Similarity Matrix of Proteins (SIMAP) is a database of protein similarities created using volunteer computing. It is freely accessible for scientific...
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BLOSUM (redirect from Blosum matrix)
bioinformatics, the BLOSUM (BLOcks SUbstitution Matrix) matrix is a substitution matrix used for sequence alignment of proteins. BLOSUM matrices are used to score...
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nucleotide similarity matrices are much simpler than protein similarity matrices. For example, a simple matrix will assign identical bases a score of +1 and...
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Germinal matrix Hair matrix cell Matrix attachment region Matrix metalloproteinase Matrix protein PAM matrix Position-specific scoring matrix Similarity matrix...
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Sequence alignment (redirect from Sequence similarity search)
alignments of proteins, the degree of similarity between amino acids occupying a particular position in the sequence can be interpreted as a rough measure of how...
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divergent proteins. The probabilities used in the matrix calculation are computed by looking at "blocks" of conserved sequences found in multiple protein alignments...
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Point accepted mutation (redirect from PAM matrix)
alignments for proteins. Each entry in a PAM matrix indicates the likelihood of the amino acid of that row being replaced with the amino acid of that column...
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determination of protein structures from NMR or X-ray crystallography. Sometimes it is more convenient to express data as a similarity matrix. It is also...
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A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry...
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multiple sequence alignment of a protein family reveals a common level of similarity throughout the lengths of the proteins, PIR refers to the family as...
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Families of Structurally Similar Proteins or FSSP is a database of structurally superimposed proteins generated using the "Distance-matrix ALIgnment"...
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family of proteases known as the metzincin superfamily. Collectively, these enzymes are capable of degrading all kinds of extracellular matrix proteins, but...
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database of RNA families IRESbase: A comprehensive database of experimentally validated internal ribosome entry sites. (See also: List of proteins in the...
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Structural alignment (redirect from Protein structural similarity)
valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by...
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protein 2, so named because it shares extensive similarity with known extracellular matrix proteins. GRCh38: Ensembl release 89: ENSG00000106823 – Ensembl...
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Circuit topology Structural classification of proteins CATH HB plot Dot plot (bioinformatics) Self-similarity matrix Pietal, MJ.; Bujnicki, JM.; Kozlowski...
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SIMAP or simap may refer to: Similarity Matrix of Proteins, a database of protein similarities simap.ch, the official gazette for Swiss government procurement...
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Gap penalty (section Scoring matrix)
algorithm is a dynamic programming algorithm. When comparing proteins, one uses a similarity matrix which assigns a score to each possible residue pair. The...
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Needleman–Wunsch algorithm (section Similarity matrix)
similarity matrix. Here, S(a, b) is the similarity of characters a and b. It uses a linear gap penalty, here called d. For example, if the similarity...
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Cytoskeleton (redirect from Cytoskeletal proteins)
Penrose suggest a role of microtubule vibrations in neurons in the origin of consciousness. Accessory proteins including motor proteins regulate and link the...
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BLAST (biotechnology) (section Types of BLAST)
amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide...
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Smith–Waterman algorithm (section Substitution matrix)
the similarity measure. The algorithm was first proposed by Temple F. Smith and Michael S. Waterman in 1981. Like the Needleman–Wunsch algorithm, of which...
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(2011-09-03). "Information on SIMAP". Retrieved 2012-02-05. "SIMAP — Similarity Matrix of Proteins". 2012. Archived from the original on 2012-01-15. Retrieved...
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Nucleoplasm (section Similarity to cytoplasm)
replication, and a variety of metabolic processes. These proteins are divided into histone proteins, a class of proteins that bind to DNA and give chromosomes...
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Sequence homology (redirect from Sequence similarity)
among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant similarity is strong evidence that...
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of all proteins in a certain genome, we could check each protein in that genome for non-overlapping regions of sequence similarity to both proteins A...
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Singular value decomposition (redirect from Matrix approximation)
factorization of a real or complex matrix into a rotation, followed by a rescaling followed by another rotation. It generalizes the eigendecomposition of a square...
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enzymes represent an ancient family of proteins with major similarities in genetic make-up that are present in a range of diverse organisms from unicellular...
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Link prediction (section Cosine similarity)
including unsupervised approaches such as similarity measures computed on the entity attributes, random walk and matrix factorization based approaches, and...
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Mitochondrion (redirect from Mitochondrial proteins)
generates ATP in the matrix Specific transport proteins that regulate metabolite passage into and out of the mitochondrial matrix It contains more than...
165 KB (18,329 words) - 21:48, 15 July 2024