ADL: Genotype and Phenotype

Malcolm Stennett mstennet at
Fri Nov 4 07:46:26 PDT 2011

      I am running auto dock 4 and would like to ask you a few questions.

 1. Could you explicitly describe what genotype and phenotype refer to in
respect to the ligand and the protein. Is the genotype a set of mapping
points and is the phenotype the bound ligand/protein complex?

2. Could you explain how the genotype is able to move to the phenotype,
then sample various local searches, and then finally form a new genotype
from the more stable local search. In other words how does the lamarckian
algorithm move forward and manage to form a new genotype? If i knew what
genotype and phenotype refers to in the respect to the ligand and protein I
would better be able to understand this.

3. What pH is the docking taking place? Did you choose to make all charged
side chains neutral, all negatively charged, all positively charged, or is
there a percentage of the later combinations? knowing the pH will help me
figure this out.

4. Is the desolvation referring to the the net free energy of water moving
out of the binding site, or does this refer to the energy needed to remove
water from the system, system meaning the whole ligand/protein complex.

Thank You for your help,
Malcolm E. Stennett

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