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
This program delineates coiled-coil domains in otherwise globular proteins, such as the leucine zipper domains in transcriptional regulators, and to predict regions of discontinuity within coiled-coil structures, such as the hinge region in myosin.
epestfind allows rapid and objective identification of PEST motifs in protein target sequences. Those proteins share high local concentrations of amino acids proline (P), glutamic acid (E), serine (S), threonine (T) and to a lesser extent aspartic acid (D). It seems that PEST motifs reduce the half-lives of proteins dramatically and hence, that they target proteins for proteolytic degradation
The MultiCoil program predicts the location of coiled-coil regions in amino acid sequences and classifies the predictions as dimeric or trimeric. The method is based on the PairCoil algorithm. To analyze your own sequences with MultiCoil, you can either use the web interface or download the program.
The Paircoil program predicts the location of coiled-coil regions in amino acid sequences.
Paircoil2 predicts the parallel coiled coil fold from sequence using pairwise residue probabilities with the Paircoil algorithm and an updated coiled coil database. Paircoil2 shows improved performance over Paircoil and other coiled-coil prediction algorithms.
The pftools are a collection of programs to build, calibrate, and search biological sequences with generalized profiles. Generalized profiles are an extension of position specific scoring matrices by including position specific scores for insertions and deletions. They correspond to a matrix representation of a multiple sequence alignment that can be used to search distant homologous sequences and precisely align sequences to the model.
RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. Many large proteins have evolved by internal duplication and many internal sequence repeats correspond to functional and structural units. Radar is uses an automatic algorithm, for segmenting your query sequence into repeats, it identifies short composition biased as well as gapped approximate repeats and complex repeat architectures involving many different types of repeats in your query sequence.
Protein search for repeats, using a collection of repeat families
REPRO is able to recognise distant repeats in a single query sequence. The technique relies on a variation of the Smith-Waterman local alignment strategy to find non-overlapping top-scoring local alignments, followed by a graph-based iterative clustering procedure to delineate the repeat set(s) based on consistency of the pairwise top-alignments.
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.
T-REKS is an algorithm for de novo detection and alignment of repeats in sequences based on K-means algorithm. Minimal length of repeat arrays is 9 for true homorepeats and 14 for other repeats with potential biological meaning.
TRUST is a method for ab-initio determination of internal repeats in proteins. The high sensitivity and accuracy of the method is achieved by exploiting the concept of transitivity of alignments.
XSTREAM is a rapid and powerful algorithm for identifying perfect and degenerate tandem repeat motifs in protein (and nucleotide) sequence data. XSTREAM also effectively models the architecture of repetitive domains in tandem repeat proteins and eliminates motif redundancy to identify "fundamental" tandem repeat patterns.