42. Privalov PL, Crane-Robinson C (2017) Role of water in the formation of macromolecular
structures. Eur Biophys J 46(3):203–224
43. Pace CN, Fu H, Lee Fryar K, Landua J, Trevino SR, Schell D, Thurlkill RL, Imura S,
Scholtz JM, Gajiwala K, Sevcik J (2014) Contribution of hydrogen bonds to protein stability.
Protein Sci 23(5):652–661
44. Irwin JJ, Shoichet BK (2005) ZINC—a free database of commercially available compounds
for virtual screening. J Chem Inf Model 45(1):177–182
45. Yuriev E, Chalmers D, Capuano B (2009) Conformational analysis of drug molecules: a
practical exercise in the medicinal chemistry course. J Chem Educ 86(4):477
46. Li J, Ehlers T, Sutter J, Varma-O’Brien S, Kirchmair J (2007) CAESAR: a new conformer
generation algorithm based on recursive buildup and local rotational symmetry consideration.
J Chem Inf Model 47(5):1923–1932
47. Lagorce D, Pencheva T, Villoutreix BO, Miteva MA (2009) DG-AMMOS: a new tool to
generate 3D conformation of small molecules using distance geometry and automated
molecular mechanics optimization for in silico screening. BMC Chem. Bio 9(1):6
48. Sefraoui O, Aissaoui M, Eleuldj M (2012) OpenStack: toward an open-source solution for
cloud computing. Int J Comput Appl 55(3):38–42
49. Stewart JJP (1990) MOPAC: a semiempirical molecular orbital program. J Comput Aided
Mol Des 4(1):1–103
50. Hawkins PC, Skillman AG, Warren GL, Ellingson BA, Stahl MT (2010) Conformer
generation with OMEGA: algorithm and validation using high quality structures from the
protein databank and cambridge structural database. J Chem Inf Model 50(4):572–584
51. Ware B (2002) Open source development with LAMP: using Linux, Apache, MySQL and
PHP. Addison-Wesley Longman Publishing Co., Inc., Reading
52. https://www.rabbitmq.com/
53. Hukushima K, Nemoto K (1996) Exchange Monte Carlo method and application to spin glass
simulations. J Phy Soc Jpn 65(6):1604–1608
54. Ashburn TT, Thor KB (2004) Drug repositioning: identifying and developing new uses for
existing drugs. Nat Rev Drug Discov 3(8):673–683
55. Novac Natalia (2013) Challenges and opportunities of drug repositioning. Trends Pharmacol
Sci 34(5):267–272
56. Smith Kelly M, Romanelli Frank (2005) Recreational use and misuse of phosphodiesterase 5
inhibitors. J Am Pharm Assoc 45(1):63–75
57. Pfister DG (2012) Off-label use of oncology drugs: the need for more data and then some.
J Clin Oncol, 584–586
58. Jin G, Wong STC (2014) Toward better drug repositioning: prioritizing and integrating
existing methods into efficient pipelines. Drug Discov Today 19(5):637–644
59. Neves SR, Ram PT, Iyengar R (2002) G protein pathways. Science 296(5573):1636–1639
60. Khrenova MG et al (2014) Modeling the role of G12 V and G13 V Ras mutations in the
Ras-GAP-catalyzed hydrolysis reaction of guanosine triphosphate. Biochemistry 53(45):
7093–7099
61. Spoerner M et al (2010) Conformational states of human rat sarcoma (Ras) protein complexed
with its natural ligand GTP and their role for effector interaction and GTP hydrolysis. J Biol
Chem 285(51):39768–39778
62. Ma J, Karplus M (1997) Molecular switch in signal transduction: reaction paths of the
conformational changes in ras p21. Proc Natl Acad Sci USA 94(22):11905–11910
63. White MA et al (1995) Multiple Ras functions can contribute to mammalian cell
transformation. Cell 80(4):533–541
64. Schubbert S, Shannon K, Bollag G (2007) Hyperactive Ras in developmental disorders and
cancer. Nat Rev Cancer 7(4):295
65. Gao C, Eriksson LA (2013) Impact of mutations on K-Ras-p 120GAP interaction. Comput
Mol BioSci 3(02):9
66. Shurki A, Warshel A (2004) Why does the Ras switch “break” by oncogenic mutations?
Proteins: Struct Funct Bioinf 55(1):1–10
Turbo Analytics: Applications of Big Data and HPC in Drug …
373
structures. Eur Biophys J 46(3):203–224
43. Pace CN, Fu H, Lee Fryar K, Landua J, Trevino SR, Schell D, Thurlkill RL, Imura S,
Scholtz JM, Gajiwala K, Sevcik J (2014) Contribution of hydrogen bonds to protein stability.
