186,197 research outputs found
Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data
No full textIn many cases of protein structure determination by NMR a high-quality structure is required. An important
contribution to structural precision is stereospecific assignment of magnetically nonequivalent prochiral methylene and
methyl groups, eliminating the need for introducing pseudoatoms and pseudoatom corrections in distance restraint lists.
Here, we introduce the stereospecific assignment program that uses the resonance assignment, a preliminary 3D structure
and 2D and/or 3D nuclear Overhauser effect spectroscopy peak lists for stereospecific assignment. For each prochiral
group the algorithm automatically calculates a score for the two different stereospecific assignment possibilities, taking
into account the presence and intensity of the nuclear Overhauser effect (NOE) peaks that are expected from the local
environment of each prochiral group (i.e., the close neighbors). The performance of the algorithm has been tested and
used on NMR data of -helical and -sheet proteins using homology models and/or X-ray structures. The program
produced no erroneus stereospecific assignments provided the NOEs were carefully picked and the 3D model was
sufficiently accurate. The set of NOE distance restraints produced by nmr2st using the results of the SSA module was
superior in generating good-quality ensembles of NMR structures (low deviations from upper limits in conjunction with
low root-mean-square-deviation values) in the first round of structure calculations. The program uses a novel approach
that employs the entire 3D structure of the protein to obtain stereospecific assignment; it can be used to speed up the
NMR structure refinement and to increase the quality of the final NMR ensemble even when no scalar or residual dipolar
coupling information is available
Semi-automatic Stereospecific Resonance and NOESY Assignment of Proteins Based on the Tertiary Structure – the Program nmr2st
No full textThe Third Intracellular Loop of the alpha1B-Adrenergic Receptor: Structural Features as derived by NMR and MD Calculations
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Solution Structure of Cytoplasmic Domains of the a1B-Adrenergic Receptor; Implications with Respect to Biological Functions
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Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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