15. Borhani DW, Shaw DE (2012) The future of molecular dynamics simulations in drug
discovery. J Comput Aided Mol Des 26(1):15–26
16. Durrant JD, McCammon JA (2011) Molecular dynamics simulations and drug discovery.
BMC Biol 9(1):71
17. Fabricant DS, Farnsworth NR (2001) The value of plants used in traditional medicine for drug
discovery. Environ Health Perspect 109(Suppl 1):69
18. http://www.chemspider.com/
19. Wishart DS et al (2006) DrugBank: a comprehensive resource for in silico drug discovery and
exploration. Nucleic Acids Res 34.suppl_1:D668–D672
20. Irwin JJ, Shoichet BK (2005) ZINC—a free database of commercially available compounds
for virtual screening. J Chem Inf Model 45(1):177–182
21. Lengauer T, Rarey M (1996) Computational methods for biomolecular docking. Curr Opin
Struct Biol 6(3):402–406
22. Sleigh Sara H, Barton Cheryl L (2010) Repurposing strategies for therapeutics. Pharm Med
24(3):151–159
23. Oprea TI, Mestres J (2012) Drug repurposing: far beyond new targets for old drugs. AAPS J
14(4):759–763
24. Sagiroglu, Seref, and Duygu Sinanc (2013) Big data: a review. In: International conference on
collaboration technologies and systems (CTS). IEEE
25. Nayak A, Poriya A, Poojary D (2013) Type of NOSQL databases and its comparison with
relational databases. Int J Appl Inf Syst 5(4):16–19
26. Hadoop A (2009) Hadoop. 2009-03-06. http://hadoop.apache.org
27. Zaharia M et al (2010) Spark: cluster computing with working sets. HotCloud 10(10-10):95
28. Allen WJ et al (2015) DOCK 6: impact of new features and current docking performance.
J Comp Chem 36(15):1132–1156
29. Jones G et al (1997) Development and validation of a genetic algorithm for flexible docking.
J Mol Biol 267(3):727–748
30. Trott Oleg, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking
with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem
31(2):455–461
31. Case DA et al (2005) The Amber biomolecular simulation programs. J Comput Chem
26.16:1668–1688
32. Brooks BR et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem
30.10:1545–1614
33. Van Der Spoel D et al (2005) GROMACS: fast, flexible, and free. J Comput Chem 26(16):
1701–1718
34. Phillips JC et al (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):
1781–1802
35. Rysavy SJ, Bromley D, Daggett V (2014) DIVE: a graph-based visual-analytics framework
for big data. IEEE Comput Graphics Appl 34(2):26–37
36. Doerr S et al (2016) HTMD: high-throughput molecular dynamics for molecular discovery.
J Chem Theory Comput 12(4):1845–1852
37. Tu T et al (2008) A scalable parallel framework for analyzing terascale molecular dynamics
simulation trajectories. In: International conference for high performance computing,
networking, storage and analysis. SC 2008. IEEE
38. Roe DR, Cheatham TE III (2013) PTRAJ and CPPTRAJ: software for processing and
analysis of molecular dynamics trajectory data. J Chem Theory Comput 9(7):3084–3095
39. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph
Model 14(1):33–38
40. Wold S, Esbensen K, Geladi P (1987) Principal component analysis. Chemometr Intell Lab
Syst 2(1–3):37–52
41. Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate
ligand-binding affinities. Expert Opin Drug Discov 10(5):449–461
372
R. R. Joshi et al.
discovery. J Comput Aided Mol Des 26(1):15–26
16. Durrant JD, McCammon JA (2011) Molecular dynamics simulations and drug discovery.
BMC Biol 9(1):71
17. Fabricant DS, Farnsworth NR (2001) The value of plants used in traditional medicine for drug
discovery. Environ Health Perspect 109(Suppl 1):69
18. http://www.chemspider.com/
19. Wishart DS et al (2006) DrugBank: a comprehensive resource for in silico drug discovery and
exploration. Nucleic Acids Res 34.suppl_1:D668–D672
20. Irwin JJ, Shoichet BK (2005) ZINC—a free database of commercially available compounds
for virtual screening. J Chem Inf Model 45(1):177–182
21. Lengauer T, Rarey M (1996) Computational methods for biomolecular docking. Curr Opin
Struct Biol 6(3):402–406
22. Sleigh Sara H, Barton Cheryl L (2010) Repurposing strategies for therapeutics. Pharm Med
24(3):151–159
23. Oprea TI, Mestres J (2012) Drug repurposing: far beyond new targets for old drugs. AAPS J
14(4):759–763
24. Sagiroglu, Seref, and Duygu Sinanc (2013) Big data: a review. In: International conference on
collaboration technologies and systems (CTS). IEEE
25. Nayak A, Poriya A, Poojary D (2013) Type of NOSQL databases and its comparison with
relational databases. Int J Appl Inf Syst 5(4):16–19
26. Hadoop A (2009) Hadoop. 2009-03-06. http://hadoop.apache.org
27. Zaharia M et al (2010) Spark: cluster computing with working sets. HotCloud 10(10-10):95
28. Allen WJ et al (2015) DOCK 6: impact of new features and current docking performance.
J Comp Chem 36(15):1132–1156
29. Jones G et al (1997) Development and validation of a genetic algorithm for flexible docking.
J Mol Biol 267(3):727–748
30. Trott Oleg, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking
with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem
31(2):455–461
31. Case DA et al (2005) The Amber biomolecular simulation programs. J Comput Chem
26.16:1668–1688
32. Brooks BR et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem
30.10:1545–1614
33. Van Der Spoel D et al (2005) GROMACS: fast, flexible, and free. J Comput Chem 26(16):
1701–1718
34. Phillips JC et al (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):
1781–1802
35. Rysavy SJ, Bromley D, Daggett V (2014) DIVE: a graph-based visual-analytics framework
for big data. IEEE Comput Graphics Appl 34(2):26–37
36. Doerr S et al (2016) HTMD: high-throughput molecular dynamics for molecular discovery.
J Chem Theory Comput 12(4):1845–1852
37. Tu T et al (2008) A scalable parallel framework for analyzing terascale molecular dynamics
simulation trajectories. In: International conference for high performance computing,
networking, storage and analysis. SC 2008. IEEE
38. Roe DR, Cheatham TE III (2013) PTRAJ and CPPTRAJ: software for processing and
analysis of molecular dynamics trajectory data. J Chem Theory Comput 9(7):3084–3095
39. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph
Model 14(1):33–38
40. Wold S, Esbensen K, Geladi P (1987) Principal component analysis. Chemometr Intell Lab
Syst 2(1–3):37–52
41. Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate
ligand-binding affinities. Expert Opin Drug Discov 10(5):449–461
372
R. R. Joshi et al.