Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations.

@article{Shi2012ProbingTE,
  title={Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations.},
  author={Yue Shi and Crystal Z Zhu and Stephen F Martin and Pengyu Y. Ren},
  journal={The journal of physical chemistry. B},
  year={2012},
  volume={116 5},
  pages={
          1716-27
        }
}
Preorganizing a ligand in the conformation it adopts upon binding to a protein has long been considered to be an effective way to improve affinity by making the binding entropy more favorable. However, recent thermodynamic studies of a series of complexes of the Grb2 SH2 domain with peptide analogues having constrained and flexible replacements for a phosphotyrosine residue revealed that less favorable binding entropies may result from constraining ligands in their biologically active… Expand
Probing the Effect of Conformational Constraints on Binding
  • Anne Bowen, Yue Shi
  • Computer Science
  • 2012 SC Companion: High Performance Computing, Networking Storage and Analysis
  • 2012
Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox.
Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method
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