Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.

ABSTRACT: Force field accuracy is still one of the "stalemates" in biomolecular modeling. Model systems with high quality experimental data are valuable instruments for the validation and improvement of effective potentials. With respect to protein-ligand binding, organic host-guest complexes have long served as models for both experimental and computational studies because of the abundance of binding affinity data available for such systems. Binding affinity data collected for cyclodextrin (CD) inclusion complexes, a popular model for molecular recognition, is potentially a more reliable resource for tuning energy parameters than hydration free energy measurements. Convergence of binding free energy calculations on CD host-guest systems can also be obtained rapidly, thus offering the opportunity to

SUBMITTER: Wickstrom L 

PROVIDER: S-EPMC4715590 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature