title: Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures.
abstract: The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of Rfree or may leave it out completely.
authors.affiliation: Department of Biochemistry and Molecular and Structural Biology, Institute Joǽef Stefan, Jamova 39, 1000 Ljubljana, Slovenia.
authors.forename: Jure
authors.initials: J
authors.lastname: Pražnikar
authors.affiliation: Department of Biochemistry and Molecular and Structural Biology, Institute Joǽef Stefan, Jamova 39, 1000 Ljubljana, Slovenia.
authors.forename: Dušan
authors.initials: D
authors.lastname: Turk
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D016013:Likelihood Functions; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D010455:Peptides; D011506:Proteins; C019529:polyalanine
keywords: Rfree; cross-validation; free-kick refinement; maximum likelihood