Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement

By Richard A. Engh, R. Huber. 1991

Subfields: Computational Biology & Bioinformatics, Computational Chemistry & Drug Discovery

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In Computational Biology & Bioinformatics

1. David Baker
2. Torsten Schwede
3. Paul D. Adams
4. Randy J. Read
5. Jeffrey J. Gray
6. Pavel V. Afonine
7. Tanja Kortemme
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In Computational Chemistry & Drug Discovery

1. Randy J. Read
2. Paul D. Adams
3. A. McCoy
4. G. Bunkoczi
5. David Baker
6. G. Murshudov
7. R. Oeffner
8. Pavel V. Afonine

Citations in the corpus

• lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests (2013, background): “…the model are defined as bond lengths and angles with values that diverge from the respective average reference value derived from highresolution experimental structures (Engh and Huber, 1991, 2006) by more than a predefined number of standard deviations (12 by default; see Supplementary Material).”
• Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “For bond lengths and angles, Phenix makes use of the CCP4 monomer library restraints (Engh & Huber, 1991; Vagin & Murshudov, 2004; Vagin et al., 2004) in protein side chains and somewhat modified classic values for nucleic acids (Clowney et al., 1996; Gelbin et al., 1996).”
• Towards automated crystallographic structure refinement with phenix.refine (2012, background): “(iv) Empirical geometry restraints: bond lengths, bond angles, dihedral angles, chiralities and planarities (Engh & Huber, 1991; Grosse-Kunstleve, Afonine et al., 2004).”
• The Rosetta all-atom energy function for macromolecular modeling and design (2017, methodology): “The ideal bond lengths and angles 89,90 were selected based on their ability to rebuild side chains observed in crystal structures (Kevin Karplus & James J. Havranek, unpublished); they were subsequently modified empirically.”
• REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. (2004, background): “Ideal values for bond lengths and bond angles for standard amino acids present in the dictionary have been taken from Engh & Huber (1991).”
• Crystal structure of vancomycin. (1996, methodology): “Distance restraints [29] were applied to the acetate ion in the binding pocket and to the disordered group.”
• Atomic resolution structures of trypsin provide insight into structural radiation damage. (2001, methodology): “The 0.95 AÊ structure of BT has the highest r.m.s. deviations compared with the Engh and Huber parameters (Engh & Huber, 1991), but the structure also has the highest fraction of re¯ections per protein atom and the lowest coordinate error and should therefore be the one most accurately de®ned.”