Improving protocols for protein mapping through proper comparison to crystallography data.

ABSTRACT: Computational approaches to fragment-based drug design (FBDD) can complement experiments and facilitate the identification of potential hot spots along the protein surface. However, the evaluation of computational methods for mapping binding sites frequently focuses upon the ability to reproduce crystallographic coordinates to within a low RMSD threshold. This dependency on the deposited coordinate data overlooks the original electron density from the experiment, thus techniques may be developed based upon subjective-or even erroneous-atomic coordinates. This can become a significant drawback in applications to systems where the location of hot spots is unknown. On the basis of comparison to crystallographic density, we previously showed that mixed-solvent molecular dynamics (MixMD) accura

SUBMITTER: Lexa KW 

PROVIDER: S-EPMC3581705 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature