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Swiss Mass Abacus is a calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations. TOF-DS Proprietary: Software by Markes International used with BenchTOF time-of-flight mass spectrometers. TopFD Open source
Protein sequences can describe larger proteins and chemical language files such as mol files can describe simple peptides. But the complexity of new research biomolecules makes describing large complex molecules difficult with chemical formats, and peptide formats are not sufficiently flexible to describe non-natural amino acids and other ...
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]
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.
Solid-phase synthesis is a common technique for peptide synthesis.Usually, peptides are synthesised from the carbonyl group side (C-terminus) to amino group side (N-terminus) of the amino acid chain in the SPPS method, although peptides are biologically synthesised in the opposite direction in cells.
In computational biology, protein pK a calculations are used to estimate the pK a values of amino acids as they exist within proteins.These calculations complement the pK a values reported for amino acids in their free state, and are used frequently within the fields of molecular modeling, structural bioinformatics, and computational biology.
A synthetic version of the target peptide containing a stable isotope label is added in a known amount to the digested sample to serve as an internal standard (SIS). Since the target peptide and SIS are chemically indistinguishable throughout the workflow, but can be measured separately by a mass spectrometer due to the mass difference of the ...
In molecular biology, protein catabolism is the breakdown of proteins into smaller peptides and ultimately into amino acids. Protein catabolism is a key function of digestion process. Protein catabolism often begins with pepsin, which converts proteins into polypeptides. These polypeptides are then further degraded.