Electronic Reprint Biological Crystallography Phenix : a Comprehensive Python-based System for Macromolecular Structure Solution

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Robust deep learning based protein sequence design using ProteinMPNN (2022, methodology): “(31) All structures were validated using MolProbity 4.”
Impact of cytosine methylation on DNA binding specificities of human transcription factors (2017, methodology): “The rigid body refinement with REFMAC5 was followed by restrain refinement with REFMAC5, as implemented in CCP4 and Phenix.refine (93).”
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “RNA ribose pucker outliers are diagnosed by a simple relationship between the well fit 30 phosphate and glycosidic bond direction (Richardson et al., 2008), which also enables puckerspecific geometry targets in refinement (Adams et al., 2010).”
I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation (2017, neutral): “Autobuild (30) for model refinement and reconstruction.”
Improvement of molecular-replacement models with Sculptor (2011, methodology): “Sculptor (including the Sculptor–Coot interface) is currently available in the PHENIX suite (http://www.phenix-online.org).”