Homology modelingHomology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence.
Sequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
Recursive definitionIn mathematics and computer science, a recursive definition, or inductive definition, is used to define the elements in a set in terms of other elements in the set (Aczel 1977:740ff). Some examples of recursively-definable objects include factorials, natural numbers, Fibonacci numbers, and the Cantor ternary set. A recursive definition of a function defines values of the function for some inputs in terms of the values of the same function for other (usually smaller) inputs.
Block size (cryptography)In modern cryptography, symmetric key ciphers are generally divided into stream ciphers and block ciphers. Block ciphers operate on a fixed length string of bits. The length of this bit string is the block size. Both the input (plaintext) and output (ciphertext) are the same length; the output cannot be shorter than the input - this follows logically from the pigeonhole principle and the fact that the cipher must be reversible - and it is undesirable for the output to be longer than the input.
