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Showing 20 records out of 375 total
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Categories: proteomics - Software type(s): website - tool
Protein Secondary Structure Prediction
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.
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 search for 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.
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, (protein modifications) - Software type(s): website - tool
Predotar was designed for systematic screening of large batches of proteins for identifying putative targeting sequences, and recognizes the N-terminal targeting sequences of classically targeted precursor proteins. It provides a probability estimate as to whether the sequence contains a mitochondrial, plastid or ER targeting sequence.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The prenylation prediction suite (PrePS) combines three predictors for protein CaaX farnesylation, CaaX geranylgeranylation and Rab geranylgeranylation in one webinterface. The predictors aim to model the substrate-enzyme interactions based on refinement of the recognition motifs for each of the prenyltransferases.
Categories: proteomics - Software type(s): library - tool
A package (R, S+) to visualize, smooth and compare receiver operating characteristic (ROC curves)
keywords:
Categories: proteomics, (protein structure) - Software type(s): website - tool
PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
ProDom is a protein domain family database constructed automatically by clustering homologous segments. Compare your sequence with ProDom by running a Blast-P or Blast-X search against: the consensus sequence provided with the ProDom families or the multiple alignments provided with each ProDom family. ProDom-CG (Complete Genomes) and ProDom-SG (Structural Genomics Candidate Search) can also be searched.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Secondary Structure Prediction System
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
Tool for searching protein sequence collections with peptide mass maps. A Bayesian algorithm is used to rank the protein sequences in the database according to their probability of producing the peptide map.
Categories: genomics, systems biology - Software type(s): website, CLI, library - database/tool
The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With >30000 cases from >1000 publications, Progenetix is the largest curated database for whole genome copy number profiles. The current dataset contains >20000 chromosomal CGH and >10000 profiles from genomic array experiments. This data covers hundreds of cancer entities.
Categories: proteomics - Software type(s): website - database
Publication électronique (en français) de vulgarisation scientifique du groupe Swiss-Prot de l'Institut Suisse de Bioinformatique dédiée aux protéines qui font parler d'elles dans l'actualité.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
ProP 1.0 server predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase (PC) prediction.
Categories: function analysis, similarity search/alignment - Software type(s): website - tool
PROPSEARCH was designed to detect functional and / or structural homologs, if the sequence identity is below about 25%. It uses the amino acid physico-chemical properties, content of bulky residues, content of small residues, average hydrophobicity, average charge a.s.o. and are used as query vector. Sequences in the database are transformed into vectors as well, and the euclidian distance between the query and database sequences is calculated.
Categories: proteomics, (protein structure) - Software type(s): website - tool
Program of error recognition in 3D structures
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - database
PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
Categories: proteomics, (protein structure, protein interactions) - Software type(s): website - tool
Comparison of asymmetric units and biological units from PDB and PQS
Categories: proteomics - Software type(s): website - tool
Protein Colourer is a tool for colouring amino acid sequences. The default settings will colour the sequence by the hydrophobicity of the amino acids. You can set the colouring scheme by changing the lists associated with each colour.
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