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.
Prediction of transmembranes helices and topology of proteins.
predicting coiled-coils in protein sequences
Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein.
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.
Classification and Secondary Structure Prediction of Membrane Proteins.
TMHMM is a membrane protein topology prediction method based on a hidden Markov model (HMM). It predicts transmembrane helices in proteins.
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
Topology prediction of membrane proteins
UniProtKB/Swiss-Prot is the manually annotated component of UniProtKB (produced by the UniProt consortium). It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis.
, disease mutation
, enzyme (catalytic activity)
, family database
, functional annotation
, gene nomenclature
, physico-chemical property
, post-translational modification (PTM)
, protein data bank (PDB)
, protein domain
, protein family
, protein function
, protein nomenclature
, protein sequence analysis (primary structure)
, protein variation (variant)
, quaternary structure
, secondary structure
, sequence alignment
, sequence analysis
, tertiary structure
, topology prediction
, transmembrane (trans-membrane)