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  • Title: Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding.
    Author: Tirado-Rives J, Jorgensen WL.
    Journal: J Med Chem; 2006 Oct 05; 49(20):5880-4. PubMed ID: 17004703.
    Abstract:
    When a ligand binds to a protein, it is typically not in the lowest-energy conformation for the unbound ligand and there is also a loss of conformational degrees of freedom. The free-energy change for this "conformer focusing" is addressed here formally, and the associated errors with its estimation or neglect are considered in the context of scoring functions for protein-ligand docking and computation of absolute free energies of binding. Specific applications for inhibition of HIV-1 reverse transcriptase are reported. It is concluded that the uncertainties from this source alone are sufficient to preclude the viability of current docking methodology for rank-ordering of diverse compounds in high-throughput virtual screening.
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