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Secondary structure prediction involves a set of methods in bioinformatics that aim to predict the local secondary structures of proteins and RNA sequences based only on knowledge of their primary structure – amino acid or nucleotide sequence, respectively.
HSAB is an acronym for "hard and soft (Lewis) acids and bases".HSAB is widely used in chemistry for explaining the stability of compounds, reaction mechanisms and pathways. It assigns the terms 'hard' or 'soft', and 'acid' or 'base' to chemical species.
Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the local secondary structures of proteins based only on knowledge of their amino acid sequence. For proteins, a prediction consists of assigning regions of the amino acid sequence as likely alpha helices , beta strands (often termed extended ...
As the name suggests, a non-nucleophilic base is a sterically hindered organic base that is a poor nucleophile.Normal bases are also nucleophiles, but often chemists seek the proton-removing ability of a base without any other functions.
For proteins, this means predicting the formation of protein structures such as alpha helices and beta strands, while for nucleic acids it means predicting the formation of nucleic acid structures like helixes and stem-loop structures through base pairing and base stacking interactions. Secondary structure prediction can refer to:
The essence of Brønsted–Lowry theory is that an acid is only such in relation to a base, and vice versa. Water is amphoteric as it can act as an acid or as a base. In the image shown at the right one molecule of H 2 O acts as a base and gains H + to become H 3 O + while the other acts as an acid and loses H + to become OH −.
However, per definition, de novo proteins lack homologous sequences, as they are evolutionarily new. [17] Thus, structure prediction software which relies on such homology can be expected to perform poorly in predicting structures of de novo proteins. [18] To improve accuracy of structure prediction for de novo proteins, new softwares have been ...
Primary structure: the amino acid sequence. A protein is a polyamide. Secondary structure: regularly repeating local structures stabilized by hydrogen bonds. The most common examples are the α-helix, β-sheet and turns. Because secondary structures are local, many regions of distinct secondary structure can be present in the same protein molecule.