ADL: Comparison: Scoring Function Autodock 4 vs. Autodock Vina.

Michael Gol golekmichal at gmail.com
Sat Nov 23 06:35:23 PST 2013


Hi,

I'm looking for MORE information about scoring funcion in this programs, and
the differences between them. I have to describe the individual members:

AD4:

ΔGbinding = ΔGvdW + ΔGelec + ΔGhbond + ΔGdesolv + Δgtors

ΔGvdW = ΔGvdW
12-6 Lennard-Jones potential (with 0.5 Å smoothing)
• ΔGelec
with Solmajer & Mehler distance-dependent dielectric
• ΔGhbond
12-10 H-bonding Potential with Goodford Directionality
• ΔGdesolv
Charge-dependent variant of Stouten Pairwise Atomic
Solvation Parameters
• ΔGtors
Number of rotatable bonds


VINA:
ΔGbinding = ΔGgauss + ΔGrepulsion + ΔGhbond + ΔGhydrophobic + ΔGtors

ΔG gauss
Attractive term for dispersion, two gaussian functions
• ΔGrepulsion
Square of the distance if closer than a threshold value
• ΔGhbond
Ramp function - also used for interactions with metal ions
• ΔGhydrophobic
Ramp function
• ΔGtors
Proportional to the number of rotatable bonds


I ask for information on this topic, materials, articles, everything that
might be useful. I searched the web, but never found detailed information.
Maybe some of you have been in contact with this topic?

Thank you very much in advance!



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