Domain Hierarchy of Protein Loop-Lock Structure (DHoPLLS): a server for decomposition of a protein structure on set of closed loops

DHoPLLS (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops, which constitute a structural basis for the protein domain hierarchy. The server was created in 2005 year on basis Prof. Trifonov’s lab in Genome Diversity Center, Institute of Evolution at University of Haifa. It is based on theory of loop-lock structure developed by Prof. Trifonov’s group in Weizmann Institute of Science. This theory declares that all globular protein can be decomposed on set of almost closed loop with mean length about 30 aminoacids. The lock is a place, where a loop meets itself. Investigations of Trifonov’s group demonstrates that some aminoacid’s sequences (about 30 aminoacids) are usually exists in proteins in form of closed loops. On basis computer programs, developed for the server, we checked the simplest assumption that most of closed loop or locks in proteins have some alphabet of consensus sequences. Unfortunately our results demonstrate that such alphabet doesn’t exist. But may be some more complicate algorithm exists for loop finding from aminoacid’s sequence of protein.