BuildBeta--a system for automatically constructing beta sheets

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.