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Showing 20 records out of 27 total
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Categories: proteomics, (protein structure) - Software type(s): website - tool
Advanced Protein Secondary Structure Prediction Server
Categories: proteomics, (protein structure) - Software type(s): website - tool
This server predicts secondary structure of protein from the amino acid sequence. In this server, Chou & Fasman algorithm has been implemented.
Categories: proteomics, (families, patterns and profiles) - 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), 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, (post-translational modification) - Software type(s): website - tool
DAS (Dense Alignment Surface) is based on low-stringency dot-plots of the query sequence against a set of library sequences - non-homologous membrane proteins - using a previously derived, special scoring matrix. The method provides a high precision hyrdophobicity profile for the query from which the location of the potential transmembrane segments can be obtained. The novelty of the DAS-TMfilter algorithm is a second prediction cycle to predict TM segments in the sequences of the TM-library.
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.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Protein secondary structure prediction
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: proteomics, (families, patterns and profiles) - Software type(s): website - tool
HeliQuest calculates from the amino acid sequence of a helix (??-helix, 3-10 helix, 3-11 helix or ?? helix) its physicochemical properties and amino acid composition and uses the results to screen any databank in order to identify protein segments possessing similar features.
Categories: proteomics, (post-translational modification) - Software type(s): website - tool
Prediction of transmembranes helices and topology of proteins.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Helical TransMembrane Segment Rotational Angle Prediction
Categories: proteomics, (protein structure) - Software type(s): website - tool
Secondary Structure Prediction Server
Categories: proteomics, (protein structure), structural bioinformatics - Software type(s): website, CLI - tool
predicting coiled-coils in protein sequences
Categories: proteomics, (families, patterns and profiles) - 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, (protein structure) - Software type(s): website - tool
NetSurfP server predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method also simultaneously predicts the reliability for each prediction, in the form of a Z-score. The Z-score is related to the surface prediction, and not the secondary structure.
Categories: proteomics, (protein structure) - Software type(s): website - tool
NetTurnP predicts if an amino acid is located in a Beta-turn or not. Optional, NetTurnP is also able to predict the nine Beta-turn subtypes.
Categories: proteomics, (families, patterns and profiles) - Software type(s): website - tool
The Paircoil program predicts the location of coiled-coil regions in amino acid sequences.
Categories: proteomics, (families, patterns and profiles) - 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 - Software type(s): website - tool
Protein Secondary Structure Prediction
Categories: proteomics, (protein characterisation and function, families, patterns and profiles, post-translational modification, protein-protein interaction) - Software type(s): website - tool
PredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intra-residue contacts, protein-protein and protein-DNA binding sites, sub-cellular localization, domain boundaries, beta-barrels, cysteine bonds, metal binding sites and disulphide bridges.
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