Features/Tools NHLBI AbDesigner EpiC IEDB DNASTAR Protean Gene Inspector Antigen Profiler Freely available + + + - - - Web application + + + - - - Interactive graphical user interface + + + + Not tested - Hydropathy + + + + + + Secondary structure + - + + + - Surface probability - + + + + - Integrated antigenic score + + + + - + Specificity assessment + + - - - + Multi-species recognition assessment + + - - - + Other protein features e.g. PTMs + + - + + + URLs: NHLBI-AbDesigner = http://helixweb.nih.gov/AbDesigner/, Epitope Choice Resource (EpiC) = http://bioware.ucd.ie/epic/, Immune Epitope Database and Analysis Resource (IEDB) = http://tools.immuneepitope.org/tools/bcell/iedb input, DNASTAR Protean = http://www.dnastar.com/t-protean.aspx, Gene Inspector = http://www. textco.com/gene-inspector.php, Antigen Profiler = http://www.pierce-antibodies.com/custom-antibodies/peptide-design-antigen-profiler.cfm

Table 1: Comparison of NHLBI-AbDesigner to other integrated antibody design tools.