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Protein-Ligand Docking

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Protein-Ligand Docking Dr. Noel O’Boyle University College Cork [email_address] Jan 2010 EBI Hands-on Training Small Molecule Bioactivity Resources at the EBI
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
Protein-ligand docking ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Images from Charaka Goonatilake’s web page, Glen Group, Unilever Centre, Cambridge
Pose vs. binding site ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Drug Discovery Pipeline C. O’Driscoll. http://www.nature.com/horizon/chemicalspace/background/pdf/odyssey.pdf
Computer-aided drug design (CADD) Known ligand(s) No known ligand Known protein structure Unknown protein structure Structure-based drug design (SBDD) Protein-ligand docking ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],De novo design CADD of no use Need experimental data of some sort
Uses of docking ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Virtual screening ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Virtual screening AR Leach, VJ Gillet, An Introduction to Cheminformatics
Components of docking software ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Final points ,[object Object],[object Object],[object Object],[object Object],[object Object]
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
The search space ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Ligand conformations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Taxol Images (from left): IUPAC Gold Book “chair, boat, twist”; “Wikipedia “Taxol”; Lakdawala et al, BMC Chem Biol , 2001 , 1 , 2.
 
Search Algorithms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The DOCK algorithm – Rigid docking ,[object Object],[object Object],[object Object],AR Leach, VJ Gillet, An Introduction to Cheminformatics
The DOCK algorithm – Rigid docking ,[object Object],[object Object],[object Object],AR Leach, VJ Gillet, An Introduction to Cheminformatics
Flexible docking ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Flexible docking using a Genetic Algorithm (GA) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Handling protein conformations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Image of Tyrosine rotamers from CMBI, Univeristy of Nijmegen at http://www.cmbi.kun.nl/mcsis/richardn/explanation.html
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
Components of docking software ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The perfect scoring function will… ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Classes of scoring function ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Empirical scoring functions
Böhm’s empirical scoring function ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Böhm’s empirical scoring function ,[object Object],[object Object],[object Object],[object Object]
Knowledge-based potentials ,[object Object],[object Object],[object Object],[object Object],[object Object]
Knowledge-based potentials For example, creating the distributions of ligand carbonyl oxygens to protein hydroxyl groups : (imagine the minimum at 3.0Ang)
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Knowledge-based potentials
Alternative scoring strategies ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
Pose prediction accuracy ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
AR Leach, VJ Gillet, An Introduction to Cheminformatics
Assess performance of a virtual screen ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
Ligand Preparation ,[object Object],[object Object],[object Object],[object Object],[object Object],Enol Ketone
Preparing the protein structure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Preparing the protein structure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Final thoughts ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Protein-Ligand Docking Dr. Noel O’Boyle University College Cork [email_address] Jan 2010 EBI Hands-on Training Small Molecule Bioactivity Resources at the EBI Questions?

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Protein-Ligand Docking

  • 1. Protein-Ligand Docking Dr. Noel O’Boyle University College Cork [email_address] Jan 2010 EBI Hands-on Training Small Molecule Bioactivity Resources at the EBI
  • 2.
  • 3.
  • 4.
  • 5.
  • 6. Drug Discovery Pipeline C. O’Driscoll. http://www.nature.com/horizon/chemicalspace/background/pdf/odyssey.pdf
  • 7.
  • 8.
  • 9.
  • 10. Virtual screening AR Leach, VJ Gillet, An Introduction to Cheminformatics
  • 11.
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  • 31. Knowledge-based potentials For example, creating the distributions of ligand carbonyl oxygens to protein hydroxyl groups : (imagine the minimum at 3.0Ang)
  • 32.
  • 33.
  • 34.
  • 35.
  • 36. AR Leach, VJ Gillet, An Introduction to Cheminformatics
  • 37.
  • 38.
  • 39.
  • 40.
  • 41.
  • 42.
  • 43. Protein-Ligand Docking Dr. Noel O’Boyle University College Cork [email_address] Jan 2010 EBI Hands-on Training Small Molecule Bioactivity Resources at the EBI Questions?

Hinweis der Redaktion

  1. Images from Wikipedia entry for Taxol
  2. Image from Wikipedia “12-6-Lennard-Jones-Potential.png”
  3. Expected = 5% of 10 = 0.5 actives Enrichment = 2 / 0.5 = 4.0