pdbFun: mass selection and fast comparison of annotated PDB residues

Abstract

pdbFun (http://pdbfun.uniroma2.it) is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. Users can select any residue subset (even including any number of PDB structures) by combining the available features. Selections can be used as probe and target in multiple structure comparison searches. For example a search could involve, as a query, all solvent-exposed, hydrophylic residues that are not in alpha-helices and are involved in nucleotide binding. Possible examples of targets are represented by another selection, a single structure or a dataset composed of many structures. The output is a list of aligned structural matches offered in tabular and also graphical format.

Figure 1

A Selection table is shown. The user has created five selections: Selection 1, all PROSITE residues with the ATP keyword in the pattern description (using the motifs feature); Selection 2, all charged residues in the PDB (D, E, H, K and R in the residues feature); Selection 3, all exposed residues (surface feature); Selection 4, all charged residues in the selected motifs (Selection 1 INTERSECT Selection 2); Selection 5, all charged residues in the selected motifs that are not solvent-exposed (Selection 4 SUBTRACT Selection 3). The estimated time for comparing the first chain (see text) of Selection 5 as query and Selection 3 as target is 18 s.

Figure 2

The first Results page of a comparison. A manual selection of 5p21 (ras protein) residues involved in GTP binding was compared with the ∼5500 chains of a non-redundant PDB (50%). The output is shown in tabular and also graphic format. In the first column of the table, the matching residues of the query PDB chain are reported; in the adjacent columns, the other PDB chains follow, and the residues aligned in three dimensions appear in the same rows. The matched PDB chains are reported in the first row; the number of matched residues in the second one. Matching residues are also displayed upon selection (pressing on the ‘draw’ button) with a Java applet.