have proven to be useful for supporting in silico hit discovery, hit to lead expansion, and lead optimization. As a structure-based approach it depends on the correct interpretation of ligand-protein interactions. There are legitimate concerns about the fidelity of the bound ligand and about non-physiological contacts with parts of the crystal and the solvent effects that influence the protein structure. A possible way to refine the structure of a protein-ligand system is to use the final structure of a given MD simulation. In this study we compare pharmacophore models built using the initial protein-ligand structure obtained from the protein data bank (PDB) with pharmacophore models built with the final structure of a molecular dynamics simulation. We show that the pharmacophore models differ in feature number and feature type and that the pharmacophore models built from the last structure of a MD simulation shows in some cases better ability to distinguish between active and decoy ligand structures. GRAPHICAL ABSTRACT:
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