Protein Sci 23(5):652–661
44. Irwin JJ, Shoichet BK (2005) ZINC—a free database of commercially available compounds
for virtual screening. J Chem Inf Model 45(1):177–182
45. Yuriev E, Chalmers D, Capuano B (2009) Conformational analysis of drug molecules: a
practical exercise in the medicinal chemistry course. J Chem Educ 86(4):477
46. Li J, Ehlers T, Sutter J, Varma-O’Brien S, Kirchmair J (2007) CAESAR: a new conformer
generation algorithm based on recursive buildup and local rotational symmetry consideration.
J Chem Inf Model 47(5):1923–1932
47. Lagorce D, Pencheva T, Villoutreix BO, Miteva MA (2009) DG-AMMOS: a new tool to
generate 3D conformation of small molecules using distance geometry and automated
molecular mechanics optimization for in silico screening. BMC Chem. Bio 9(1):6
48. Sefraoui O, Aissaoui M, Eleuldj M (2012) OpenStack: toward an open-source solution for
cloud computing. Int J Comput Appl 55(3):38–42
49. Stewart JJP (1990) MOPAC: a semiempirical molecular orbital program. J Comput Aided
Mol Des 4(1):1–103
50. Hawkins PC, Skillman AG, Warren GL, Ellingson BA, Stahl MT (2010) Conformer
generation with OMEGA: algorithm and validation using high quality structures from the
protein databank and cambridge structural database. J Chem Inf Model 50(4):572–584
51. Ware B (2002) Open source development with LAMP: using Linux, Apache, MySQL and
PHP. Addison-Wesley Longman Publishing Co., Inc., Reading
52. https://www.rabbitmq.com/
53. Hukushima K, Nemoto K (1996) Exchange Monte Carlo method and application to spin glass
simulations. J Phy Soc Jpn 65(6):1604–1608
54. Ashburn TT, Thor KB (2004) Drug repositioning: identifying and developing new uses for
existing drugs. Nat Rev Drug Discov 3(8):673–683
55. Novac Natalia (2013) Challenges and opportunities of drug repositioning. Trends Pharmacol
Sci 34(5):267–272
56. Smith Kelly M, Romanelli Frank (2005) Recreational use and misuse of phosphodiesterase 5
inhibitors. J Am Pharm Assoc 45(1):63–75
57. Pfister DG (2012) Off-label use of oncology drugs: the need for more data and then some.
J Clin Oncol, 584–586
58. Jin G, Wong STC (2014) Toward better drug repositioning: prioritizing and integrating
existing methods into efficient pipelines. Drug Discov Today 19(5):637–644
59. Neves SR, Ram PT, Iyengar R (2002) G protein pathways. Science 296(5573):1636–1639
60. Khrenova MG et al (2014) Modeling the role of G12 V and G13 V Ras mutations in the
Ras-GAP-catalyzed hydrolysis reaction of guanosine triphosphate. Biochemistry 53(45):
7093–7099
61. Spoerner M et al (2010) Conformational states of human rat sarcoma (Ras) protein complexed
with its natural ligand GTP and their role for effector interaction and GTP hydrolysis. J Biol
Chem 285(51):39768–39778
62. Ma J, Karplus M (1997) Molecular switch in signal transduction: reaction paths of the
conformational changes in ras p21. Proc Natl Acad Sci USA 94(22):11905–11910
63. White MA et al (1995) Multiple Ras functions can contribute to mammalian cell
transformation. Cell 80(4):533–541
64. Schubbert S, Shannon K, Bollag G (2007) Hyperactive Ras in developmental disorders and
cancer. Nat Rev Cancer 7(4):295
65. Gao C, Eriksson LA (2013) Impact of mutations on K-Ras-p 120GAP interaction. Comput
Mol BioSci 3(02):9
66. Shurki A, Warshel A (2004) Why does the Ras switch “break” by oncogenic mutations?
Proteins: Struct Funct Bioinf 55(1):1–10
Turbo Analytics: Applications of Big Data and HPC in Drug …
373