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@ARTICLE{FernandezBallester:93926,
      author       = {Fernandez-Ballester, G. and Beltrao, P. and Gonzalez, J. M.
                      and Song, Y.-H. and Wilmanns, M. and Valencia, A. and
                      Serrano, L. and DESY},
      title        = {{S}tructure-based prediction of the {S}accharomyces
                      cerevisiae {SH}3-ligand interactions},
      journal      = {Journal of molecular biology},
      volume       = {388},
      issn         = {0022-2836},
      address      = {Amsterdam [u.a.]},
      publisher    = {Elsevier},
      reportid     = {PHPPUBDB-12664},
      pages        = {902-916},
      year         = {2009},
      note         = {© Elsevier Ltd.; Post referee fulltext in progress 2;
                      Embargo 12 months from publication},
      abstract     = {A great challenge in the proteomics and structural genomics
                      era is to discover protein structure and function, including
                      the identification of biological partners. Experimental
                      investigation is costly and time-consuming, making
                      computational methods very attractive for predicting protein
                      function. In this work, we used the existing structural
                      information in the SH3 family to first extract all SH3
                      structural features important for binding and then used this
                      information to select the right templates to homology model
                      most of the Saccharomyces cerevisiae SH3 domains. Second, we
                      classified, based on ligand orientation with respect to the
                      SH3 domain, all SH3 peptide ligands into 29 conformations,
                      of which 18 correspond to variants of canonical type I and
                      type II conformations and 11 correspond to non-canonical
                      conformations. Available SH3 templates were expanded by
                      chimera construction to cover some sequence variability and
                      loop conformations. Using the 29 ligand conformations and
                      the homology models, we modelled all possible complexes.
                      Using these complexes and in silico mutagenesis scanning, we
                      constructed position-specific ligand binding matrices. Using
                      these matrices, we determined which sequences will be
                      favorable for every SH3 domain and then validated them with
                      available experimental data. Our work also allowed us to
                      identify key residues that determine loop conformation in
                      SH3 domains, which could be used to model human SH3 domains
                      and do target prediction. The success of this methodology
                      opens the way for sequence-based, genome-wide prediction of
                      protein-protein interactions given enough structural
                      coverage.},
      keywords     = {Algorithms / Amino Acid Sequence / Computer Simulation /
                      Humans / Ligands / Models, Molecular / Molecular Sequence
                      Data / Peptides: chemistry / Peptides: metabolism / Protein
                      Binding / Protein Conformation / Reproducibility of Results
                      / Saccharomyces cerevisiae: chemistry / Saccharomyces
                      cerevisiae: metabolism / Saccharomyces cerevisiae Proteins:
                      chemistry / Saccharomyces cerevisiae Proteins: genetics /
                      Saccharomyces cerevisiae Proteins: metabolism / Sequence
                      Alignment / src Homology Domains / Ligands (NLM Chemicals) /
                      Peptides (NLM Chemicals) / Saccharomyces cerevisiae Proteins
                      (NLM Chemicals)},
      cin          = {EMBL(-2012)},
      ddc          = {570},
      cid          = {$I:(DE-H253)EMBL_-2012_-20130307$},
      pnm          = {FS Beamline without reference (POF1-550)},
      pid          = {G:(DE-H253)POF1-No-Ref-20130405},
      experiment   = {EXP:(DE-H253)Unknown-BL-20150101},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:19324052},
      UT           = {WOS:000266302500018},
      doi          = {10.1016/j.jmb.2009.03.038},
      url          = {https://bib-pubdb1.desy.de/record/93926},
}