MedusaScore: An accurate force field-based scoring function for virtual drug screening

Shuangye Yin, Lada Biedermannova, Jiri Vondrasek, Nikolay Dokholyan

Research output: Contribution to journalArticle

91 Citations (Scopus)

Abstract

Virtual screening is becoming an important tool for drug discovery. However, the application of virtual screening has been limited by the lack of accurate scoring functions. Here, we present a novel scoring function, MedusaScore, for evaluating protein-ligand binding. MedusaScore is based on models of physical interactions that include van der Waals, solvation, and hydrogen bonding energies. To ensure the best transferability of the scoring function, we do not use any protein-ligand experimental data for parameter training. We then test the MedusaScore for docking decoy recognition and binding affinity prediction and find superior performance compared to other widely used scoring functions. Statistical analysis indicates that one source of inaccuracy of MedusaScore may arise from the unaccounted entropic loss upon ligand binding, which suggests avenues of approach for further MedusaScore improvement.

Original languageEnglish (US)
Pages (from-to)1656-1662
Number of pages7
JournalJournal of Chemical Information and Modeling
Volume48
Issue number8
DOIs
StatePublished - Aug 1 2008

Fingerprint

Screening
drug
Ligands
Pharmaceutical Preparations
Proteins
Solvation
statistical analysis
Statistical methods
Hydrogen bonds
energy
lack
interaction
performance

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Chemical Engineering(all)
  • Computer Science Applications
  • Library and Information Sciences

Cite this

Yin, Shuangye ; Biedermannova, Lada ; Vondrasek, Jiri ; Dokholyan, Nikolay. / MedusaScore : An accurate force field-based scoring function for virtual drug screening. In: Journal of Chemical Information and Modeling. 2008 ; Vol. 48, No. 8. pp. 1656-1662.
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MedusaScore : An accurate force field-based scoring function for virtual drug screening. / Yin, Shuangye; Biedermannova, Lada; Vondrasek, Jiri; Dokholyan, Nikolay.

In: Journal of Chemical Information and Modeling, Vol. 48, No. 8, 01.08.2008, p. 1656-1662.

Research output: Contribution to journalArticle

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