3D-partner is a fast web tool to predict interacting partners and binding models of a query protein sequence through structure complexes and a knowledge-based scoring function. 3D-partner first utilizes IMPALA to identify homologous structures (templates) of this query from a two-chain complex profile library. The interacting-partner sequences of these templates are then used to search interacting candidates from protein sequence databases (e.g. SwissProt) by PSI-BLAST. We have developed a new knowledge-based scoring function, which consists of steric and template specific scores (hydrogen-bonding and couple-conserved residue scores), to evaluate how well the interfaces between the query and interacting candidates. Based on this scoring function, 3D-partner provides the statistic significance (Z-value), the binding models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners. 3D-partner shows the binding model of the query and its interacting partner by aligning them to respective template sequences and structures. The important contact residues in the interface are indicated in the following formats: hydrogen-bond residues (gray); conserved residues (yellow) and both (green). 3D-partner is an easy-to-use web server and helps users to analyze the binding model.