Programming new geometry restraints: parallelity of atomic groups

By O. Sobolev, Pavel V. Afonine, Paul D. Adams, Alexandre Urzhumtsev. 2015

13 citations recorded by the source corpus.

Details are described of the calculation of new parallelity restraints recently introduced in cctbx and PHENIX.

Subfields: Materials Chemistry, Molecular Biology

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In Materials Chemistry

1. Paul D. Adams
2. Pavel V. Afonine
3. Randy J. Read
4. T. C. Terwilliger
5. Nigel W. Moriarty
6. T. Croll
7. A. McCoy
8. Jane S. Richardson

In Molecular Biology

1. Paul D. Adams
2. Pavel V. Afonine
3. Randy J. Read
4. T. C. Terwilliger
5. Nigel W. Moriarty
6. T. Croll
7. A. McCoy
8. Jane S. Richardson

Citations in the corpus

• Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, background): “Parallelity restraints keep the atom groups parallel (Sobolev et al., 2015; Richardson, 2015).”
• Real-space refinement in PHENIX for cryo-EM and crystallography (2018, background): “…restraints on idealized protein secondary structure fragments; - Restraints to maintain stacking bases in RNA/DNA parallel (parallelity restraints; Sobolev et al., 2015); - Ramachandran plot restraint (Headd et al., 2012); - Amino-acid side-chain rotamer-specific restraints; - Cβ deviation…”
• Q|R: quantum-based refinement. (2017, methodology): “…these problems, additional restraints have been used to augment (2) (see, for example, Oldfield, 2001; Echols et al., 2010; Headd et al., 2012; Sobolev et al., 2015), Trestraints plus ¼ Trestraints þ TSS þ TRamachandran þ Trotamer þ Treference: ð3Þ Here, TSS represents secondary-structure…”