Crystallographic R Factor Refinement by Molecular Dynamics
By Axel T. BR�NGER, J. Kuriyan, Martin Karplus. 1987
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
- Nigel W. Moriarty
- D. Liebschner
- T. C. Terwilliger
- O. Sobolev
- Nathaniel Echols
- R. Grosse-Kunstleve
Citations in the corpus
- Towards automated crystallographic structure refinement with phenix.refine (2012, background): “…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.”
- Real-space refinement in PHENIX for cryo-EM and crystallography (2018, methodology): “Other non-default tasks allow optimization using simulated annealing (SA; Brunger et al., 1987), morphing (Terwilliger at al., 2013), rigid-body refinement (see Afonine et al., 2009 and references within) and systematic residue side-chain optimizations using grid searches in torsion χ-angle space…”
- Protein sidechain conformer prediction: a test of the energy function. (1998, background): “In only three cases did some part of the refinement involve energy-based procedures: X-PLOR [62] in 1hiv; EREF [63] in 5pti; and an early empirical function of Levitt [64] in 4fxn.”
- Comparison of anionic and cationic trypsinogens: The anionic activation domain is more flexible in solution and differs in its mode of BPTI binding in the crystal structure (2008, methodology): “The structures were refined using the X-PLOR package~Brünger et al., 1987! with 10% of the data set aside to computeRfree ~Brünger, 1992!. Initially an overall temperature factor of 20 Å2 was used.”
- Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules (2009, methodology): “The use of molecular-dynamics simulated annealing can be used to reduce the dangers of local minima by increasing the radius of convergence (Brünger et al., 1987; Adams et al., 1997; Brunger & Adams, 2002).”