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Showing 6 records out of 6 total

Categories: proteomics, (function analysis) - Software type(s): website - tool
GPMAW lite is a protein bioinformatics tool to perform basic bioinformatics calculations on any protein amino acid sequence, including predicted molecular weight, molar absorbance and extinction coefficient, isoelectric point and hydrophobicity index, as well as amino acid composition and protease digest.
Categories: proteomics - Software type(s): website - tool
The HCA method is based on the use of a bidimensional plot, called the HCA plot. The bidimensional plot is associated with an alpha helicoidal pitch (3.6 residue/turn, connectivity distance of 4) which has been shown to offer the best correspondence between clusters and regular secondary structures. Examination of the HCA plot of a protein sequence allow to easily identify globular regions from non globular ones and, in globular regions, to identify secondary structures.
Categories: function analysis, similarity search/alignment - Software type(s): website - tool
PROPSEARCH was designed to detect functional and / or structural homologs, if the sequence identity is below about 25%. It uses the amino acid physico-chemical properties, content of bulky residues, content of small residues, average hydrophobicity, average charge a.s.o. and are used as query vector. Sequences in the database are transformed into vectors as well, and the euclidian distance between the query and database sequences is calculated.
Categories: proteomics, (function analysis) - Software type(s): website - tool
Compute various physical and chemical parameters for a given protein sequence. The computed parameters include the molecular weight, theoretical pI (isoelectric point), amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).
Categories: proteomics, (function analysis) - Software type(s): website - tool
Compute and represent the profile produced by any amino acid scale on a selected protein sequence. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but ProtScale provides more than 50 predefined scales entered from the literature.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website, GUI - tool
WeStBESel is a tool to help selecting the most relevant B-cell epitopes according to the user needs (i.e. vaccines, diagnostic test, etc). We use a mixed approach by combining : physico-chemical property-based approaches (conservation intra and interspecies, PTM, hydrophobicity, solvent accessibility, disorder and mutations), sliding windows algorithm paired with five of the best B-cell epitopes prediction tools (ABCPred, AAP, BCPred, BepiPred, SVMTrip).