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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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Published on: October 26, 2015

Improved docking of polypeptides with Glide.

Ivan Tubert-Brohman1, Woody Sherman, Matt Repasky

  • 1Schrödinger, Inc., 120 West 45th street, New York, New York 10036, USA.

Journal of Chemical Information and Modeling
|June 27, 2013
PubMed
Summary
This summary is machine-generated.

This study enhances peptide-protein docking by optimizing the Glide program for flexible polypeptides. The improved protocol significantly boosts prediction accuracy, offering a faster alternative to existing methods.

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Area of Science:

  • Computational biology
  • Structural biology
  • Biophysics

Background:

  • Predicting polypeptide-protein binding modes is crucial but challenging for standard docking tools.
  • Existing methods often struggle with the flexibility of polypeptides.

Purpose of the Study:

  • To adapt and improve the Glide docking program for accurate prediction of flexible polypeptide binding modes.
  • To enhance sampling and scoring strategies for peptide-protein docking.

Main Methods:

  • Utilized the Glide docking program, enhancing its sampling for flexible polypeptides.
  • Applied post-processing with MM-GBSA calculations for improved pose scoring.
  • Evaluated performance using RMSD on 19 non-α-helical peptides, including redocking and cross-docking scenarios.

Main Results:

  • Success rate for redocking to native structures increased from 21% to 58% with the optimized protocol.
  • Achieved accuracy comparable to Rosetta FlexPepDock but over 100 times faster.
  • Cross-docking achieved a 40% success rate with unbound receptor structures.

Conclusions:

  • The enhanced Glide protocol offers a rapid and accurate method for flexible polypeptide-protein docking.
  • The protocol is most effective for extended peptides with limited size and formal charges.
  • This approach expands the applicability of small molecule docking tools to peptide ligands.