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Showing 20 records out of 27 total
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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
SCRATCH is a server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Secondary Structure Prediction System
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, (protein structure) - Software type(s): website - tool
Secondary structure prediction.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Protein secondary structure prediction
Categories: proteomics, (protein structure) - Software type(s): website - tool
Advanced Protein Secondary Structure Prediction Server
Categories: proteomics, (protein structure) - Software type(s): website - tool
Secondary Structure Prediction Server
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, (function analysis, protein modifications) - Software type(s): website - tool
Classification and secondary structure srediction of membrane proteins.
Categories: proteomics, (function analysis, sequence sites, features and motifs, protein modifications, protein interactions) - 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.
Categories: proteomics - Software type(s): website - tool
Protein Secondary Structure Prediction
Categories: proteomics, (protein structure) - Software type(s): website, CLI - tool
The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occurring transmembrane proteins
Categories: proteomics, (protein structure), structure analysis - Software type(s): website, CLI - tool
predicting coiled-coils in protein sequences
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.
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: glycomics - Software type(s): website - database
UniCarb-DB stores data and information on glycan structures and associated fragment data characterised by LC-MS/MS strategies. It is annotated with high-quality datasets.
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, (sequence sites, features and motifs) - Software type(s): website, GUI - tool
WeStBESel is a tool to help selecting the most relevant B-cell epitopes according to the user needs (i.e. vaccines, diagnostic test, etc). We use a mixed approach by combining : physico-chemical property-based approaches (conservation intra and interspecies, PTM, hydrophobicity, solvent accessibility, disorder and mutations), sliding windows algorithm paired with five of the best B-cell epitopes prediction tools (ABCPred, AAP, BCPred, BepiPred, SVMTrip).
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