Predicting interresidue contacts using templates and pathways

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Abstract
We present a novel method, HMMSTR‐CM, for protein contact map predictions. Contact potentials were calculated by using HMMSTR, a hidden Markov model for local sequence structure correlations. Targets were aligned against protein templates using a Bayesian method, and contact maps were generated by using these alignments. Contact potentials then were used to evaluate these templates. An ab initio method based on the target contact potentials using a rule‐based strategy to model the protein‐folding pathway was developed. Fold recognition and ab initio methods were combined to produce accurate, protein‐like contact maps. Pathways sometimes led to an unambiguous prediction of topology, even without using templates. The results on CASP5 targets are discussed. Also included is a brief update on the quality of fully automated ab initio predictions using the I‐sites server. Proteins 2003;53:497–502.