The MolProbity website provides macromolecular model validation services, and this paper describes the current update on the services offered, highlighting the changes and additions since the previous review in 2010. The update includes infrastructure improvements, such as the rewrite of previous Java utilities to use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This enhances the thorough integration of MolProbity-style validation within Phenix and improves long-term maintainability.
Furthermore, there is now a complete MolProbity mirror site at [http://molprobity.manchester.ac.uk](http://molprobity.manchester.ac.uk/), and GitHub serves their open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. The paper also notes that coordinate output after Asn/Gln/His "flip" correction is now more idealized since the post-refinement step has apparently often been skipped in the past.
Additionally, two sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Cα-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused.
Structure prediction;Nucleic acid structure analysis;Nucleic acids;Protein structural motifs and surfaces;Sequence composition, complexity and repeats
Operation: Validation;Protein geometry calculation;Molecular model refinement;Protein model validation;Protein geometry validation
Software interface: Web user interface
Language: Python, Java, ...
Version name: 4.5.2
Credit: NIH Grant GM-15000, funding Richardson Lab research for over 34 years, NIH Grant GM-61302, funding RLab for over 3 years, A HHMI Predoctoral Fellowship
Contact: Richardson laboratory
- KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program.
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- Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
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- NGL viewer: web-based molecular graphics for large complexes.
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- PMID: 29850778
- PMC: PMC6198858
Download and documentation
Home page: http://molprobity.biochem.duke.edu/
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