228 Genome Informatics 14: 228–237 (2003) Development of an ab initio Protein Structure Prediction System ABLE
Abstract:
An ab initio protein structure prediction system called ABLE is described. It is based on the fragment assembly method, which consists of two steps: dividing a target sequence into overlapping subsequences (fragments) of short length and assigning a local structure to each fragment; and generating models by assembling the local structures and selecting the models with low potential energy. One of the most important problems in conventional fragment assembly methods is the difficulty of selecting native-like structures by energy minimization only. ABLE thus employs a structural clustering method to select the native-like models from among the generated models. By applying the unit-vector root mean square distance (URMS) as a measure of structure similarity, we achieve more robust, effective structural clustering. When no enough clusters of good quality are obtained, ABLE runs the energy minimization procedure again by incorporating structural restraint conditions obtained from the consensus substructures in the previously generated models. This approach is based on our observation that there is a high probability that the consensus substructures of the generated models have native-like structures. Another feature of ABLE is that in assigning local structures to fragments, it assigns mainchain dihedral angles (φ, ψ) to the central
