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 β-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 β-pairing scores, this method creates all possible β-sheet arrangements including those that have the correct packing of β-strands. It uses the IK algorithms of ProteinShop to move α-helices and β-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 β-sheet topology although this number may increase if the protein has long loops or complex α-helical regions. Proteins 2010. © Published 2009 Wiley-Liss, Inc.