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Results for DC.creator="A." AND DC.creator="A." AND DC.creator="Vagin" in section 21.2.2 of volume F |
Deviations from standard atomic volumes as a quality measure for protein crystal structures
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.2.3, pp. 664-665 [ doi:10.1107/97809553602060000880 ]
Deviations from standard atomic volumes as a quality measure for protein crystal structures 21.2.2.2.3. Deviations from standard atomic volumes as a quality measure for protein crystal structures The observations that protein ... found that the packing values of the NMR models displayed a much larger scatter than those of the corresponding crystal ...
Validation using knowledge-based interaction potentials and profiles
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.2.2, pp. 663-664 [ doi:10.1107/97809553602060000880 ]
... using knowledge-based interaction potentials and profiles These methods represent a distinct set of approaches to the validation of the non ... relative frequencies of residue-residue or atom-atom contacts from a set of high-quality protein structures and evaluating how the contacts in a given protein deviate from these standard frequencies. Most often, ...
Validation of stereochemical and non-bonded parameters
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.2.1, p. 663 [ doi:10.1107/97809553602060000880 ]
... is described in detail in Chapter 21.4 of this volume. A very important evaluation criterion is the Ramachandran-plot quality, where the distribution of the backbone [varphi], [psi] angles of a given protein structure is compared to that in high-quality ... odds (G-factor) value, which measures how normal or unusual a residue's location is in the plot for a ...
Comparisons against standard values derived from surveys of other macromolecules
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.2, pp. 663-665 [ doi:10.1107/97809553602060000880 ]
... values derived from surveys of other macromolecules This involves computing a number of stereochemical, geometric and energy parameters from the atomic ... properties, and the aim is to evaluate the quality of a model by measuring the extent to which it departs from ... in order to assess the quality of the structure as a whole, and on the local level, to identify specific ...
Comparisons against standard values derived from crystals of small molecules
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.1, pp. 662-663 [ doi:10.1107/97809553602060000880 ]
... of programs (Collaborative Computational Project, Number 4, 1994). As a result, the bond distances and angles of the final model ... used in molecular dynamics force fields, such as that of a recent version of CHARMM (MacKerell et al., 1998). In these force fields, covalent-geometry parameters are obtained by a different strategy. They are optimized together with non-bonded ...
Validating the geometric and stereochemical parameters of the model
International Tables for Crystallography (2012). Vol. F, Section 21.2.2, pp. 662-665 [ doi:10.1107/97809553602060000880 ]
... of programs (Collaborative Computational Project, Number 4, 1994). As a result, the bond distances and angles of the final model ... used in molecular dynamics force fields, such as that of a recent version of CHARMM (MacKerell et al., 1998). In these force fields, covalent-geometry parameters are obtained by a different strategy. They are optimized together with non-bonded ...
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.2.3, pp. 664-665 [ doi:10.1107/97809553602060000880 ]
Deviations from standard atomic volumes as a quality measure for protein crystal structures 21.2.2.2.3. Deviations from standard atomic volumes as a quality measure for protein crystal structures The observations that protein ... found that the packing values of the NMR models displayed a much larger scatter than those of the corresponding crystal ...
Validation using knowledge-based interaction potentials and profiles
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.2.2, pp. 663-664 [ doi:10.1107/97809553602060000880 ]
... using knowledge-based interaction potentials and profiles These methods represent a distinct set of approaches to the validation of the non ... relative frequencies of residue-residue or atom-atom contacts from a set of high-quality protein structures and evaluating how the contacts in a given protein deviate from these standard frequencies. Most often, ...
Validation of stereochemical and non-bonded parameters
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.2.1, p. 663 [ doi:10.1107/97809553602060000880 ]
... is described in detail in Chapter 21.4 of this volume. A very important evaluation criterion is the Ramachandran-plot quality, where the distribution of the backbone [varphi], [psi] angles of a given protein structure is compared to that in high-quality ... odds (G-factor) value, which measures how normal or unusual a residue's location is in the plot for a ...
Comparisons against standard values derived from surveys of other macromolecules
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.2, pp. 663-665 [ doi:10.1107/97809553602060000880 ]
... values derived from surveys of other macromolecules This involves computing a number of stereochemical, geometric and energy parameters from the atomic ... properties, and the aim is to evaluate the quality of a model by measuring the extent to which it departs from ... in order to assess the quality of the structure as a whole, and on the local level, to identify specific ...
Comparisons against standard values derived from crystals of small molecules
International Tables for Crystallography (2012). Vol. F, Section 21.2.2.1, pp. 662-663 [ doi:10.1107/97809553602060000880 ]
... of programs (Collaborative Computational Project, Number 4, 1994). As a result, the bond distances and angles of the final model ... used in molecular dynamics force fields, such as that of a recent version of CHARMM (MacKerell et al., 1998). In these force fields, covalent-geometry parameters are obtained by a different strategy. They are optimized together with non-bonded ...
Validating the geometric and stereochemical parameters of the model
International Tables for Crystallography (2012). Vol. F, Section 21.2.2, pp. 662-665 [ doi:10.1107/97809553602060000880 ]
... of programs (Collaborative Computational Project, Number 4, 1994). As a result, the bond distances and angles of the final model ... used in molecular dynamics force fields, such as that of a recent version of CHARMM (MacKerell et al., 1998). In these force fields, covalent-geometry parameters are obtained by a different strategy. They are optimized together with non-bonded ...
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