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@ARTICLE{Capelli:866016,
      author       = {Capelli, Riccardo and Carloni, Paolo and Parrinello,
                      Michele},
      title        = {{E}xhaustive {S}earch of {L}igand {B}inding {P}athways via
                      {V}olume-{B}ased {M}etadynamics},
      journal      = {The journal of physical chemistry letters},
      volume       = {10},
      number       = {12},
      issn         = {1948-7185},
      address      = {Washington, DC},
      publisher    = {ACS},
      reportid     = {FZJ-2019-05276},
      pages        = {3495 - 3499},
      year         = {2019},
      abstract     = {Determining the complete set of ligands’
                      binding–unbinding pathways is important for drug discovery
                      and for rational interpretation of mutation data. Here we
                      have developed a metadynamics-based technique that addresses
                      this issue and allows estimating affinities in the presence
                      of multiple escape pathways. Our approach is shown on a
                      lysozyme T4 variant in complex with a benzene molecule. The
                      calculated binding free energy is in agreement with
                      experimental data. Remarkably, not only were we able to find
                      all the previously identified ligand binding pathways, but
                      also we identified three pathways previously not identified
                      as such. These results were obtained at a small
                      computational cost, making this approach valuable for
                      practical applications, such as screening of small compound
                      libraries.},
      cin          = {IAS-5 / JARA-HPC / INM-9},
      ddc          = {530},
      cid          = {I:(DE-Juel1)IAS-5-20120330 / $I:(DE-82)080012_20140620$ /
                      I:(DE-Juel1)INM-9-20140121},
      pnm          = {574 - Theory, modelling and simulation (POF3-574) / HBP
                      SGA2 - Human Brain Project Specific Grant Agreement 2
                      (785907) / HPC-aided design of drugs with improved kinetics
                      of binding $(jias5d_20181101)$},
      pid          = {G:(DE-HGF)POF3-574 / G:(EU-Grant)785907 /
                      $G:(DE-Juel1)jias5d_20181101$},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:31188006},
      UT           = {WOS:000472804700048},
      doi          = {10.1021/acs.jpclett.9b01183},
      url          = {https://juser.fz-juelich.de/record/866016},
}