Crystallization detection software tools | Protein structure data analysis
Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error.
Offers a platform dedicated to the analysis of X-Ray diffraction data, including crystals with very high mosaicity. HKL-2000 proposes a toolkit composed of three different applications coordinated to allow users to perform mosaicity refinement during processing as well as 3D processing. Besides, the program can generate a report which compiles statistics and graphs usable in further publications.
Reduces and analyzes raw crystallographic data. xia2 is a standalone software able to automate the study of X-ray diffraction data from images to scaled intensities and structure factor amplitudes. This software can be applied for tasks in pharmaceutics or in benchmarking for guiding choices of equipment. Additionally, the program can be extendable in a way to be fitted to specific needs of crystallographers.
Performs analysis of X-Ray diffraction data, encompassing crystals with very high mosaicity. HKL-3000 furnishes an assortment of more than 10 software including those provided by the HKL-2000 software merged with supplementary macromolecular crystallographic applications such as Coot or Buccaneer. Besides, the program is able to output reports proposing statistics and graphs that can be included in publications.
Contains fundamental algorithms for computational crystallography that are designed for integration into highly automated software systems, but are also suitable for smaller systems, including educational software. cctbx provides three main modules. The eltbx (element toolbox) is a collection of tables of various X-ray and neutron scattering factors, element names, atomic numbers, atomic weights, ionic radii, and characteristic X-ray wavelengths. The uctbx (unit-cell toolbox) provides tools for the description and manipulation of unit cells, and is organized around the UnitCell class. The sgtbx (space-group toolbox) where a large variety of space-group symbols can be used to derive the corresponding symmetry operations. The entire community is invited to actively participate in the development of the code base.
Allows users to visualize solid shaded ribbon models of macromolecules. RIBBONS is a standalone software that includes features for (i) analyzing crystallographic results, (ii) displaying molecular models, and (iii) generating publication quality images. The application is able to handle files to create lists of spheres, cylinders, or triangles for display as well as restore the current orientation of submitted files.
Discovers the presence of RNA stems in macromolecular crystals. RIBER/DIBER employs diffraction data alone to determine nucleic acid content of a crystal. It aims to retrieve double-stranded B-DNA and not double-stranded A-RNA. This tool can be useful to choose most promising crystals for the diffraction and structure solution, that is an essential factor to optimize the success in structure determination.
A web server for prediction of protein crystallizability. The prediction is made by comparing several features of the protein with distributions of these features in TargetDB and combining the results into an overall probability of crystallization. XtalPred provides: (1) a detailed comparison of the protein's features to the corresponding distribution from TargetDB; (2) a summary of protein features and predictions that indicate problems that are likely to be encountered during protein crystallization; (3) prediction of ligands; and (4) (optional) lists of close homologs from complete microbial genomes that are more likely to crystallize.