Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

  title={Generalized Fragment Picking in Rosetta: Design, Protocols and Applications},
  author={Dominik Gront and Daniel W. Kulp and Robert McCoy Vernon and Charlie E. M. Strauss and David Baker},
  booktitle={PloS one},
The Rosetta de novo structure prediction and loop modeling protocols begin with coarse grained Monte Carlo searches in which the moves are based on short fragments extracted from a database of known structures. Here we describe a new object oriented program for picking fragments that greatly extends the functionality of the previous program (nnmake) and opens the door for new approaches to structure modeling. We provide a detailed description of the code design and architecture, highlighting… CONTINUE READING

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