NDO (Normalized Domain Overlap) scoring scheme was developed when we assessed the domain boundary prediction, a new category, in the sixth community-wide experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP6). A mathematical description of the scoring scheme and the source code is available for download here. For a detailed description of the scoring scheme, please refer to the paper "Tai CH, Lee WJ, Vincent JJ, Lee B. Evaluation of domain prediction in CASP6. Proteins. 61 Suppl 7: 183-92, 2005."