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Showing 20 records out of 30 total
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Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
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
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
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.
Categories: proteomics, (protein structure), Genomics, (characterisation/annotation), Structure analysis - 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 structure) - Software type(s): website - tool
DLP-SVM is a domain linker predictor. It is composed of three loop-length dependent SVM predictors of domain linkers (SVM-All, SVM-Long and SVM-Short), and SVM-Joint, which combines the results of SVM-Short and SVM-Long into a single consolidated prediction.
ELM
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
Eukaryotic Linear Motif resource for functional sites in proteins
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
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
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
The program scans a protein sequence against the PRINTS Protein Fingerprint Database.
Categories: Genomics, (characterisation/annotation), Evolutionary biology - Software type(s): website - database
A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
InterProScan is a tool that combines different protein signature recognition methods into one resource. The number of signature databases and their associated scanning tools, as well as the further refinement procedures, increases the complexity of the problem.
Categories: proteomics, (protein structure), Structure analysis - Software type(s): website, CLI - tool
predicting coiled-coils in protein sequences
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
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.
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
Image Creator for linear (multi) domain views
keywords: protein domain
Categories: proteomics, (Sequence sites, features and motifs, similarity search/alignment) - Software type(s): website - database/tool
Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models.
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
The Paircoil program predicts the location of coiled-coil regions in amino acid sequences.
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
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.
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
PattInProt allows to scan a protein database of one or several sequences for one or several patterns written in PROSITE syntax. The tool allows to specify an allowed number of mismatches or a similarity threshold towards the pattern.
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
Scans a sequence against the Pfam protein families database.
Categories: proteomics, (Sequence sites, features and motifs, similarity search/alignment) - Software type(s): library - tool
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.
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
Search your query sequence for protein motifs, rapidly compare your query protein sequence against all patterns stored in the PROSITE pattern database and determine what the function of an uncharacterised protein is. This tool requires a protein sequence as input, but DNA/RNA may be translated into a protein sequence using transeq and then queried. Allows a graphical output.
Categories: proteomics, (Sequence sites, features and motifs) - Software type(s): website - tool
An important problem in sequence analysis is to find patterns matching sets or subsets of sequences. This tool allows the user to discover patterns conserved in sets of unaligned protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported. The patterns are reported using PROSITE syntax.
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