Protean 3D supports the following protein sequence file formats: *.aa, *.fap, *.fas, *.fasta, *.gp, *.gbk, *.sbd, and *.pro. Protean 3D also supports protein structure files from the Protein Data Bank (*.pdb, *.ent, *.pdb.gz, *.ent.gz, *.zip, *.txt), as well as structure files created by Protean 3D (*.structure) or one of our Nova Applications (*.novafold, *.antibody, *.novadock).

Protean 3D offers three methods for creating hydropathy profiles for protein sequence analysis:

• Hopp-Woods – predicts protein antigenic determinants by searching protein sequences for the area of greatest local hydrophilicity. Hopp and Woods, 1981, make two assumptions in using hydrophilicity to find antigenic determinants: 1) antigenic determinants are usually found on regions with a high degree of exposure to solvents and 2) antigenic determinants commonly possess charged hydrophilic side chains. Each residue is assigned a hydrophilicity value and these values are averaged over a hexamer window.
• Kyte-Doolittle – predicts regional hydropathy of proteins from their amino acid sequences, using the approach of Kyte and Doolittle, 1982. Hydropathy values are assigned for all amino acids and are then averaged over a user-defined window. The average is plotted at the midpoint of the window. Residue hydropathy assignments are derived from water-vapor transfer free energies and the interior-exterior distribution of residue side-chains.
• Parker – uses the method of Parker et al., 1986, which is a hydrophilicity scale based on high-performance liquid chromatography retention times of model synthetic peptides. Hydrophilicity measures have been used extensively in the prediction of antigenic amino acid residues. The Parker method uses a modified Hopp-Woods algorithm together with a new set of hydrophilicity options.

Protean 3D offers four methods for predicting secondary structures:

• Chou-Fasman – predicts secondary structure of proteins from the crystallographic structures of their amino acid sequences.
• Deléage-Roux – predicts secondary structure using the approach of Deléage and Roux, 1987. The method uses an independent prediction of the protein’s structural class to bias the prediction of its secondary structure.
• Garnier-Robson – predicts protein structure from the amino acid sequence. The method examines the propensity of a given residue to exist in a certain structure.
• Coiled Coil – predicts structures according to the formula of Lupas et al., 1991. You may use this track with the Transmembrane – Goldman-Engleman-Steitz track to predict transmembrane alpha helices.