bookmark DomainParser A computer program using network flow algorithms for protein domain decomposition. DomainParser partitions a protein structure into domains. Through utilization of various types of structural information including hydrophobic moment profile, we have developed an effective method for assessing the most probable number of domains a structure may have. The core of this method is a neural network, which is trained to discriminate correctly partitioned domains from incorrectly partitioned domains. When compared with the manual decomposition results given in the SCOP database, DomainParser algorithm achieves higher decomposition accuracy (81.9%) on the same data set.