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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Augmenting Structure-Based Design with Experimental Protein-Ligand Interaction Data: Molecular Recognition,

Andreas Tosstorff1, Jason C Cole2, Richard Bartelt3

  • 1Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland.

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Summary

The ratio of frequencies (RF) framework reveals atomic interaction preferences in protein-ligand complexes for drug design. This method enhances molecular recognition analysis and improves docking predictions, aiding structure-based drug discovery.

Keywords:
amide stackingmolecular recognitionprotein-ligand interactionsstructure-based designweak hydrogen bonding

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Area of Science:

  • Computational chemistry and structural biology
  • Drug discovery and medicinal chemistry

Background:

  • The ratio of frequencies (RF) framework quantifies relative atomic interaction preferences in crystal structures.
  • Understanding these interactions is crucial for structure-based drug design.

Purpose of the Study:

  • To apply the RF framework to protein-ligand complexes for analyzing molecular recognition.
  • To investigate specific interactions: heteroaromatic stacking, acidified C-H groups, and carboxylate lone pairs.
  • To introduce a visualization tool for drug design and assess RF as a rescoring tool.

Main Methods:

  • Application of the RF framework to analyze protein-ligand interactions.
  • Development of an interactive visualization tool for design idea generation.
  • Utilizing RF analysis as a rescoring tool post-docking.

Main Results:

  • The RF framework provides statistically sound insights into molecular recognition.
  • Analysis revealed details on stacking, C-H, and carboxylate lone pair interactions.
  • The visualization tool aids in design idea generation.
  • RF rescoring improved enrichment factors in docking for DUD-E targets.

Conclusions:

  • The RF framework is a valuable tool for analyzing molecular interactions in drug design.
  • The approach supports structure-enabled drug discovery by enhancing interaction analysis and docking performance.