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biology. J Chem Inf Model 52:1757–1768. https://doi.org/10.1021/ci3001277
59. Sterling T, Irwin JJ (2015) ZINC 15–ligand discovery for everyone. J Chem Inf Model
55:2324–2337. https://doi.org/10.1021/acs.jcim.5b00559
60. Hong H, Chen M, Ng HW, Tong W (2016) QSAR models at the US FDA/NCTR. Methods
Mol Biol 1425:431–459. https://doi.org/10.1007/978-1-4939-3609-0_18
61. Hecker N, Ahmed J, von Eichborn J et al (2012) SuperTarget goes quantitative: update on drugtarget interactions. Nucleic Acids Res 40:D1113–D1117. https://doi.org/10.1093/nar/gkr912
62. Schmidt U, Struck S, Gruening B et al (2009) SuperToxic: a comprehensive database of toxic
compounds. Nucleic Acids Res 37:D295–D299. https://doi.org/10.1093/nar/gkn850
63. Lim E, Pon A, Djoumbou Y et al (2010) T3DB: a comprehensively annotated database of
common toxins and their targets. Nucleic Acids Res 38:D781–D786. https://doi.org/10.1093/
nar/gkp934
64. Wishart D, Arndt D, Pon A et al (2015) T3DB: the toxic exposome database. Nucleic Acids
Res 43:D928–D934. https://doi.org/10.1093/nar/gku1004
65. Sandhu KS, Veeramachaneni V, Yao X et al (2015) Release of (and lessons learned from
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doi.org/10.2217/pgs.15.38
66. Fowler S, Schnall JG (2014) TOXNET: information on toxicology and environmental health.
Am J Nurs 114:61–63. https://doi.org/10.1097/01.NAJ.0000443783.75162.79
67. Wexler P (2001) TOXNET: an evolving web resource for toxicology and environmental health
information. Toxicology 157:3–10
68. OECD (2018) Users’ handbook supplement to the guidance document for developing and
assessing AOPs. France, Paris
69. Burley SK, Berman HM, Kleywegt GJ et al (2017) Protein data bank (PDB): the single global
macromolecular structure archive. Methods Mol Biol 1607:627–641. https://doi.org/10.1007/
978-1-4939-7000-1_26
70. Boutet E, Lieberherr D, Tognolli M et al (2007) UniProtKB/Swiss-Prot. Methods Mol Biol
406:89–112
71. Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol
215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
72. Fiser A, Sali A (2003) Modeller: generation and refinement of homology-based protein structure
models. Methods Enzymol 374:461–491. https://doi.org/10.1016/S0076-6879(03)74020-8
73. Biasini M, Bienert S, Waterhouse A et al (2014) SWISS-MODEL: modelling protein tertiary
and quaternary structure using evolutionary information. Nucleic Acids Res 42:W252–W258.
https://doi.org/10.1093/nar/gku340
74. Laskowski RA (2001) PDBsum: summaries and analyses of PDB structures. Nucleic Acids
Res 29:221–222
75. Benkert P, Biasini M, Schwede T (2011) Toward the estimation of the absolute quality
of individual protein structure models. Bioinformatics 27:343–350. https://doi.org/10.1093/
bioinformatics/btq662
76. Xu D, Zhang Y (2012) Ab initio protein structure assembly using continuous structure fragments
and optimized knowledge-based force field. Proteins Struct Funct Bioinforma 80:1715–1735.
https://doi.org/10.1002/prot.24065
77. Brylinski M, Skolnick J (2008) A threading-based method (FINDSITE) for ligand-binding site
prediction and functional annotation. Proc Natl Acad Sci U S A 105:129–134. https://doi.org/
10.1073/pnas.0707684105
78. Levitt DG, Banaszak LJ (1992) POCKET: a computer graphics method for identifying and
displaying protein cavities and their surrounding amino acids. J Mol Graph 10:229–234
