Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement

By L. Rice, A. Brünger. 1994

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Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “…(IAS) model can be used to model bonding features (Afonine et al., 2004, 2007), to low resolution, where the use of torsion-angle parameterization (Rice & Brünger, 1994; Grosse-Kunstleve et al., 2009) and specific restraints for coordinates [reference-model, secondarystructure,…”
The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “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].”
Torsion angle dynamics for NMR structure calculation with the new program DYANA. (1997, methodology): “…to differences in the implementation of TAD and the force calculation: DYANA uses the TAD algorithm of Jain et al. (1993), whereas XPLOR employs the algorithm of Bae & Haug (1987) and follows a fourth-order Runge-Kutta scheme for integration of the equations of motion (Rice & Bru È nger, 1994 ).”
Crystal Structure of the Cytosolic C2a-C2b Domains of Synaptotagmin III (1999, unknown): “Refinement included several rounds of conjugate gradient minimization, torsion angle simulated annealing at 3,000 K (Rice and Brunger, 1994), grouped B-factor refinement for both domains, and individual B-factor refinement for the C2A domain only (Table III, A and B).”