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TPP also does: Protein Quantification with XPRESS (calculates relative peptide/protein abundances from isotopically labeled MS/MS samples); ASAPRatio (Automated Statistical Analysis on Protein Ratio, an alternative to XPRESS); and Libra (quantification of isobarically-labeled samples (e.g. iTraq, TMT, etc.) for any number of channels).
Mascot identifies proteins by interpreting mass spectrometry data. The prevailing experimental method for protein identification is a bottom-up approach, where a protein sample is typically digested with trypsin to form smaller peptides. While most proteins are too large, peptides usually fall within the limited mass range that a typical mass ...
The peak list obtained through spectrometric means is used as the query in a database search using the software MASCOT. [11] The MASCOT software uses an algorithm that looks for significant peptide sequence homology to present the most statistically likely protein in the sample, based on the results.
The number of such isolated non-degenerate singularities will be the number of points that have been infinitesimally glued. Precisely, another function germ g which is non-singular at the origin is taken and considered the new function germ h := f + εg where ε is very small. When ε = 0 then h = f.
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.
This list of protein subcellular localisation prediction tools includes software, databases, and web services that are used for protein subcellular localization prediction. Some tools are included that are commonly used to infer location through predicted structural properties, such as signal peptide or transmembrane helices , and these tools ...
The possible peptide that has the most similar spectrum will have the highest chance to be the right sequence. However, the number of possible peptides may be large. For example, a precursor peptide with a molecular weight of 774 has 21,909,046 possible peptides. Even though it is done in the computer, it takes a long time. [17] [18]
The number of notable protein-ligand docking programs currently available is high and has been steadily increasing over the last decades. The following list presents an overview of the most common notable programs, listed alphabetically, with indication of the corresponding year of publication, involved organisation or institution, short description, availability of a webservice and the license.