HUMAN FAMSD-BASE: High Quality Protein Structure Model Databasefor the Human Genome Using the FAMSD Homology Modeling Method

摘要

Almost all proteins express their biological functions through the structural conformation of their specificamino acid sequences. Therefore, acquiring the three-dimensional structures of proteins is very important to elu-cidate the role of a particular protein. We had built protein structure model databases, which is called RIKENFAMSBASE (http://famshelp.gsc.riken.jp/famsbase/). The RIKEN FAMSBASE is a genome-wide protein struc-ture model database that contains a large number of protein models from many organisms. The HUMAN FAMS-BASE that is one part of the RIKEN FAMSBASE contains many protein models for human genes, which aresignificant in the pharmaceutical and medicinal fields. We have now implemented an update of the human pro-tein modeling database consisting of 242918 constructed models against the number of 20743 human proteinsequences with an improved modeling method called Full Automatic protein Modeling System Developed(FAMSD). The results of our benchmark test of the FAMSD method indicated that it has an excellent capabilityto pack amino acid side-chains with correct torsion angles in addition to the main-chain, while avoiding the for-mation of atom-atom collisions that are not found in experimental structures. This new protein structure modeldatabase for human genes, which is named HUMAN FAMSD-BASE, is open to the public as a component partof the RIKEN FAMSBASE at http://mammalia.gsc.riken.jp/human_famsd/. A significant improvement of theHUMAN FAMSD-BASE in comparison with the preceding HUMAN FAMSBASE was verified in the benchmarktest of this paper. The HUMAN FAMSD-BASE will have an important impact on the progress of biologicalscience.