LOOPER: a molecular mechanics-based algorithm for protein loop prediction.

  title={LOOPER: a molecular mechanics-based algorithm for protein loop prediction.},
  author={Velin Z. Spassov and Paul K. Flook and Lisa Yan},
  journal={Protein engineering, design & selection : PEDS},
  volume={21 2},
We describe a new ab initio method and corresponding program, LOOPER, for the prediction of protein loop conformations. The method is based on a multi-step algorithm (developed as a set of CHARMm scripts) and uses standard CHARMm force field parameters for energy minimization and scoring. One of the main obstacles to ab initio computational loop modeling is the exponential growth of the backbone conformational states with the number of residues in the loop fragment. In contrast to many ab… CONTINUE READING

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