2008 NOV 3 - (VerticalNews.com) -- "A database with details of the geometry of metal sites in proteins has been set up. The data are derived from metalloprotein structures that are in the Protein Data Bank [PDB; Berman, Henrick, Nakamura & Markley (2006). Nucleic Acids Res. 35, D301-D303] and have been determined at 2.5 angstrom resolution or better," researchers in Scotland report.

  "The database contains all contacts within the crystal asymmetric unit considered to be chemical bonds to any of the metals Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu or Zn. The stored information includes PDB code, crystal data, resolution of structure determination, refinement program and R factor, protein class (from PDB header), contact distances, atom names of metal and interacting atoms as they appear in the PDB, site occupancies, B values, coordination numbers, information on coordination shapes, and metal-metal distances. This may be accessed by SQL queries, or by a user-friendly web interface which searches for contacts between specified types of atoms [for example Ca and carboxylate O of aspartate, Co and imidazole N delta of histidine] or which delivers details of all the metal sites in a specified protein. The web interface allows graphical display of the metal site, on its own or within the whole protein molecule, and may be accessed at http://eduliss.bch.ed.ac.uk/MESPEUS/," wrote K. Hsin and colleagues, University of Edinburgh ...read more

  2008 SEP 8 - (VerticalNews.com) -- According to a study from Fisciano, Italy, "A new procedure for performing structural analysis of crystalline materials from diffraction data, using internal coordinates, is described. For starting information only unit-cell content, space group, chemical formula, molecular connectivity and a limited amount of diffraction data are required."

  "After first selecting a number of solutions using a Monte Carlo approach with severe filters, which reject the most unrealistic solutions, genetic algorithms (crossover and mutations) are applied. In fact, the initial selection step alone is, frequently, a powerful tool for discovering structures, without recourse to the genetic algorithms. The procedure, while suffering from the limitation that connectivity must be known, is effective in cases where direct methods are not applicable because the diffraction data are scarce, are limited to low diffraction angles or are missing in specific portions of the reciprocal space. The main features of the algorithm are described and examples of validation given. The routines are now available as part of the freely distributed general-purpose program TRY," wrote A. Immirzi and colleagues, University of Salerno ...read more

  2008 JAN 21 - (VerticalNews.com) -- "Since its discovery, the direct-methods origin-free modulus sum function S, originally denoted Z(R) by Rius [ Acta Cryst. ( 1993), A49, 406-409], has been used for solving some relatively complex crystal structures from powder X-ray diffraction data. In these applications, phase refinement was normally carried out by maximizing the function S with a modified tangent formula," scientists writing in the Journal of Applied Crystallography report ...read more