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
- 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 - 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 - 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 - 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 - 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 - Rodrigues JPGLM, Bonvin AMJJ (2014) Inte-
grative computational modeling of protein
interactions. FEBS J 281:1988–2003.
https://doi.org/10.1111/febs.12771 - Selent J, Kaczor AA (2011) Oligomerization of
G protein-coupled receptors: computational
methods. Curr Med Chem 18:4588–4605 - 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 - Wodak SJ, Janin J (1978) Computer analysis of
protein-protein interaction. J Mol Biol
124:323–342 - Janin J (2010) Protein-protein docking tested
in blind predictions: the CAPRI experiment.
Mol Biosyst 6:2351–2362.https://doi.org/
10.1039/c005060c - Lensink MF, Wodak SJ (2013) Docking, scor-
ing, and affinity prediction in CAPRI. Proteins
81:2082–2095. https://doi.org/10.1002/
prot.24428 - 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 - 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 - 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 - 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 - 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