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The Wimley–White whole residue hydrophobicity scales are significant for two reasons. First, they include the contributions of the peptide bonds as well as the sidechains, providing absolute values. Second, they are based on direct, experimentally determined values for transfer free energies of polypeptides.
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
Color-coding: hydrophobicity from microenvironment in folded proteins [10] The classical table/wheel of the standard genetic code is arbitrarily organized based on codon position 1. Saier, [ 11 ] following observations from, [ 12 ] showed that reorganizing the wheel based instead on codon position 2 (and reordering from UCAG to UCGA) better ...
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]
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.
The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide bond planar. [3] The figure in the top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and ...
The HOMA model was originally designed as a special case of a more general structural (HOMA-CIGMA) model that includes the continuous infusion of glucose with model assessment (CIGMA) approach; both techniques use mathematical equations to describe the functioning of the major effector organs influencing glucose/insulin interactions.
The peptide length is limited due to the cyclical derivatization not always going to completion. The derivatization problem can be resolved by cleaving large peptides into smaller peptides before proceeding with the reaction. It is able to accurately sequence up to 30 amino acids with modern machines capable of over 99% efficiency per amino acid.