The leucine zipper is a dimerisation domain occurring mostly in regulatory and thus in many oncogenic proteins. 2ZIP combines a standard coiled coil prediction algorithm with an approximate search for the characteristic leucine repeat. No further information from homologues is required for prediction. This approach improves significantly over existing methods, especially in that the coiled coil prediction turns out to be highly informative and avoids large numbers of false positives
The 3of5 application aims at the analysis of protein sequences to find user-defined patterns, described via complex regular expressions-like terms, e.g. to search for a motif with 3 basic AAs in 5 positions.
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.
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.
Agadir predicts the helical behaviour of monomeric peptides. It only considers short range interactions. Conditions such as pH, temperature and ionic strength are used in the calculation. Modifications of the termini are also allowed.
Keep in mind that Agadir is not a program to predict secondary structure of proteins.
ALF simulates a wide range of evolutionary forces that act on genomes, such as character substitutions, indels, gene duplication, gene loss, lateral gene transfer and genome rearrangement.
Four tools for multiple alignments.
The AllAll server takes as input a set of protein sequences and returns various comparisons and visualizations- a distance-based phylogenetic tree, a split tree, some variation indices, some visualizations, the pairwise sequence distances and the most probable ancestral sequence.
ANOLEA (Atomic Non-Local Environment Assessment) is a server that performs energy calculations on a protein chain, evaluating the "Non-Local Environment" of each heavy atom in the molecule. The energy of each pairwise interaction is taken from a distance-dependent knowledge-based mean force potential that has been derived from a database of 147 non-redundant protein chains with a sequence identity below 25% and solved by X-Ray crystallography with a resolution lower than 3 A.
Advanced Protein Secondary Structure Prediction Server
Arlequin provides the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples. The graphical interface is designed to allow users to rapidly select the different analyses they want to perform on their data. One can explore the data, and analyze several times the same data set from different perspectives, with different selected options.
Ascalaph is a general purpose molecular modeling software that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics simulations in the gas or in condensed phase. It can interact with external molecular modeling packages (MDynaMix, NWChem, CP2K and PC GAMESS/Firefly).
AssociationViewer is a Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.
BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model.
GPI modification site prediction
Digitized version of the Roche Applied Science "Biochemical Pathways" wall chart. The map, linked to relevant ENZYME database entries, can be browsed online, and keyword searches are available.
Neighbor Joining (NJ) algorithm improved for molecular sequences
BLAST sequence similarity search (blastp or tblastn) against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB, EMBL, ESTs
BLAST sequence similarity search against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB or UniParc - on the UniProt web site.
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.