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Detection of errors in protein models
Dym, O., Eisenberg, D. and Yeates, T. O.  International Tables for Crystallography (2012). Vol. F, ch. 21.3, pp. 677-683 [ doi:10.1107/97809553602060000881 ]
... amino-acid side chains in the monomeric and oligomeric state (Eisenberg et al., 1992). The third application is to identify ... All non-glycine residues outside the allowed regions are marked. (d) Ramachandran plot for the refined RuBisCO structure. The archive of ... All non-glycine residues outside the allowed regions are marked. (d) Ramachandran diagram for the revised structure. The potential usefulness ...

Summary
Dym, O., Eisenberg, D. and Yeates, T. O.  International Tables for Crystallography (2012). Vol. F, Section 21.3.6, p. 682 [ doi:10.1107/97809553602060000881 ]
Summary 21.3.6. Summary In order to ensure the quality of the growing protein structure databases, models must be evaluated carefully during and after the structure determination process. Model evaluation can incorporate two types of measures: agreement between the model and the experimental diffraction data, and agreement between the model and the ...

Survey of old and revised structures
Dym, O., Eisenberg, D. and Yeates, T. O.  International Tables for Crystallography (2012). Vol. F, Section 21.3.5.2, p. 682 [ doi:10.1107/97809553602060000881 ]
Survey of old and revised structures 21.3.5.2. Survey of old and revised structures The past two decades have seen a surge of development in the experimental techniques of crystal structure determination. As a consequence, many structures originally solved at low resolution were later determined at higher resolution, often starting with improved ...
     [more results from section 21.3.5 in volume F]

Selection of database
Dym, O., Eisenberg, D. and Yeates, T. O.  International Tables for Crystallography (2012). Vol. F, Section 21.3.4, p. 679 [ doi:10.1107/97809553602060000881 ]
Selection of database 21.3.4. Selection of database Regardless of the specific approach or the specific criteria for validating structural models, a reliable reference database has to be chosen by careful selection of known structures. Suitable criteria to consider when selecting a database are: protein structures determined to resolutions of 2.5Ċ or ...

ERRAT
Dym, O., Eisenberg, D. and Yeates, T. O.  International Tables for Crystallography (2012). Vol. F, Section 21.3.3.4, pp. 678-679 [ doi:10.1107/97809553602060000881 ]
ERRAT 21.3.3.4. ERRAT The program ERRAT (Colovos & Yeates, 1993) analyses the relative frequencies of noncovalent interactions between atoms of various types. It can be viewed as an extension of the earlier 3D profile approach from the residue level to the atom level. Three types of atoms are considered (C, N and ...
     [more results from section 21.3.3 in volume F]

Separating evaluation from refinement
Dym, O., Eisenberg, D. and Yeates, T. O.  International Tables for Crystallography (2012). Vol. F, Section 21.3.2, p. 677 [ doi:10.1107/97809553602060000881 ]
Separating evaluation from refinement 21.3.2. Separating evaluation from refinement Any property that has been constrained or heavily restrained during refinement of the atomic model, and any property that has been closely monitored during rebuilding, cannot be used as the sole criterion to assess or `prove' the quality of the model. The ...

Motivation and introduction
Dym, O., Eisenberg, D. and Yeates, T. O.  International Tables for Crystallography (2012). Vol. F, Section 21.3.1, p. 677 [ doi:10.1107/97809553602060000881 ]
... the refinement function. References Bowie, J. U., Lüthy, R. & Eisenberg, D. (1991). A method to identify protein sequences that fold ... 2, 1511-1519. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK: a program ...

Availability of software
Dym, O., Eisenberg, D. and Yeates, T. O.  International Tables for Crystallography (2012). Vol. F, Section 21.3.7, p. 682 [ doi:10.1107/97809553602060000881 ]
... shown in this chapter. References Bennett, M. J., Choe, S. & Eisenberg, D. (1994). Domain swapping: entangling alliances between proteins. Proc. Natl ...

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