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 Results for 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
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  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
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  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
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  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
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  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
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  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
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  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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