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STAP / Statistical Torsion Angle Potentials

A public database of 2405 refined NMR solution structures from the Protein Data Bank (PDB). A simulated annealing protocol was employed to obtain refined structures with target potentials, including the newly developed STAP. The refined database was extensively analysed using various quality indicators from several assessment programs to determine the nuclear Overhauser effect (NOE) completeness, Ramachandran appearance, chi(1)-chi(2) rotamer normality, various parameters for protein stability and other indicators.

Vivaldi / VIsualization and VALidation Display

A web-based service for the analysis, visualization and validation of nuclear magnetic resonance (NMR) structures in the Protein Data Bank. Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information. A user-friendly interface, including a 3D viewer, tightly coupled with charts and tables, enables both experts and non-experts in NMR structure determination to analyze NMR ensembles and to assess their quality. The service presents information about the modeled NMR ensemble, validation of experimental chemical shifts, residual dipolar couplings, distance and dihedral angle constraints, as well as validation scores based on empirical knowledge and databases.