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A beta hairpin is a common supersecondary motif composed of two anti-parallel beta strands connected by a loop. The structure resembles a hairpin and is often found in globular proteins. The loop between the beta strands can range anywhere from 2 to 16 residues. However, most loops contain less than seven residues. [2]
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
Local structure motif library: Protein JCoils Prediction of Coiled coil and Leucine Zipper: Protein MEME/MAST Motif discovery and search: Both CUDA-MEME GPU accelerated MEME (v4.4.0) algorithm for GPU clusters: Both MERCI Discriminative motif discovery and search: Both PHI-Blast Motif search and alignment tool: Both Phyloscan: Motif search tool ...
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An alpha-helix with hydrogen bonds (yellow dots) The α-helix is the most abundant type of secondary structure in proteins. The α-helix has 3.6 amino acids per turn with an H-bond formed between every fourth residue; the average length is 10 amino acids (3 turns) or 10 Å but varies from 5 to 40 (1.5 to 11 turns).
To do this it marks a local motif alignment with flags to indicate which residues simultaneously satisfy more stringent criteria: 1) Local structure overlap 2) regular secondary structure 3) 3D-superposition 4) same ordering in primary sequence.
The resulting structure is a key building block of many RNA secondary structures. Cruciform DNA Cruciform DNA is a form of non-B DNA that requires at least a 6 nucleotide sequence of inverted repeats to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative DNA supercoiling. [3]
I-TASSER is a template-based method for protein structure and function prediction. [1] The pipeline consists of six consecutive steps: 1, Secondary structure prediction by PSSpred; 2, Template detection by LOMETS [6] 3, Fragment structure assembly using replica-exchange Monte Carlo simulation [7]