Rigidity Strengthening: A Mechanism for Protein-Ligand Binding

Duc D. Nguyen, Tian Xiao, Menglun Wang, Guo Wei Wei

Research output: Contribution to journalArticlepeer-review

76 Scopus citations

Abstract

Protein-ligand binding is essential to almost all life processes. The understanding of protein-ligand interactions is fundamentally important to rational drug and protein design. Based on large scale data sets, we show that protein rigidity strengthening or flexibility reduction is a mechanism in protein-ligand binding. Our approach based solely on rigidity is able to unveil a surprisingly apparently long-range contribution of apparently four residue layers to protein-ligand binding, which has ramifications for drug and protein design. Additionally, the present work reveals that among various pairwise interactions, the short-range ones within the distance of the van der Waals diameter are most important. It is found that the present approach outperforms all other state-of-the-art scoring functions for protein-ligand binding affinity predictions of two benchmark test sets.

Original languageEnglish
Pages (from-to)1715-1721
Number of pages7
JournalJournal of Chemical Information and Modeling
Volume57
Issue number7
DOIs
StatePublished - Jul 24 2017

Bibliographical note

Publisher Copyright:
© 2017 American Chemical Society.

ASJC Scopus subject areas

  • General Chemistry
  • General Chemical Engineering
  • Computer Science Applications
  • Library and Information Sciences

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