Computational modeling of small molecule ligand binding interactions and affinities

Marino Convertino, Nikolay Dokholyan

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Abstract

Understanding and controlling biological phenomena via structure-based drug screening efforts often critically rely on accurate description of protein–ligand interactions. However, most of the currently available computational techniques are affected by severe deficiencies in both protein and ligand conformational sampling as well as in the scoring of the obtained docking solutions. To overcome these limitations, we have recently developed MedusaDock, a novel docking methodology, which simultaneously models ligand and receptor flexibility. Coupled with MedusaScore, a physical force field-based scoring function that accounts for the protein–ligand interaction energy, MedusaDock, has reported the highest success rate in the CSAR 2011 exercise. Here, we present a standard computational protocol to evaluate the binding properties of the two enantiomers of the non-selective β-blocker propanolol in the β2 adrenergic receptor’s binding site. We describe details of our protocol, which have been successfully applied to several other targets.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages23-32
Number of pages10
DOIs
StatePublished - May 1 2016

Publication series

NameMethods in Molecular Biology
Volume1414
ISSN (Print)1064-3745

Fingerprint

Ligands
Biological Phenomena
Preclinical Drug Evaluations
Propranolol
Adrenergic Receptors
Binding Sites
Proteins

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Convertino, M., & Dokholyan, N. (2016). Computational modeling of small molecule ligand binding interactions and affinities. In Methods in Molecular Biology (pp. 23-32). (Methods in Molecular Biology; Vol. 1414). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-3569-7_2
Convertino, Marino ; Dokholyan, Nikolay. / Computational modeling of small molecule ligand binding interactions and affinities. Methods in Molecular Biology. Humana Press Inc., 2016. pp. 23-32 (Methods in Molecular Biology).
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Convertino, M & Dokholyan, N 2016, Computational modeling of small molecule ligand binding interactions and affinities. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1414, Humana Press Inc., pp. 23-32. https://doi.org/10.1007/978-1-4939-3569-7_2

Computational modeling of small molecule ligand binding interactions and affinities. / Convertino, Marino; Dokholyan, Nikolay.

Methods in Molecular Biology. Humana Press Inc., 2016. p. 23-32 (Methods in Molecular Biology; Vol. 1414).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Convertino M, Dokholyan N. Computational modeling of small molecule ligand binding interactions and affinities. In Methods in Molecular Biology. Humana Press Inc. 2016. p. 23-32. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-3569-7_2