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Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein-Protein Docking.

Nicola ScafuriMiguel A SolerAndrea SpitaleriWalter Rocchia
Published in: Journal of chemical theory and computation (2021)
Protein-protein docking typically consists of the generation of putative binding conformations, which are subsequently ranked by fast heuristic scoring functions. The simplicity of these functions allows for computational efficiency but has severe repercussions on their discrimination capabilities. In this work, we show the effectiveness of suitable descriptors calculated along short scaled molecular dynamics runs in recognizing the nearest-native bound conformation among a set of putative structures generated by the HADDOCK tool for eight protein-protein systems.
Keyphrases
  • protein protein
  • molecular dynamics
  • small molecule
  • density functional theory
  • randomized controlled trial
  • systematic review
  • high resolution
  • early onset
  • dna binding
  • transcription factor
  • crystal structure