Structure quality and target parameters

By Richard A. Engh, R. Huber. 2006

88 citations recorded by the source corpus.

Subfields: Condensed Matter Physics, Materials Chemistry, Radiation

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Condensed Matter Physics

In Materials Chemistry

In Radiation

Citations in the corpus

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests (2013, methodology): “Here, stereochemical violations in the model are defined as bond lengths and angles with values that diverge from the respective average reference value derived from high-resolution experimental structures (Engh and Huber, 1991, 2006) by more than a predefined number of standard deviations (12 (cid”
Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures (2022, background): “To build a full atom 3D structure, we construct the coordinates of N, Cα, C, O, and side-chain Cβ (except glycine that does not have Cβ) according to their ideal local coordinates relative to the Cα position and orientation of each amino acid [14].”
MolProbity: More and better reference data for improved all‐atom structure validation (2018, background): “By default, the expected values for bond geometry are drawn from a single-value library derived from Engh and Huber.”
SE(3) diffusion model with application to protein backbone generation (2023, background): “Each fixed coordinate assumes chemically idealized bond angles and lengths measured experimentally (Engh & Huber, 2012).”
The Phenix Software for Automated Determination of Macromolecular Structures (2011, background): “Universally, refinement programs use some form of restraints derived from prior knowledge about macromolecular chemistry[51-53], for example the ideal lengths of bonds between atoms.”
A New Generation of Crystallographic Validation Tools for the Protein Data Bank (2011, background): “These Ramachandran distributions had converged on the outline of the ‘‘favored’’ regions, now generally taken as including 98% of the high-quality data.”