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The tendency for proteins to remain attached to a surface depends largely on the material properties such as surface energy, texture, and relative charge distribution. Larger proteins are more likely to adsorb and remain attached to a surface due to the higher number of contact sites between amino acids and the surface (Figure 1).
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).
Method that uses the distribution of hydrophobic and electrostatic patches on the surface of the protein, factoring in the intensity and relative orientation of the respective surface patches into an aggregation propensity function that has been trained on a benchmark set of 31 adnectin proteins. sequence - Amyloidogenic regions AggreRATE-Pred [48]
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.
This list of protein subcellular localisation prediction tools includes software, databases, and web services that are used for protein subcellular localization prediction. Some tools are included that are commonly used to infer location through predicted structural properties, such as signal peptide or transmembrane helices , and these tools ...
Usually, the active site of a protein locates on its center of action and, the key to its function. The first step is the detection of active sites on the protein surface and an exact description of their features and boundaries. These specifications are vital inputs for subsequent target druggability prediction or target comparison.
This difference is due to the different methods used to measure hydrophobicity. The method used to obtain the Janin and Rose et al. scales was to examine proteins with known 3-D structures and define the hydrophobic character as the tendency for a residue to be found inside of a protein rather than on its surface.
Relative accessible surface area or relative solvent accessibility (RSA) of a protein residue is a measure of residue solvent exposure. It can be calculated by formula: It can be calculated by formula: