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10. Yuriev E, Agostino M, Ramsland PA (2011) Challenges and advances in computational
docking: 2009 in review. J Mol Recognit 24:149–164. https://doi.org/10.1002/jmr.1077
11. Yuriev E, Holien J, Ramsland PA (2015) Improvements, trends, and new ideas in molecular
docking: 2012–2013 in review. J Mol Recognit 28:581–604. https://doi.org/10.1002/jmr.
2471
12. Taylor RD, Jewsbury PJ, Essex JW (2002) A review of protein-small molecule docking
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13. Huang SY, Zou X (2010) Advances and challenges in protein-ligand docking. Int J Mol Sci
11:3016–3034. https://doi.org/10.3390/ijms11083016
14. Chen Y-C (2015) Beware of docking! Trends Pharmacol Sci 36:78–95. https://doi.org/10.
1016/j.tips.2014.12.001
15. Acharya KR, Lloyd MD (2005) The advantages and limitations of protein crystal structures.
Trends Pharmacol Sci 26:10–14. https://doi.org/10.1016/j.tips.2004.10.011
16. Petukh M, Stefl S, Alexov E (2013) The role of protonation states in ligand-receptor
recognition and binding. Curr Pharm Des 19:4182–4190. https://doi.org/10.2174/
1381612811319230004
17. Onufriev AV, Alexov E (2013) Protonation and pK changes in protein–ligand binding.
Q Rev Biophys 46:181–209. https://doi.org/10.1017/s0033583513000024
18. Srivastava J, Barreiro G, Groscurth S et al (2008) Structural model and functional
significance of pH-dependent talin-actin binding for focal adhesion remodeling. Proc Natl
Acad Sci U S A 105:14436–14441. https://doi.org/10.1073/pnas.0805163105
19. Ferrara P, Gohlke H, Price DJ et al (2004) Assessing scoring functions for protein-ligand
interactions. J Med Chem 47:3032–3047. https://doi.org/10.1021/jm030489h
20. Warren GL, Andrews CW, Capelli AM et al (2006) A critical assessment of docking
programs and scoring functions. J Med Chem 49:5912–5931. https://doi.org/10.1021/
jm050362n
21. Rask-Andersen M, Almén MS, Schiöth HB (2011) Trends in the exploitation of novel drug
targets. Nat Rev Drug Discov 10:579–590. https://doi.org/10.1038/nrd3478
22. Finan C, Gaulton A, Kruger FA et al (2017) The druggable genome and support for target
identification and validation in drug development. Sci Transl Med 9:1–16. https://doi.org/10.
1126/scitranslmed.aag1166
23. Civelek M, Lusis AJ (2014) Systems genetics approaches to understand complex traits. Nat
Rev Genet 15:34–48. https://doi.org/10.1038/nrg3575
24. Csermely P, Korcsmáros T, Kiss HJM et al (2013) Structure and dynamics of molecular
networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther
138:333–408. https://doi.org/10.1016/j.pharmthera.2013.01.016
25. Zhu P, Aliabadi HM, Uludağ H, Han J (2016) Identification of potential drug targets in
cancer signaling pathways using stochastic logical models. Sci Rep 6:23078. https://doi.org/
10.1038/srep23078
26. Torkamani A, Topol EJ, Schork NJ (2008) Pathway analysis of seven common diseases
assessed by genome-wide association. Genomics 92:265–272. https://doi.org/10.1016/j.
ygeno.2008.07.011
27. Druker BJ, Tamura S, Buchdunger E et al (1996) Effects of a selective inhibitor of the Abl
tyrosine kinase on the growth of Bcr-Abl positive cells. Nat Med 2:561–566. https://doi.org/
10.1038/nm0596-561
28. Fabian MA, Biggs WH, Treiber DK et al (2005) A small molecule-kinase interaction map
for clinical kinase inhibitors. Nat Biotechnol 23:329–336. https://doi.org/10.1038/nbt1068
162
S. K. Panday and I. Ghosh
screening for drug discovery: methods and applications. Nat Rev Drug Discov 3:935–949.
https://doi.org/10.1038/nrd1549
9. Yuriev E, Ramsland PA (2013) Latest developments in molecular docking: 2010–2011 in
review. J Mol Recognit 26:215–239. https://doi.org/10.1002/jmr.2266
10. Yuriev E, Agostino M, Ramsland PA (2011) Challenges and advances in computational
docking: 2009 in review. J Mol Recognit 24:149–164. https://doi.org/10.1002/jmr.1077
11. Yuriev E, Holien J, Ramsland PA (2015) Improvements, trends, and new ideas in molecular
docking: 2012–2013 in review. J Mol Recognit 28:581–604. https://doi.org/10.1002/jmr.
