Search results
Results from the WOW.Com Content Network
Algorithm and program for comparing primary biological sequence information, including DNA and protein sequences. Cross-platform: Public domain: National Center for Biotechnology Information: CP2K: Perform atomistic simulations of solid state, liquid, molecular and biological systems, written in Fortran 2003. Linux, macOS, Windows: GPL and LGPL
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.
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 ...
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.
Example multiple sequence alignment. There are millions of protein and nucleotide sequences known. These sequences fall into many groups of related sequences known as protein families or gene families. Relationships between these sequences are usually discovered by aligning them together and assigning this alignment a score.
Loop modeling is a problem in protein structure prediction requiring the prediction of the conformations of loop regions in proteins with or without the use of a structural template. Computer programs that solve these problems have been used to research a broad range of scientific topics from ADP to breast cancer .
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 ...
For protein sequence spaces, each residue in the protein is represented by a dimension with 20 possible positions along that axis corresponding to the possible amino acids. [ 3 ] [ 4 ] Hence there are 400 possible dipeptides arranged in a 20x20 space but that expands to 10 130 for even a small protein of 100 amino acids arranged in a space with ...