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98. Kuenemann MA, Sperandio O, Labbe CM, Lagorce D, Miteva MA, Villoutreix BO (2015)
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mapping. J Am Chem Soc 133(2):200–202
79. Jazayeri A, Dias JM, Marshall FH (2015) From G protein-coupled receptor structure
resolution to rational drug design. J Biol Chem 290(32):19489–19495
80. Singh R, Singh S, Nath Pandey P (2016) In-silico analysis of Sirt2 from Schistosoma
monsoni:structures, conformations and interactions with inhibitors. J Biomol Struct Dyn
34(5):1042–1051. https://doi.org/10.1080/07391102.2015.1065205
81. Sliwoski G, Kothiwale S, Meiler J, Lowe EW Jr (2014) Computational methods in drug
discovery. Pharmacol Rev 66(1):334–395
82. Alvarez Dorta D, Sivignon A, Chalopin T et al (2016) The antiadhesive strategy in Crohn’s
disease: orally active mannosides to decolonize pathogenic Escherichia coli from the gut.
ChemBioChem 17(10):936–952
83. Amin KM, Anwar MM, Kamel MM, Kassem EM, Syam YM, Elseginy SA (2013)
Synthesis, cytotoxic evaluation and molecular docking study of novel quinazoline
derivatives as PARP-1 inhibitors. Acta Pol Pharm 70(5):833–849
84. Sabbah DA, Saada M, Khalaf RA et al (2015) Molecular modeling based approach,
synthesis, and cytotoxic activity of novel benzoin derivatives targeting phosphoinostide
3-kinase (PI3Kalpha). Bioorg Med Chem Lett 25(16):3120–3124
85. Frederick R, Robert S, Charlier C et al (2005) 3,6-disubstituted coumarins as
mechanism-based inhibitors of thrombin and factor Xa. J Med Chem 48(24):7592–7603
86. Dong MH, Chen HF, Ren YJ, Shao FM (2016) Molecular modeling studies, synthesis and
biological evaluation of dabigatran analogues as thrombin inhibitors. Bioorg Med Chem 24
(2):73–84
87. Mena-Ulecia K, Tiznado W, Caballero J (2015) Study of the differential activity of thrombin
inhibitors using docking, QSAR, molecular dynamics, and MM-GBSA. PLoS ONE 10(11):
e0142774
88. Vitoria M, Granich R, Gilks CF et al (2009) The global fight against HIV/AIDS,
tuberculosis, and malaria: current status and future perspectives. Am J Clin Pathol 131(6):
844–848
89. Wodak SJ, Janin J (1978) Computer analysis of protein-protein interaction. J Mol Biol 124
(2):323–342
90. Janin J, Henrick K, Moult J et al (2003) CAPRI: a critical assessment of predicted
interactions. Proteins. 52(1):2–9
91. Lensink MF, Wodak SJ (2010) Blind predictions of protein interfaces by docking
calculations in CAPRI. Proteins 78(15):3085–3095
92. Fleishman SJ, Whitehead TA, Strauch EM et al (2011) Community-wide assessment of
protein-interface modeling suggests improvements to design methodology. J Mol Biol 414
(2):289–302
93. Dominguez C, Boelens R, Bonvin AM (2003) HADDOCK: a protein-protein docking
approach based on biochemical or biophysical information. J Am Chem Soc 125(7):1731–
1737
94. May A, Zacharias M (2007) Protein-protein docking in CAPRI using ATTRACT to account
for global and local flexibility. Proteins 69(4):774–780
95. Sable R, Jois S (2015) Surfing the protein-protein interaction surface using docking methods:
application to the design of PPI inhibitors. Molecules 20(6):11569–11603
96. Bier D, Thiel P, Briels J, Ottmann C (2015) Stabilization of protein-protein interactions in
chemical biology and drug discovery. Prog Biophys Mol Biol 119(1):10–19
97. Persico M, Di Dato A, Orteca N et al (2015) From protein communication to drug discovery.
Curr Top Med Chem 15(20):2019–2031
98. Kuenemann MA, Sperandio O, Labbe CM, Lagorce D, Miteva MA, Villoutreix BO (2015)
In silico design of low molecular weight protein-protein interaction inhibitors: overall
concept and recent advances. Prog Biophys Mol Biol 119(1):20–32
99. Pons C, Glaser F, Fernandez-Recio J (2011) Prediction of protein-binding areas by
small-world residue networks and application to docking. BMC Bioinform 12:378
Structure-Based Drug Design…
299