Quality assessment for molecular models: Difference between revisions
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The orientation of the sidechains of Asn, Gln, and His cannot be determined from the electron density in a crystallographic experiment at typical resolution, because of the similarity in electron densities of carbon vs. nitrogen. It is usually straightforward to determine the correct orientation by examining the local environment and optimising hydrogen bonding. Unfortunately, is is common for these determinations not to be made in published crystallographic models. Fortunately, [[MolProbity]] does these determinations automatically, and corrects the model by flipping the sidechains of Asn, Gln and HIs when this is warranted. | The orientation of the sidechains of Asn, Gln, and His cannot be determined from the electron density in a crystallographic experiment at typical resolution, because of the similarity in electron densities of carbon vs. nitrogen. It is usually straightforward to determine the correct orientation by examining the local environment and optimising hydrogen bonding. Unfortunately, is is common for these determinations not to be made in published crystallographic models. Fortunately, [[MolProbity]] does these determinations automatically, and corrects the model by flipping the sidechains of Asn, Gln and HIs when this is warranted. | ||
==Local Quality Scores of Protein Models in Cryo-EM Maps== | |||
[DAQ-Score Database|https://daqdb.kiharalab.org/] provides pre-computed residue-wise local quality scores for structure models in PDB that were derived from cryo-EM maps<ref>PMID: 35953671</ref>. | |||
==Improving Published Models== | ==Improving Published Models== | ||