Likelihood-based refinement. I. Irremovable model errors.

By Vladimir Y. Lunin, Pavel V. Afonine, Alexandre G. Urzhumtsev. 2002

49 citations recorded by the source corpus.

Subfields: Applied Mathematics, Materials Chemistry, Statistics and Probability

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Applied Mathematics

1. T. J. Lane

In Materials Chemistry

1. Paul D. Adams
2. Pavel V. Afonine
3. T. C. Terwilliger
4. Nigel W. Moriarty
5. Randy J. Read
6. Alexandre Urzhumtsev
7. Nathaniel Echols
8. R. Grosse-Kunstleve

In Statistics and Probability

1. Nigel W. Moriarty
2. Paul D. Adams
3. Pavel V. Afonine
4. T. J. Lane
5. T. C. Terwilliger

Citations in the corpus

• Towards automated crystallographic structure refinement with phenix.refine (2012, background): “It is well known that refining an incomplete model can have a negative effect on all model parameters: positional and B factors, for example (Lunin et al., 2002; Afonine et al., 2004).”
• Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models (2007, background): “The maximum-likelihood estimate of overall coordinate uncertainty for the 1cqp model is 0.41 Å (Read, 1986; Lunin et al., 2002).”
• Protein structure prediction has reached the single-structure frontier (2023, methodology): “Experimental coordiante errors are estimated by the refinement software REFMAC (orange) 5 and PHENIX (blue) 6,7 .”
• Automatic multiple-zone rigid-body refinement with a large convergence radius (2009, unknown): “Least-squares refinement (LS) is expected to be more affected than maximum-likelihood refinement (ML), since the latter is designed to automatically weight down terms with poor model-to-data correspondence (Lunin et al., 2002), i.e. data at high resolution at the beginning of refinement.”
• Biological Crystallography Structure of Acostatin, a Dimeric Disintegrin from Southern Copperhead (agkistrodon Contortrix Contortrix), at 1.7 a ˚ Resolution (methodology): “In fact, the IAS-refinement with the Maximum Likelihood target (Lunin et al., 2002; to our knowledge never previously applied in this context), improved the models further as measured by the rigid-bond test, however that analysis is beyond the scope of this paper.”