BuildBeta--a system for automatically constructing beta sheets

Proteins. 2010 Feb 15;78(3):559-74. doi: 10.1002/prot.22578.

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Models, Chemical*
  • Models, Molecular
  • Protein Structure, Secondary*
  • Proteins / chemistry*
  • Proteins / genetics
  • Software*

Substances

  • Proteins