2471
12. Taylor RD, Jewsbury PJ, Essex JW (2002) A review of protein-small molecule docking
methods. J Comput Aided Mol Des 16:151–166. https://doi.org/10.1023/a:1020155510718
13. Huang SY, Zou X (2010) Advances and challenges in protein-ligand docking. Int J Mol Sci
11:3016–3034. https://doi.org/10.3390/ijms11083016
14. Chen Y-C (2015) Beware of docking! Trends Pharmacol Sci 36:78–95. https://doi.org/10.
1016/j.tips.2014.12.001
15. Acharya KR, Lloyd MD (2005) The advantages and limitations of protein crystal structures.
Trends Pharmacol Sci 26:10–14. https://doi.org/10.1016/j.tips.2004.10.011
16. Petukh M, Stefl S, Alexov E (2013) The role of protonation states in ligand-receptor
recognition and binding. Curr Pharm Des 19:4182–4190. https://doi.org/10.2174/
1381612811319230004
17. Onufriev AV, Alexov E (2013) Protonation and pK changes in protein–ligand binding.
Q Rev Biophys 46:181–209. https://doi.org/10.1017/s0033583513000024
18. Srivastava J, Barreiro G, Groscurth S et al (2008) Structural model and functional
significance of pH-dependent talin-actin binding for focal adhesion remodeling. Proc Natl
Acad Sci U S A 105:14436–14441. https://doi.org/10.1073/pnas.0805163105
19. Ferrara P, Gohlke H, Price DJ et al (2004) Assessing scoring functions for protein-ligand
interactions. J Med Chem 47:3032–3047. https://doi.org/10.1021/jm030489h
20. Warren GL, Andrews CW, Capelli AM et al (2006) A critical assessment of docking
programs and scoring functions. J Med Chem 49:5912–5931. https://doi.org/10.1021/
jm050362n
21. Rask-Andersen M, Almén MS, Schiöth HB (2011) Trends in the exploitation of novel drug
targets. Nat Rev Drug Discov 10:579–590. https://doi.org/10.1038/nrd3478
22. Finan C, Gaulton A, Kruger FA et al (2017) The druggable genome and support for target
identification and validation in drug development. Sci Transl Med 9:1–16. https://doi.org/10.
1126/scitranslmed.aag1166
23. Civelek M, Lusis AJ (2014) Systems genetics approaches to understand complex traits. Nat
Rev Genet 15:34–48. https://doi.org/10.1038/nrg3575
24. Csermely P, Korcsmáros T, Kiss HJM et al (2013) Structure and dynamics of molecular
networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther
138:333–408. https://doi.org/10.1016/j.pharmthera.2013.01.016
25. Zhu P, Aliabadi HM, Uludağ H, Han J (2016) Identification of potential drug targets in
cancer signaling pathways using stochastic logical models. Sci Rep 6:23078. https://doi.org/
10.1038/srep23078
26. Torkamani A, Topol EJ, Schork NJ (2008) Pathway analysis of seven common diseases
assessed by genome-wide association. Genomics 92:265–272. https://doi.org/10.1016/j.
ygeno.2008.07.011
27. Druker BJ, Tamura S, Buchdunger E et al (1996) Effects of a selective inhibitor of the Abl
tyrosine kinase on the growth of Bcr-Abl positive cells. Nat Med 2:561–566. https://doi.org/
10.1038/nm0596-561
28. Fabian MA, Biggs WH, Treiber DK et al (2005) A small molecule-kinase interaction map
for clinical kinase inhibitors. Nat Biotechnol 23:329–336. https://doi.org/10.1038/nbt1068
162
S. K. Panday and I. Ghosh