Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement.
By Paul D. Adams, Navraj S. Pannu, Randy J. Read, A. Brunger. 1997
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
- Pavel V. Afonine
- Paul D. Adams
- T. C. Terwilliger
- G. Bunkoczi
- Randy J. Read
- Nigel W. Moriarty
- Nathaniel Echols
- D. Liebschner
Citations in the corpus
- Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “…can reach only the nearest local minimum; therefore, sophisticated search algorithms such as rotamer optimization (recently implemented in phenix.refine) or simulated annealing (Brünger et al., 1987; Adams et al., 1997; Brunger et al., 2001; Brunger & Adams, 2002) may need to be applied.”
- Crystallography & NMR system: A new software suite for macromolecular structure determination. (1998, methodology): “Therefo becomes important to recalculate the cross-validated σA error estimates (Kleywegt & Brünger, 1996; Read, 1997), and the weight between X-ray diffraction target function and the geome energy function in the course of the refinement (Adams et al., 1997).”
- Structural mechanism for rifampicin inhibition of bacterial rna polymerase. (2001, methodology): “:) using CNS (Adams et al., 1997), yielding an initial R factor ofbacterial and eukaryotic RNAPs, combined with the fact 0.354 (Rfree 5 0.41, where the identical reflections was set aside asthat so many RifR mutations have been discovered, indifor the Rfree determination of the native structure) for”
- The Phenix Software for Automated Determination of Macromolecular Structures (2011, background): “Simulated annealing (SA) refinement can push this limit to approximately 1.5 Å [46] but is typically best applied at the start of structure refinement when model errors are largest[47, 48].”
- Modelling dynamics in protein crystal structures by ensemble refinement (2012, unknown): “Ensemble refinement of 20 datasets from the PDB We performed MD simulations, in which the model was restrained by a time-averaged X-ray ( Gros et al., 1990 ), maximum-likelihood ( Pannu and Read, 1996 ; Adams et al., 1997 ; Murshudov et al., 1997 ) target function (see ‘Materials and methods’).”