Probabilistic Models of Local Biomolecular Structure and Their Applications
In 1951, before the first experimental determination of a complete protein structure, Corey and Pauling predicted that certain typical local structural motifs would arise from specific hydrogen bond patterns . These motifs, referred to as α-helices and β-sheets, were later confirmed experimentally, and are now known to exist in almost all proteins. The fact that proteins display such strong local structural preferences has an immediate consequence for protein structure simulation and prediction. The efficiency of simulations can be enhanced by focusing on candidate structures that exhibit realistic local structure, thus effectively reducing the conformational search space. Probabilistic models that capture local structure are also the natural building blocks for the development of more elaborate models of protein structure.
KeywordsHide Markov Model Dihedral Angle Hide Node Conformational Space Acceptance Probability
The authors acknowledge funding by the Danish Research Council for Technology and Production Sciences (FTP, project: Protein structure ensembles from mathematical models, 274-09-0184) and the Danish Council for Independent Research (FNU, project: A Bayesian approach to protein structure determination, 272-08-0315).