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Showing 11 records out of 11 total

Categories: proteomics, (protein sequences and identification, mass spectrometry and 2-DE data) - Software type(s): website - tool
Protein identification by amino acid composition, and optionally pI, Mw, species, UniProtKB keyword and calibration protein. Several constellations are available, corresponding to various amino acid analysis techniques.
Categories: proteomics, (protein characterisation and function) - Software type(s): website - tool
Compare amino acid composition of a UniProtKB entry with some or all other UniProtKB entries. Several constellations are available, corresponding to various amino acid analysis techniques.
Categories: proteomics, (protein structure), genomics, (characterisation/annotation), structural bioinformatics - Software type(s): website, CLI - tool
COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.
Categories: proteomics, (protein characterisation and function) - 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: protein characterisation and function, 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, (protein characterisation and function) - 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, (protein characterisation and function) - 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 - Software type(s): website - tool
Random protein sequence generator
Categories: proteomics, (protein characterisation and function) - Software type(s): website - tool
SAPS (Statistical Analysis of Protein Sequences) evaluates a wide variety of protein sequence properties using statistics. Properties considered include compositional biases, clusters and runs of charge and other amino acid types, different kinds and extents of repetitive structures, locally periodic motifs, and anomalous spacings between identical residue types.
Categories: proteomics, (protein structure), structural bioinformatics, biophysics, drug design - Software type(s): website - database
SwissSidechain is a structural and molecular mechanics database of hundreds of non-natural amino-acid sidechains that can be used to study in silico their insertion into natural peptides or proteins.