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Protein Sequence Analysis Tools
Molecular server that is dedicated to the analysis of protein and nucleic acid sequence. *Protein identification and characterization:Identification and characterization with peptide mass fingerprinting data; Identification and characterization with MS/MS data; Identification with isoelectric point, molecular weight and/or amino acid composition; Other prediction or characterization tools; Other tools for MS data (vizualisation, quantitation, analysis, etc.); Other tools for 2-DE data (image analysis, data publishing, etc.). *DNA -> Protein *Similarity searches *Pattern and profile searches *Post-translational modification prediction *Topology prediction *Primary structure analysis *Secondary structure prediction *Tertiary structure: Tertiary structure analysis; Tertiary structure prediction; Assessing tertiary structure prediction; Quaternary structure; Molecular modeling and visualization tools; Molecular modeling and visualization tools; Prediction of disordered regions. *Sequence alignment: Binary; Multiple; Alignment analysis. *Gateways *Phylogenetic analysis *Biological text analysis
Protein coding region prediction in Bacterial DNA.
Welcome to Membrane Protein Explorer (MPEx), a tool for exploring the topology and other features of membrane proteins by means of hydropathy plots based upon thermodynamic principles.
PredictProtein is an Internet service for sequence analysis and the prediction of protein structure and function. Users submit protein sequences or alignments; PredictProtein returns multiple sequence alignments, PROSITE sequence motifs, low-complexity regions (SEG), nuclear localisation signals, regions lacking regular structure (NORS) and predictions of secondary structure, solvent accessibility, globular regions, transmembrane helices, coiled-coil regions, structural switch regions, disulfide-bonds, sub-cellular localization, and functional annotations.Upon request fold recognition by prediction-based threading, CHOP domain assignments, predictions of transmembrane strands and inter-residue contacts are also available. For all services, users can submit their query either by electronic mail, or interactively from World Wide Web.
ProDom is a protein domain family database constructed automatically by clustering homologous segments. The ProDom building procedure MKDOM2 is based on recursive PSI-BLAST searches [ALTS2]. The source protein sequences are non-fragmentary sequences derived from SWISS-PROT and TrEMBL databases.
ProtScale allows you to compute and represent the profile produced by any amino acid scale on a selected protein. An amino acid scale is defined by a numerical value assigned to each type of amino acid. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but many other scales exist which are based on different chemical and physical properties of the amino acids. This program provides 57 predefined scales entered from the literature.
Sequence Manipulation Suite (SMS)
Worldwide Protein Data Bank (wwPDB)
The wwPDB maintains a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.