79. Trott O, Olson AJ (2010) AutoDock Vina. J Comput Chem 31:445–461. https://doi.org/10.
1002/jcc.21334
80. Case DA, Cheatham TE, Darden T et al (2005) The Amber biomolecular simulation programs.
J Comput Chem 26:1668–1688. https://doi.org/10.1002/jcc.20290
115
58. Irwin JJ, Sterling T, Mysinger MM et al (2012) ZINC: a free tool to discover chemistry for
biology. J Chem Inf Model 52:1757–1768. https://doi.org/10.1021/ci3001277
59. Sterling T, Irwin JJ (2015) ZINC 15–ligand discovery for everyone. J Chem Inf Model
55:2324–2337. https://doi.org/10.1021/acs.jcim.5b00559
60. Hong H, Chen M, Ng HW, Tong W (2016) QSAR models at the US FDA/NCTR. Methods
Mol Biol 1425:431–459. https://doi.org/10.1007/978-1-4939-3609-0_18
61. Hecker N, Ahmed J, von Eichborn J et al (2012) SuperTarget goes quantitative: update on drugtarget interactions. Nucleic Acids Res 40:D1113–D1117. https://doi.org/10.1093/nar/gkr912
62. Schmidt U, Struck S, Gruening B et al (2009) SuperToxic: a comprehensive database of toxic
compounds. Nucleic Acids Res 37:D295–D299. https://doi.org/10.1093/nar/gkn850
63. Lim E, Pon A, Djoumbou Y et al (2010) T3DB: a comprehensively annotated database of
common toxins and their targets. Nucleic Acids Res 38:D781–D786. https://doi.org/10.1093/
nar/gkp934
64. Wishart D, Arndt D, Pon A et al (2015) T3DB: the toxic exposome database. Nucleic Acids
Res 43:D928–D934. https://doi.org/10.1093/nar/gku1004
65. Sandhu KS, Veeramachaneni V, Yao X et al (2015) Release of (and lessons learned from
mining) a pioneering large toxicogenomics database. Pharmacogenomics 16:779–801. https://
doi.org/10.2217/pgs.15.38
66. Fowler S, Schnall JG (2014) TOXNET: information on toxicology and environmental health.
Am J Nurs 114:61–63. https://doi.org/10.1097/01.NAJ.0000443783.75162.79
67. Wexler P (2001) TOXNET: an evolving web resource for toxicology and environmental health
information. Toxicology 157:3–10
68. OECD (2018) Users’ handbook supplement to the guidance document for developing and
assessing AOPs. France, Paris
69. Burley SK, Berman HM, Kleywegt GJ et al (2017) Protein data bank (PDB): the single global
macromolecular structure archive. Methods Mol Biol 1607:627–641. https://doi.org/10.1007/
978-1-4939-7000-1_26
70. Boutet E, Lieberherr D, Tognolli M et al (2007) UniProtKB/Swiss-Prot. Methods Mol Biol
406:89–112
71. Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol
215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
72. Fiser A, Sali A (2003) Modeller: generation and refinement of homology-based protein structure
models. Methods Enzymol 374:461–491. https://doi.org/10.1016/S0076-6879(03)74020-8
73. Biasini M, Bienert S, Waterhouse A et al (2014) SWISS-MODEL: modelling protein tertiary
and quaternary structure using evolutionary information. Nucleic Acids Res 42:W252–W258.
https://doi.org/10.1093/nar/gku340
74. Laskowski RA (2001) PDBsum: summaries and analyses of PDB structures. Nucleic Acids
Res 29:221–222
75. Benkert P, Biasini M, Schwede T (2011) Toward the estimation of the absolute quality
of individual protein structure models. Bioinformatics 27:343–350. https://doi.org/10.1093/
bioinformatics/btq662
76. Xu D, Zhang Y (2012) Ab initio protein structure assembly using continuous structure fragments
and optimized knowledge-based force field. Proteins Struct Funct Bioinforma 80:1715–1735.
https://doi.org/10.1002/prot.24065
77. Brylinski M, Skolnick J (2008) A threading-based method (FINDSITE) for ligand-binding site
prediction and functional annotation. Proc Natl Acad Sci U S A 105:129–134. https://doi.org/
10.1073/pnas.0707684105
78. Levitt DG, Banaszak LJ (1992) POCKET: a computer graphics method for identifying and
displaying protein cavities and their surrounding amino acids. J Mol Graph 10:229–234
79. Trott O, Olson AJ (2010) AutoDock Vina. J Comput Chem 31:445–461. https://doi.org/10.
1002/jcc.21334
80. Case DA, Cheatham TE, Darden T et al (2005) The Amber biomolecular simulation programs.
J Comput Chem 26:1668–1688. https://doi.org/10.1002/jcc.20290