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Showing 20 records out of 375 total
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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, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Multiple alignment server
keywords: sequence alignment
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, (protein modifications) - Software type(s): website - tool
Predict N-terminal myristoylation of proteins by neural networks. Myristoylator uses ensembles of neural networks, in order to learn to discriminate positive and negative sequences for N-myristoylation.
Categories: proteomics, (proteomics experiment), glycomics - Software type(s): CLI, API - tool
MzJava is an open-source Java library for the analysis of mass spectrometry data. It provides algorithms and data structures for processing mass spectra and their associated biological molecules, such as small molecules, glycans, proteins, and peptides with post-translational modifications. MzJava includes methods to perform mass calculation, protein digestion, peptide and glycan fragmentation, MS/MS signal processing, and scoring for spectra-spectra and peptide/glycan-spectra matches.
Categories: proteomics, genomics - Software type(s): CLI, GUI - tool
MzVar is a Java tool allowing the compilation of customized variant protein and peptide databases in the FASTA format for database searching of MS/MS data, using a VCF file as variant input and a FASTA file as transcript input. The tool is compatible with transcript sequences retrieved from either Ensembl or the UCSC Table Browser.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
NetAcet predicts substrates of N-acetyltransferase A (NatA). The method was trained on yeast data but it obtains similar performance values on mammalian substrates acetylated by NatA orthologs.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
Neural network predictions of C-mannosylation sites in mammalian proteins.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
NetCorona predicts coronavirus 3C-like proteinase (or protease) cleavage sites using artificial neural networks on amino acid sequences. Every potential site is scored and a list is compiled in addition to a graphical representation.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Predicts glycation of epsilon amino groups of lysines in mammalian proteins.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
NetNES 1.1 server predicts leucine-rich nuclear export signals (NES) in eukaryotic proteins using a combination of neural networks and hidden Markov models.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
NetNGlyc predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
Neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
NetPhos produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The NetPhosK 1.0 server produces neural network predictions of kinase specific eukaryotic protein phosphorylation sites. Currently NetPhosK covers the following kinases: PKA, PKC, PKG, CKII, Cdc2, CaM-II, ATM, DNA PK, Cdk5, p38 MAPK, GSK3, CKI, PKB, RSK, INSR, EGFR and Src.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
predict serine and threonine phosphorylation sites in yeast proteins
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The NetPicoRNA 1.0 server produces neural network predictions of cleavage sites of picornaviral proteases.
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.
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