ArticlebioRxiv : the preprint server for biology2025
KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.
Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
The number of structures deposited in the Protein Data Bank (PDB) has increased exponentially in recent years due to the availability of new methods to visualize increasingly complex macromolecules and their complexes in atomic detail. However, accurately refining atomic models from experimental maps remains a challenge due to limitations of current approaches for efficient model refinement. Standard PHENIX refinement can partially address these limitations with its speed and broad accessibility but often fails to yield the best model compared to those generated by more computationally intensive approaches. We therefore developed "KNexPHENIX", a customized semi-automated PHENIX-based workflow to support optimal macromolecular model building. KNexPHENIX can be used to refine macromolecular structures obtained from both cryo-electron microscopy (cryo-EM) and X-ray crystallography and is independent of the nature or size of the molecule. We evaluated KNexPHENIX on deposited structures as well as on
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