LiveBench provides simple evaluation of the structure prediction servers from the point of view of a potential user. The evaluation of sensitivity and specificity of the available servers can help the user develop sequence analysis strategies and assess the confidence of the obtained predictions.
NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures and corrects them.
The PoPMuSiC program is a tool for the computer-aided design of mutant proteins with controlled stability properties. It evaluates the changes in stability of a given protein or peptide under single-site mutations, on the basis of the protein's structure.
PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.
Program of error recognition in 3D structures
Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
TLS Motion Determination analyzes a macromolecular crystal structure for evidence of flexibility, e.g. local or inter-domain motions. It does this by partitioning individual chains into multiple segments that are modeled as rigid bodies undergoing TLS (Translation/Libration/Screw) vibrational motion. It generates all possible partitions up to a maximum number of segments.
Computational tools for the alignment and superposition of protein structures are essential instruments in structural biology. TopMatch-web provides an easy-to-use interface to a suite of techniques for protein structure alignments. Given a pair of protein structures, TopMatch calculates a list of alignments ordered by structural similarity. The corresponding superpositions can be explored in a 3D molecule viewer which highlights the structurally equivalent parts of the proteins.
TopSearch is a new powerful gateway to protein structures and their structural relationships. Given a query structure the search engine instantly returns a list of known protein structures sorted by structural similarity. TopSearch operates on three structural levels: chains, biological assemblies and quaternary structures, and asymmetric units.