Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

By J. Headd, Nathaniel Echols, Pavel V. Afonine, R. Grosse-Kunstleve, Vincent B. Chen, Nigel W. Moriarty, David C Richardson, Jane S. Richardson, Paul D. Adams. 2012

232 citations recorded by the source corpus.

Recent developments in PHENIX are reported that allow the use of reference-model torsion restraints, secondary-structure hydrogen-bond restraints and Ramachandran restraints for improved macromolecular refinement in phenix.refine at low resolution.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “Restraining the hydrogen bonds in the secondary-structure element can help to maintain the regular structure (Headd et al., 2012).”
Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “All these tools have recently been implemented in phenix.reﬁne and details are discussed in this issue (Headd et al. , 2012).”
Real-space refinement in PHENIX for cryo-EM and crystallography (2018, background): “…plot restraint (Headd et al., 2012); - Amino-acid side-chain rotamer-specific restraints; - Cβ deviation restraints; - Reference model restraints, where a reference model may be a similar structure of better quality or the initial position of the model being refined (Headd et al., 2012).”
Programming new geometry restraints: parallelity of atomic groups (2015, methodology): “…restraint target, the sum in equation (1), is the sum of contributions from all restraint types If additional information about the molecule or its environment is available and deemed necessary to use, additional terms can be added to equation (22) (Echols et al. , 2010; Headd et al. , 2012, 2014).”
Integrating model simulation tools and cryo‐electron microscopy (2022, result): “These restraints include tightly restricting Ramachandran angles and backbone angles.(232) Model refinement methods that integrate MD simulations also intrinsically restrain some stereochemical properties through the force fields used in refinement, leading to models with less outliers, compared to ”
Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM (2018, methodology): “Such structural information has also been exploited in a similar way by other software packages (Headd et al. , 2014, 2012; Schro¨der et al. , 2010; Sheldrick, 2015; Smart et al. , 2012).”
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta (2016, methodology): “Unlike other approaches [9,21], our approach can automatically perform largescale backbone reorganization, correcting backbone placement errors common in these 3-4.”
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement (2014, methodology): “…these restraints resemble a simple harmonic near the target values, tapering off to no restraint as the distance increases, similar to the reference-model restraint implementations in BUSTER (Smart et al., 2012), REFMAC5 (Nicholls et al., 2012) and phenix.refine (Headd et al., 2012).”