Computational Drug Discovery and Design

(backadmin) #1

Acknowledgments


The chapter was developed using the equipment purchased within
the project “The equipment of innovative laboratories doing
research on new medicines used in the therapy of civilization and
neoplastic diseases” within the Operational Program Development
of Eastern Poland 2007–2013, Priority Axis I Modern Economy,
operations I.3 Innovation promotion. T.S. and J.S. acknowledge
support from Instituto de Salud Carlos III FEDER (CP12/03139
and PI15/00460). A.A.K., T.S. and J.S. participate in the
European COST Action CM1207 (GLISTEN).
T.S. acknowledges financial support from Hospital del Mar Medical
Research Institute.

References



  1. Andreani J, Guerois R (2014) Evolution of
    protein interactions: from interactomes to
    interfaces. Arch Biochem Biophys 554:65–75.
    https://doi.org/10.1016/j.abb.2014.05.010

  2. Petta I, Lievens S, Libert C et al (2016) Mod-
    ulation of protein-protein interactions for the
    development of novel therapeutics. Mol Ther J
    Am Soc Gene Ther 24:707–718.https://doi.
    org/10.1038/mt.2015.214

  3. Gromiha MM, Yugandhar K, Jemimah S
    (2016) Protein-protein interactions: scoring
    schemes and binding affinity. Curr Opin Struct
    Biol 44:31–38. https://doi.org/10.1016/j.
    sbi.2016.10.016

  4. Moal IH, Moretti R, Baker D, Ferna ́ndez-
    Recio J (2013) Scoring functions for protein-
    protein interactions. Curr Opin Struct Biol
    23:862–867. https://doi.org/10.1016/j.sbi.
    2013.06.017

  5. Huang S-Y (2015) Exploring the potential of
    global protein-protein docking: an overview
    and critical assessment of current programs
    for automatic ab initio docking. Drug Discov
    Today 20:969–977. https://doi.org/10.
    1016/j.drudis.2015.03.007

  6. Rodrigues JPGLM, Bonvin AMJJ (2014) Inte-
    grative computational modeling of protein
    interactions. FEBS J 281:1988–2003.
    https://doi.org/10.1111/febs.12771

  7. Selent J, Kaczor AA (2011) Oligomerization of
    G protein-coupled receptors: computational
    methods. Curr Med Chem 18:4588–4605

  8. Kaczor AA, Selent J, Poso A (2013) Structure-
    based molecular modeling approaches to
    GPCR oligomerization. Methods Cell Biol
    117:91–104. https://doi.org/10.1016/
    B978-0-12-408143-7.00005-0
    9. Kuntz ID, Blaney JM, Oatley SJ et al (1982) A
    geometric approach to macromolecule-ligand
    interactions. J Mol Biol 161:269–288

  9. Wodak SJ, Janin J (1978) Computer analysis of
    protein-protein interaction. J Mol Biol
    124:323–342

  10. Janin J (2010) Protein-protein docking tested
    in blind predictions: the CAPRI experiment.
    Mol Biosyst 6:2351–2362.https://doi.org/
    10.1039/c005060c

  11. Lensink MF, Wodak SJ (2013) Docking, scor-
    ing, and affinity prediction in CAPRI. Proteins
    81:2082–2095. https://doi.org/10.1002/
    prot.24428

  12. Lensink MF, Velankar S, Wodak SJ (2017)
    Modeling protein-protein and protein-peptide
    complexes: CAPRI 6th edition. Proteins
    85:359–377. https://doi.org/10.1002/prot.
    25215

  13. Bohnuud T, Luo L, Wodak SJ et al (2017) A
    benchmark testing ground for integrating
    homology modeling and protein docking. Pro-
    teins 85:10–16. https://doi.org/10.1002/
    prot.25063

  14. Park H, Lee H, Seok C (2015) High-
    resolution protein-protein docking by global
    optimization: recent advances and future chal-
    lenges. Curr Opin Struct Biol 35:24–31.
    https://doi.org/10.1016/j.sbi.2015.08.001

  15. Kaczor AA, Selent J, Sanz F, Pastor M (2013)
    Modeling complexes of transmembrane pro-
    teins: systematic analysis of protein-protein
    docking tools. Mol Inform 32:717–733.
    https://doi.org/10.1002/minf.201200150

  16. Zacharias M (2010) Accounting for conforma-
    tional changes during protein-protein docking.
    Curr Opin Struct Biol 20:180–186.https://
    doi.org/10.1016/j.sbi.2010.02.001


Protein-Protein Docking 301
Free download pdf