VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb2, we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Φ–Ψ (Phi–Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence–structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.

No abstract

No abstract

P. J. BAKER et al. 725resolution increases. Therefore, the anomalous-scattering signal is clearly better for the short-wavelength data rather than the longer-wavelength data. Furthermore, the ratio of w" /w" where is the ~t ncalc/J--, , FHcalc anomalous contribution of the anomalous-scattering atoms to the structure factor and E" is the r.m.s, lack of closure for the anomalous case, as a function of resolution (Fig. 4) is greater, on average by a factor of two, for the EMP derivative and this pattern is extended to the F,L~ R factor (47.1% EMP; 51.0% DBMMF) and the overall figure of merit for the resultant phase set (0.58 EMP; 0.51 DBMMF). These results indicate that, for these two very similar derivatives, the anomalous-scattering signal to noise has been enhanced for the EMP data set, for which the wavelength was chosen to illuminate the LII absorption edge of the Hg atom in conjunction with a reduction in the overall protein crystal absorption at 0.86/~. On PX9.6 it is easy to move between the absorption edges of commonly used heavy ions, such as mercury, platinum and gold, so that MIROAS is routinely useable. The results from this present study with SIROAS illustrate the ease and effectiveness of the procedure. The two benefits of reduced absorption and increased anomalous-scattering signal have increased the phasing power of the EMP derivative of GDH and hence improved the quality of the resultant GDH electron density maps.We thank the SERC for their financial support of this work and for use of the SRS. We also thank J. M. A. Smith for helping to set up station PX9.6 and for subsequent consultations and also all the support staff at Daresbury. DWR is a Lister Institute Research Fellow. AbstractAn analysis of the distribution of organic crystal structures with more than one formula unit in the asymmetric unit among the 230 space groups has been carried out for the compounds listed in the Cambridge