title: BuildBeta--a system for automatically constructing beta sheets.
abstract: We describe a method that can thoroughly sample a protein conformational space given the protein primary sequence of amino acids and secondary structure predictions. Specifically, we target proteins with beta-sheets because they are particularly challenging for ab initio protein structure prediction because of the complexity of sampling long-range strand pairings. Using some basic packing principles, inverse kinematics (IK), and beta-pairing scores, this method creates all possible beta-sheet arrangements including those that have the correct packing of beta-strands. It uses the IK algorithms of ProteinShop to move alpha-helices and beta-strands as rigid bodies by rotating the dihedral angles in the coil regions. Our results show that our approach produces structures that are within 4-6 A RMSD of the native one regardless of the protein size and beta-sheet topology although this number may increase if the protein has long loops or complex alpha-helical regions.
authors.affiliation: Department of Computer Science, University of California, Davis, California 95616, USA.
authors.forename: Nelson
authors.initials: N
authors.lastname: Max
authors.forename: Chengcheng
authors.initials: C
authors.lastname: Hu
authors.forename: Oliver
authors.initials: O
authors.lastname: Kreylos
authors.forename: Silvia
authors.initials: S
authors.lastname: Crivelli
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D012984:Software
chemical_list: D011506:Proteins