Top 10 similar words or synonyms for hexapeptides

pentapeptides    0.840392

tetrapeptides    0.838832

heptapeptides    0.836183

decapeptides    0.822079

heptapeptide    0.800110

octapeptides    0.797251

hexapeptide    0.787524

nonapeptides    0.758150

pentapeptide    0.755877

cyclopeptides    0.739182

Top 30 analogous words or synonyms for hexapeptides

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Sequence alignment The DALI method, or distance matrix alignment, is a fragment-based method for constructing structural alignments based on contact similarity patterns between successive hexapeptides in the query sequences. It can generate pairwise or multiple alignments and identify a query sequence's structural neighbors in the Protein Data Bank (PDB). It has been used to construct the FSSP structural alignment database (Fold classification based on Structure-Structure alignment of Proteins, or Families of Structurally Similar Proteins). A DALI webserver can be accessed at DALI and the FSSP is located at The Dali Database.
Catgrip Catgrips are small cation-binding molecular features of proteins and peptides. Each consists of the main chain atoms only of three consecutive amino acid residues. The first and third main chain CO groups bind the cations, often calcium, potassium or sodium, with no side chain involvement. Some catgrips bind a water molecule instead of a cation; it is hydrogen-bonded to the first and third main chain CO groups. Catgrips are found as calcium-binding features in annexins, matrix metalloproteinases (e.g.serralysins), subtilisins and phospholipase A2. They are also observed in synthetic peptides and in cyclic hexapeptides made from alternating D,L amino acids.
Rosetta@home A component of the Rosetta software suite, RosettaDesign, was used to accurately predict which regions of amyloidogenic proteins were most likely to make amyloid-like fibrils. By taking hexapeptides (six amino acid-long fragments) of a protein of interest and selecting the lowest energy match to a structure similar to that of a known fibril forming hexapeptide, RosettaDesign was able to identify peptides twice as likely to form fibrils as are random proteins. Rosetta@home was used in the same study to predict structures for amyloid beta, a fibril-forming protein that has been postulated to cause Alzheimer's disease. Preliminary but as yet unpublished results have been produced on Rosetta-designed proteins that may prevent fibrils from forming, although it is unknown whether it can prevent the disease.
Siderophore The soil is a rich source of bacterial and fungal genera. Common Gram-positive species are those belonging to the Actinomycetales and species of the genera "Bacillus", "Arthrobacter" and "Nocardia". Many of these organisms produce and secrete ferrioxamines which lead to growth promotion of not only the producing organisms, but also other microbial populations that are able to utilize exogenous siderophores . Soil fungi include "Aspergillus" and "Penicillium" which predominately produce ferrichromes. This group of siderophores consist of cyclic hexapeptides and consequently are highly resistant to environmental degradation associated with the wide range of hydrolytic enzymes that are present in humic soil. Soils containing decaying plant material possess pH values as low as 3–4. Under such conditions organisms that produce hydroxamate siderophores have an advantage due to the extreme acid stability of these molecules. The microbial population of fresh water is similar to that of soil, indeed many bacteria are washed out from the soil. In addition, fresh-water lakes contain large populations of "Pseudomonas", "Azomonas", "Aeromonos" and "Alcaligenes" species.
Glycosaminoglycan Unlike HSGAGs and CSGAGs, the third class of GAGs, those belonging to keratan sulfate types, are driven towards biosynthesis through particular protein sequence motifs. For example, in the cornea and cartilage, the keratan sulfate domain of aggrecan consists of a series of tandemly repeated hexapeptides with a consensus sequence of E(E/L)PFPS. Additionally, for three other keratan sulfated proteoglycans, lumican, keratocan, and mimecan (OGN), the consensus sequence NX(T/S) along with protein secondary structure was determined to be involved in "N"-linked oligosaccharide extension with keratan sulfate. Keratan sulfate elongation begins at the nonreducing ends of three linkage oligosaccharides, which define the three classes of keratan sulfate. Keratan sulfate I (KSI) is "N" -linked via a high mannose type precursor oligosaccharide. Keratan sulfate II (KSII) and keratan sulfate III (KSIII) are "O"-linked, with KSII linkages identical to that of mucin core structure, and KSIII linked to a 2-"O" mannose. Elongation of the keratan sulfate polymer occurs through the glycosyltransferase addition of Gal and GlcNAc. Galactose addition occurs primarily through the β-1,4-galactosyltransferase enzyme (β4Gal-T1) while the enzymes responsible for β-3-Nacetylglucosamine have not been clearly identified. Finally, sulfation of the polymer occurs at the 6-position of both sugar residues. The enzyme KS-Gal6ST (CHST1) transfers sulfate groups to galactose while N-acetylglucosaminyl-6-sulfotransferase (GlcNAc6ST) (CHST2) transfers sulfate groups to terminal GlcNAc in keratan sulfate.