Nuclear overhauser effect assignment and structure calculation | NMR-based proteomics data analysis
The major bottleneck in the determination of solution NMR structures is the assignment of NOE peaks (nuclear Overhauser effect). NOE assignment and structure calculation are often combined together to calculate final structures.
A package to generate and manipulate molecular structures. Protein and nucleic acid structures, including bond and angle definitions can be generated from sequence-only information, and the coordinate statement can be used to read and write PDB structure coordinate files. Xplor-NIH is achieved by seeking the minimum of a target function comprising terms for the experimental NMR restraints, covalent geometry and non-bonded contacts using a variety of minimization procedures, monte carlo methods and conventional gradient-based minimization.
Consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion.
Handles and visualizes large molecules with a focus on nuclear magnetic resonance (NMR) structure detection. VMD-XPLOR merges XPLOR and VMD programs with the aim of supplying an interface able to transfer structures and animation sequences towards VMD. It allows users to view NMR experimental data and its corresponding molecular structure and to perform an interactive handling of coordinates such as torsion angles.
A web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications.
Performs prediction of protein backbone torsion angles from chemical shifts. TALOS uses a two-level feed-forward multilayer artificial neural network (ANN) to predict the location in phi/psi space, or the secondary structure, based on a residue’s nuclear magnetic resonance (NMR) chemical shifts and amino acid type, and those of its adjacent residues.
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