PSF: an online search engine for protein segment motifs in the PDB
To assist the task of finding related conformations in the Protein Data Bank (PDB), I designed a search engine named protein segment finder (PSF) (1). The search engine uses a compact database to quickly identify protein segments obeying a set of primary, secondary and tertiary structure constraints. The database contains information such as amino acid sequence, secondary structure, disulfide bonds, hydrogen bonds, and atoms in contact as calculated from all protein structures in the PDB. The search engine parses the database and returns hits that match the queried parameters. PSF which is notable for its high speed and interactive feedback, is expected to assist scientists in discovering conformation homologs and predicting protein structure. PSF is publicly available online at http://ari.stanford.edu/psf
PHI-DAC: Protein Homology Database through Dihedral Angle Conservation
Finding related conformations in the Protein Data Bank (PDB) is essential in many areas of bioscience. To assist this task, we designed a dihedral angle database for searching protein segment homologs. The search engine relies on encoding of the protein coordinates into text characters representing amino-acid sequence, φ, and ψ dihedral angles. The search engine is advantageous due to its high speed and interactive nature and is expected to assist scientists in discovering conformation homologs and evolutionary kinship. The search engine is fast with query times lasting a few seconds, and freely available at http://tarshish.md.biu.ac.il/~samsona
Helical Wheel Projection
Helical wheel is a program produce visual representation used to illustrate the properties of alpha helices in proteins. The sequence of amino acids that make up a helical region of the protein's secondary structure are plotted in a rotating manner where the angle of rotation between consecutive amino acids is 100°, so that the final representation looks down the helical axis. Helical Wheel Projection is publicly available online at http://tarshish.md.biu.ac.il/~genadif/index_new.html
References
1. Samson, A. O. & Levitt, M. (2009). Protein segment finder: an online search engine for segment motifs in the PDB. Nucleic Acids Res 37, D224-8.
