TopSearch is a new powerful gateway to protein structures and their structural relationships. The core of TopSearch is a novel search engine that uses ultra-fast structure matching techniques for structure searches: given a query structure the search engine instantly returns a list of all (really all!) known protein structures sorted by structural similarity. TopSearch operates on three structural levels: chains, biological assemblies and quaternary structures (yes, including ribosomes!), and asymmetric units. All at the same speed! In working with structures, numbers are not enough - with TopSearch you see what you get. Immediately!
An effective tool for protein structure alignment and visualization of structural similarities.
Is a powerful tool in protein structure research. ProSa supports and guides your studies aimed at the determination of a protein's native fold. It is helpful for experimental structure determinations and modeling studies... read more
Validates and corrects asparagine and glutamine side-chain amide rotamers in protein structures solved by X-ray crystallography.
The decomposition of proteins into structurally distinct units is a common tool for classification and examination of protein structures. TopDomain-Web provides an easy-to-use albeit powerful interface to a suite of techniques for the decomposition of protein structures.
RefDens relates electron densities computed from a structural model to densities expected from prior observations on identical or closely related molecular environments. Strong deviations of computed from expected densities reveal unrealistic molecular structures. The electron densities solely depend on the molecular model, so that structure analysis and error detection are independent and hence complementary to experimental data.
Canonical distributions of electrons can be used in the refinement of structural models obtained from X-ray, NMR, cryo-EM, and other imaging techniques, as well as structure prediction and molecular modeling. Difference density maps for structural models of any origin can be computed and downloaded. In addition, hybrid density maps are provided that combine canonical electron density maps with experimentally derived densities to aid in the real space refinement of crystal structures.
Most common approaches to extract structural information from NMR chemical shifts are based on chemical shifts comparison. Therefore, consistent chemical shift referencing is required, as two chemical shift sets calculated using different reference compounds or referencing methods may not be compared in a meaningful way. CheckShift reliably re-references uploaded chemical shift data to conform with the IUPAC standard.
Provides a convenient and easy to use standard reference for the analysis of sequence alignment methods, homology search tools and fold recognition techniques. Any method can be immediately related to several popular methods (BLAST, PSI-BLAST, FASTA, SSearch, COMPASS and HHsearch).
Signal peptide prediction by sequence alignment using BLAST. Predictions returned by Signal-BLAST are transparent and easy to analyze.
COPS - Classification of Protein Structures
Quantitative classification of protein structures, efficient navigation through fold space and instantaneous visualization of pairwise structure similarities. Instant classification of newly determined protein structures and characterization of their novelty. New structural information found in the weekly releases of PDB, the public repository of known protein structure.
Chemical shifts are the mileposts of NMR spectroscopy. They include a wealth of structural information, however encoded in a way that prevents straightforward calculation of three-dimensional structures. Supplied with a set of chemical shifts SimShiftDB finds similar structures from the PDB based on comparison of amino acid sequence and chemical shifts. Alignments calculated by SimShiftDB give reliable structural models for the aligned regions of the query protein.
Endows classic SCOP with quantified structural information.