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Here, is the probability of two amino acids and replacing each other in a homologous sequence, and and are the background probabilities of finding the amino acids and in any protein sequence. The factor λ {\displaystyle \lambda } is a scaling factor, set such that the matrix contains easily computable integer values.
Download as PDF; Printable version; ... Category for molecular biology sequencing in proteomics, such as protein sequencing. Subcategories. This category has the ...
In mass spectrometry, de novo peptide sequencing is the method in which a peptide amino acid sequence is determined from tandem mass spectrometry. Knowing the amino acid sequence of peptides from a protein digest is essential for studying the biological function of the protein. In the old days, this was accomplished by the Edman degradation ...
Because the Edman degradation proceeds from the N-terminus of the protein, it will not work if the N-terminus has been chemically modified (e.g. by acetylation or formation of pyroglutamic acid). Sequencing will stop if a non-α-amino acid is encountered (e.g. isoaspartic acid), since the favored five-membered ring intermediate is unable to be ...
Protein sequence interpretation: a scheme new protein to be engineered in a yeast. It is often desirable to know the unordered amino acid composition of a protein prior to attempting to find the ordered sequence, as this knowledge can be used to facilitate the discovery of errors in the sequencing process or to distinguish between ambiguous results.
For full 3-D threading, the problem of identifying the best alignment is very difficult (it is an NP-hard problem for some models of threading). [ citation needed ] Researchers have made use of many combinatorial optimization methods such as conditional random fields , simulated annealing , branch and bound , and linear programming , searching ...
The Chou–Fasman method predicts helices and strands in a similar fashion, first searching linearly through the sequence for a "nucleation" region of high helix or strand probability and then extending the region until a subsequent four-residue window carries a probability of less than 1.
A typical workflow of a peptide mass fingerprinting experiment. Peptide mass fingerprinting (PMF), also known as protein fingerprinting, is an analytical technique for protein identification in which the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer such as MALDI-TOF or ESI-TOF. [1]