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Structure determination by NMR has traditionally been a time-consuming process, requiring interactive analysis of the data by a highly trained scientist. There has been considerable interest in automating the process to increase the throughput of structure determination and to make protein NMR accessible to non-experts (See structural genomics ...
The Collaborative Computing Project for NMR (CCPN) is a project that aims to bring together computational aspects of the scientific community involved in NMR spectroscopy, especially those who work in the field of protein NMR. The general aims are to link new and existing NMR software via a common data standard and provide a forum within the ...
SEQUEST is a MS data analysis program used for protein identification. It correlates collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences. [21] SIMS Open source: SIMS was designed to perform unrestricted PTM searches over tandem mass spectra. [22] SimTandem Freeware
All chemical shifts in RefDB have been computationally re-referenced to DSS (a common NMR chemical shift standard). [1] RefDB is a continuously updated resource that uses web-bots to query public databases (BMRB, GenBank, Protein Data Bank) and fetch assignment, sequence and structure data on a weekly basis.
The database contains also a smaller amount of NMR data from carbohydrates, cofactors and ligands. [1] These data are crossreferenced to 3D structures in the PDB when available. The NMR data are provided in the NMR-STAR file format and a number of format conversion tools are available at the site to convert files from NMR-STAR to other formats. [1]
The Protein Data Bank was announced in October 1971 in Nature New Biology [10] as a joint venture between Cambridge Crystallographic Data Centre, UK and Brookhaven National Laboratory, US. Upon Hamilton's death in 1973, Tom Koetzle took over direction of the PDB for the subsequent 20 years.
Example of chemical shift index. The chemical shift index or CSI is a widely employed technique in protein nuclear magnetic resonance spectroscopy that can be used to display and identify the location (i.e. start and end) as well as the type of protein secondary structure (beta strands, helices and random coil regions) found in proteins using only backbone chemical shift data [1] [2] The ...
PROSESS (Protein Structure Evaluation Suite & Server) is a new web server that offers an assessment of protein structural models by NMR chemical shifts as well as NOEs, geometrical, and knowledge-based parameters. LACS Linear analysis of chemical shifts is used for absolute referencing of chemical shift data.