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Edelmiro Moman
DEFINITION
APPLICATIONS
http://www.rcsb.org/
introduction to molecular docking edelmiro moman
● The final goal uses to be to predict the biological activity of a given ligand
POSING
The process of determining whether a given conformation and orientation of a ligand
fits the active site. This is usually a fuzzy procedure that returns many alternative results.
SCORING
The pose score is a measure of the fit of a ligand into the active site. Scoring during the posing phase
usually involves simple energy calculations (electrostatic, van der Waals, ligand strain). Further
re-scoring might attempt to estimate more accurately the free energy of binding (G, and therefore KA)
perhaps including properties such as entropy and solvation.
introduction to molecular docking edelmiro moman
van der Waals ΔGvdW = WvdW ∑i, j ( Aij / rij12 - Bij / rij6 )
Hydrogen Bonding ΔGH-bond = WH-bond ∑i, j E(t) * ( Cij / rij12 - Dij / rij10 + Ehbond )
Electrostatics ΔGelec = Welec ∑i, j ( qi * qj ) / ( ε(rij) * rij )
Desolvation ΔGdesolv = Wdesolv ∑i (C), j (Si * Vj * exp ( -rij2 / (2 * σ2) )
Change in Torsional Free Energy when the Ligand goes from Unbound to Bound
MOLECULAR REPRESENTATIONS
Atomic
Surfaces
Grid
introduction to molecular docking edelmiro moman
PROTEIN FLEXIBILITY
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● Molecular Dynamics
Usually in combination with other methods
● Energy Minimisation
● Monte Carlo
● Normal Modes
● Rotamer Libraries
● Soft Potentials
http://flipdock.scripps.edu/
introduction to molecular docking edelmiro moman
● Tautomers
DOCKING SOFTWARE
RESOURCES:
http://www.imb-jena.de/jcb/ppi/jcb_ppi_software.html
http://www.ks.uiuc.edu/Development/biosoftdb/biosoft.cgi
http://mgl.scripps.edu/people/gmm/
http://www.dockingserver.com/web
http://bioinfo3d.cs.tau.ac.il/PatchDock/
● My Website:
http://www.edelmiromoman.eu/
CONCLUDING REMARKS
● Critically analyse all this stuff in view of existing (and your own)
hypotheses