References
- Esko JD, Kimata K, Lindahl U (2009) Proteo-
glycans and sulfated glycosaminoglycans. In:
Varki A, Cummings RD, Esko JD et al (eds)
Essentials of glycobiology, 2nd edn. Cold
Spring Harbor Laboratory Press, New York - Perrimon N, Bernfield M (2000) Specificities
of heparan sulphate proteoglycans in develop-
mental processes. Nature 404:725–728 - Habuchi H, Habuchi O, Kimata K (2004) Sul-
fation pattern in glycosaminoglycan: does it
have a code? Glycoconj J 21:47–52 - Sattelle B, Hansen S, Gardiner J et al (2010)
Free energy landscapes of iduronic acid and
related monosaccharides. J Am Chem Soc
132:13132–13134 - Imberty A, Lortat-Jacob H, Pe ́rez S (2007)
Structural view of glycosaminoglycan–protein
interactions. Carbohydr Res 342:430–439 - Samsonov SA, Pisabarro MT (2016) Compu-
tational analysis of interactions in structurally
available protein-glycosaminoglycan com-
plexes. Glycobiology 26:850–861 - Sepuru KM, Nagarajan B, Desai U et al (2016)
Molecular basis of chemokine CXCL5-
glycosaminoglycan interactions. J Biol Chem.
https://doi.org/10.1074/jbc.M116.745265 - Teyra J, Samsonov SA, Schreiber S et al (2011)
SCOWLP update: 3D classification of protein-
protein, -peptide, -saccharide and -nucleic acid
interactions, and structure-based binding infer-
ences across folds. BMC Bioinformatics
12:398 - Roberts B, Mancera R (2008) Ligand-protein
docking with water molecules. J Chem Inf
Model 48:397–408 - Thilagavathi R, Mancera R (2010) Ligand-
protein cross-docking with water molecules. J
Chem Inf Model 50:415–421 - van Dijk A, Bonvin A (2006) Solvated docking:
introducing water into the modelling of
biomolecular complexes. Bioinformatics
22:2340–2347- Samsonov S, Teyra J, Pisabarro MT (2008) A
molecular dynamics approach to study the
importance of solvent in protein interactions.
Proteins 73:515–525 - Samsonov S, Teyra J, Pisabarro MT (2011)
Docking glycosaminoglycans to proteins: anal-
ysis of solvent inclusion. J Comput Aided Mol
Des 25:477–489 - Samsonov S, Gehrcke JP, Pisabarro MT (2014)
Flexibility and explicit solvent in molecular
dynamics-based docking of protein-
glycosaminoglycan systems. J Chem Inf
Model 54:582–592 - Molecular Operating Environment (MOE),
2013.08; Chemical Computing Group Inc.,
1010 Sherbooke St. West, Suite #910, Mon-
treal, QC, Canada, H3A 2R7, 2016 - Goodford P (1985) A computational proce-
dure for determining energetically favorable
binding sites on biologically important macro-
molecules. J Med Chem 28:849–857 - Case DA, Berryman JT, Betz RM et al (2015)
AMBER 14. University of California, San
Francisco - Kirschner K, Yongye A, Tschampel S et al
(2008) GLYCAM06: a generalizable biomo-
lecular force field. carbohydrates. J Comput
Chem 29:622–655 - Ester M, Kriegel HP, Sander J et al (1996) A
density-based algorithm for discovering clus-
ters in large spatial databases with noise. In:
Proceedings of 2nd international conference
on knowledge discovery and data mining
(KDD-96). American Association for Artificial
Intelligence, Menlo Park, CA - O’Boyle NM, Banck M, James CA et al (2011)
Open babel: an open chemical toolbox. J Che-
minform 3:33
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