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Showing 20 records out of 369 total
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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.
Categories: genomics, (sequence alignment), evolutionary biology - Software type(s): CLI - tool
The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.
Categories: proteomics, (protein sequences and identification, function analysis) - Software type(s): website - database
neXtProt is an innovative knowledge platform dedicated to human proteins. This resource contains a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt is continuously extended so as to provide many more carefully selected data sets and analysis tools.
Categories: IT infrastructure - Software type(s): CLI - tool
Nfswatch is a command-line tool for monitoring NFS traffic. Nfswatch can capture and analyze the NFS packets on a particular network interface or on all interfaces.
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Categories: proteomics, (protein modifications) - Software type(s): website - tool
Prediction of N-terminal N-myristoylation of proteins
Categories: proteomics, (protein structure) - Software type(s): website - tool
NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures and corrects them.
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