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Using graphlet degree vectors to predict atomic displacement parameters in protein structures.

ABSTRACT: In structural biology, atomic displacement parameters, commonly used in the form of B values, describe uncertainties in atomic positions. Their distribution over the structure can provide hints on local structural reliability and mobility. A spatial macromolecular model can be represented by a graph whose nodes are atoms and whose edges correspond to all interatomic contacts within a certain distance. Small connected subgraphs, called graphlets, provide information about the wiring of a particular atom. The multiple linear regression approach based on this information aims to predict a distribution of values of isotropic atomic displacement parameters (B values) within a protein structure, given the atomic coordinates and molecular packing. By modeling the dynamic component of atomic uncertainties, this method allows the B values obtained from experimental crystallographic or cryo-electron microscopy studies to be reproduced relatively well.

SUBMITTER: Praznikar J

PROVIDER: S-EPMC10833351 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

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Using graphlet degree vectors to predict atomic displacement parameters in protein structures.

Pražnikar Jure J

Acta crystallographica. Section D, Structural biology 20231121 Pt 12

In structural biology, atomic displacement parameters, commonly used in the form of B values, describe uncertainties in atomic positions. Their distribution over the structure can provide hints on local structural reliability and mobility. A spatial macromolecular model can be represented by a graph whose nodes are atoms and whose edges correspond to all interatomic contacts within a certain distance. Small connected subgraphs, called graphlets, provide information about the wiring of a particul ...[more]

PMID: 37987168

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