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Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
Software by NIST for compression of structure with mass spectra. The program seeks to find mechanisms and their rates for all fragmentation types (EI, Tandem positive and negative mode) and correlates mass spectral peaks to a probable origin structure. It contains an isotope calculator and other features and on-line help.
For a database of that size, by applying a Bonferroni correction to account for multiple comparisons, the significance threshold drops to 5*10 −8. [1] In addition to the calculated peptide scores, Mascot also estimates the False Discovery Rate (FDR) by searching against a decoy database. When performing a decoy search, Mascot generates a ...
Levinthal's paradox is a thought experiment in the field of computational protein structure prediction; protein folding seeks a stable energy configuration. An algorithmic search through all possible conformations to identify the minimum energy configuration (the native state) would take an immense duration; however in reality protein folding happens very quickly, even in the case of the most ...
The peptide's intact mass is known from the mass spectrum, and Sequest uses this information to determine the set of candidate peptides sequences that could meaningfully be compared to the spectrum by including only those near the mass of the observed peptide ion.
Point a is an ordinary point when functions p 1 (x) and p 0 (x) are analytic at x = a. Point a is a regular singular point if p 1 (x) has a pole up to order 1 at x = a and p 0 has a pole of order up to 2 at x = a. Otherwise point a is an irregular singular point.
A peptide library is a tool for studying proteins.Peptide libraries typically contain a large number of peptides that have a systematic combination of amino acids.Usually, solid phase synthesis, e.g. resin as a flat surface or beads, is used for peptide library generation.
Peptide bond formation via dehydration reaction. When two amino acids form a dipeptide through a peptide bond, [1] it is a type of condensation reaction. [2] In this kind of condensation, two amino acids approach each other, with the non-side chain (C1) carboxylic acid moiety of one coming near the non-side chain (N2) amino moiety of the other.