% IMPORTANT: The following is UTF-8 encoded.  This means that in the presence
% of non-ASCII characters, it will not work with BibTeX 0.99 or older.
% Instead, you should use an up-to-date BibTeX implementation like “bibtex8” or
% “biber”.

@ARTICLE{Kynast:818246,
      author       = {Kynast, Philipp and Derreumaux, Philippe and Strodel,
                      Birgit},
      title        = {{E}valuation of the coarse-grained {OPEP} force field for
                      protein-protein docking},
      journal      = {BMC Biophysics},
      volume       = {9},
      number       = {1},
      issn         = {2046-1682},
      address      = {London},
      publisher    = {BioMed Central},
      reportid     = {FZJ-2016-04724},
      pages        = {4},
      year         = {2016},
      abstract     = {Background: Knowing the binding site of protein–protein
                      complexes helps understand their function and shows possible
                      regulation sites. The ultimate goal of protein–protein
                      docking is the prediction of the three-dimensional structure
                      of a protein–protein complex. Docking itself only produces
                      plausible candidate structures, which must be ranked using
                      scoring functions to identify the structures that are most
                      likely to occur in nature. Methods: In this work, we rescore
                      rigid body protein–protein predictions using the optimized
                      potential for efficient structure prediction (OPEP), which
                      is a coarse-grained force field. Using a force field based
                      on continuous functions rather than a grid-based scoring
                      function allows the introduction of protein flexibility
                      during the docking procedure. First, we produce
                      protein–protein predictions using ZDOCK, and after energy
                      minimization via OPEP we rank them using an OPEP-based soft
                      rescoring function. We also train the rescoring function for
                      different complex classes and demonstrate its improved
                      performance for an independent dataset. Results: The trained
                      rescoring function produces a better ranking than ZDOCK for
                      more than 50 $\%$ of targets, rising to over 70 $\%$ when
                      considering only enzyme/inhibitor complexes. Conclusions:
                      This study demonstrates for the first time that energy
                      functions derived from the coarse-grained OPEP force field
                      can be employed to rescore predictions for protein–protein
                      complexes.},
      cin          = {ICS-6},
      ddc          = {570},
      cid          = {I:(DE-Juel1)ICS-6-20110106},
      pnm          = {551 - Functional Macromolecules and Complexes (POF3-551)},
      pid          = {G:(DE-HGF)POF3-551},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000374457200001},
      pubmed       = {pmid:27103992},
      doi          = {10.1186/s13628-016-0029-y},
      url          = {https://juser.fz-juelich.de/record/818246},
}