MOTIVATION: Kotai Antibody Builder is a Web service for tertiary structural modeling of antibody variable regions. It consists of three main steps: hybrid template selection by sequence alignment and canonical rules, 3D rendering of alignments and CDR-H3 loop modeling. For the last step, in addition to rule-based heuristics used to build the initial model, a refinement option is available that uses fragment assembly followed by knowledge-based scoring. Using targets from the Second Antibody Modeling Assessment, we demonstrate that Kotai Antibody Builder generates models with an overall accuracy equal to that of the best-performing semi-automated predictors using expert knowledge. AVAILABILITY AND IMPLEMENTATION: Kotai Antibody Builder is available at http://kotaiab.org CONTACT: [email protected].

UNLABELLED: PreDs is a WWW server that predicts the dsDNA-binding sites on protein molecular surfaces generated from the atomic coordinates in a PDB format. The prediction was done by evaluating the electrostatic potential, the local curvature and the global curvature on the surfaces. Results of the prediction can be interactively checked with our original surface viewer. AVAILABILITY: PreDs is available free of charge from http://pre-s.protein.osaka-u.ac.jp/~preds/ CONTACT: [email protected].