Shirai H, Prades C, Vita R, Marcatili P, Popovic B, Xu J, Overington JP, Hirayama K, Soga S, Tsunoyama K, Clark D, Lefranc MP, Ikeda K. Antibody informatics for drug discovery. Biochimica et Biophysica Acta. Nov 2014, 1844 (11): 2002–2015. PMID 25110827. doi:10.1016/j.bbapap.2014.07.006.
Tollenaere JP. The role of structure-based ligand design and molecular modelling in drug discovery. Pharmacy World & Science. Apr 1996, 18 (2): 56–62. PMID 8739258. S2CID 21550508. doi:10.1007/BF00579706.
Waring MJ, Arrowsmith J, Leach AR, Leeson PD, Mandrell S, Owen RM, Pairaudeau G, Pennie WD, Pickett SD, Wang J, Wallace O, Weir A. An analysis of the attrition of drug candidates from four major pharmaceutical companies. Nature Reviews Drug Discovery. 2015, 14 (7): 475–86. PMID 26091267. S2CID 25292436. doi:10.1038/nrd4609.
Yu H, Adedoyin A. ADME-Tox in drug discovery: integration of experimental and computational technologies. Drug Discovery Today. Sep 2003, 8 (18): 852–61. PMID 12963322. doi:10.1016/S1359-6446(03)02828-9.
Imming P, Sinning C, Meyer A. Drugs, their targets and the nature and number of drug targets. Nature Reviews. Drug Discovery. Oct 2006, 5 (10): 821–34. PMID 17016423. S2CID 8872470. doi:10.1038/nrd2132.
Recanatini M, Bottegoni G, Cavalli A. In silico antitarget screening. Drug Discovery Today: Technologies. Dec 2004, 1 (3): 209–15. PMID 24981487. doi:10.1016/j.ddtec.2004.10.004.
Scomparin A, Polyak D, Krivitsky A, Satchi-Fainaro R. Achieving successful delivery of oligonucleotides - From physico-chemical characterization to in vivo evaluation. Biotechnology Advances. Apr 2015, 33 (6): 1294–309. PMID 25916823. doi:10.1016/j.biotechadv.2015.04.008.
Yuan Y, Pei J, Lai L. Binding site detection and druggability prediction of protein targets for structure-based drug design. Current Pharmaceutical Design. Dec 2013, 19 (12): 2326–33. PMID 23082974. doi:10.2174/1381612811319120019.
de Azevedo WF, Dias R. Computational methods for calculation of ligand-binding affinity. Current Drug Targets. Dec 2008, 9 (12): 1031–9. PMID 19128212. doi:10.2174/138945008786949405.
Singh J, Chuaqui CE, Boriack-Sjodin PA, Lee WC, Pontz T, Corbley MJ, Cheung HK, Arduini RM, Mead JN, Newman MN, Papadatos JL, Bowes S, Josiah S, Ling LE. Successful shape-based virtual screening: the discovery of a potent inhibitor of the type I TGFbeta receptor kinase (TbetaRI). Bioorganic & Medicinal Chemistry Letters. Dec 2003, 13 (24): 4355–9. PMID 14643325. doi:10.1016/j.bmcl.2003.09.028.
Becker OM, Dhanoa DS, Marantz Y, Chen D, Shacham S, Cheruku S, Heifetz A, Mohanty P, Fichman M, Sharadendu A, Nudelman R, Kauffman M, Noiman S. An integrated in silico 3D model-driven discovery of a novel, potent, and selective amidosulfonamide 5-HT1A agonist (PRX-00023) for the treatment of anxiety and depression. Journal of Medicinal Chemistry. Jun 2006, 49 (11): 3116–35. PMID 16722631. doi:10.1021/jm0508641.
Oda A, Tsuchida K, Takakura T, Yamaotsu N, Hirono S. Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes. Journal of Chemical Information and Modeling. 2006, 46 (1): 380–91. PMID 16426072. doi:10.1021/ci050283k.
Deng Z, Chuaqui C, Singh J. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. Journal of Medicinal Chemistry. Jan 2004, 47 (2): 337–44. PMID 14711306. doi:10.1021/jm030331x.
Amari S, Aizawa M, Zhang J, Fukuzawa K, Mochizuki Y, Iwasawa Y, Nakata K, Chuman H, Nakano T. VISCANA: visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening. Journal of Chemical Information and Modeling. 2006, 46 (1): 221–30. PMID 16426058. doi:10.1021/ci050262q.
Wang R, Gao Y, Lai L. LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design. Journal of Molecular Modeling. 2000, 6 (7–8): 498–516. S2CID 59482623. doi:10.1007/s0089400060498.
Schneider G, Fechner U. Computer-based de novo design of drug-like molecules. Nature Reviews. Drug Discovery. Aug 2005, 4 (8): 649–63. PMID 16056391. S2CID 2549851. doi:10.1038/nrd1799.
Yuan Y, Pei J, Lai L. Binding site detection and druggability prediction of protein targets for structure-based drug design. Current Pharmaceutical Design. Dec 2013, 19 (12): 2326–33. PMID 23082974. doi:10.2174/1381612811319120019.Yuan Y, Pei J, Lai L (Dec 2013). "Binding site detection and druggability prediction of protein targets for structure-based drug design". Current Pharmaceutical Design. 19 (12): 2326–33. doi:10.2174/1381612811319120019. PMID23082974 (页面存档备份,存于互联网档案馆).
Leis S, Schneider S, Zacharias M. In silico prediction of binding sites on proteins. Current Medicinal Chemistry. 2010, 17 (15): 1550–62. PMID 20166931. doi:10.2174/092986710790979944.
Böhm HJ. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. Journal of Computer-Aided Molecular Design. Jun 1994, 8 (3): 243–56. Bibcode:1994JCAMD...8..243B. PMID 7964925. S2CID 2491616. doi:10.1007/BF00126743.
Liu J, Wang R. Classification of Current Scoring Functions. Journal of Chemical Information and Modeling. 23 March 2015, 55 (3): 475–482. PMID 25647463. doi:10.1021/ci500731a.
Ajay, Murcko MA. Computational methods to predict binding free energy in ligand-receptor complexes. J. Med. Chem. 1995, 38 (26): 4953–67. PMID 8544170. doi:10.1021/jm00026a001.
Greer J, Erickson JW, Baldwin JJ, Varney MD. Application of the three-dimensional structures of protein target molecules in structure-based drug design. Journal of Medicinal Chemistry. Apr 1994, 37 (8): 1035–54. PMID 8164249. doi:10.1021/jm00034a001.
Capdeville R, Buchdunger E, Zimmermann J, Matter A. Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug. Nature Reviews. Drug Discovery. Jul 2002, 1 (7): 493–502. PMID 12120256. S2CID 2728341. doi:10.1038/nrd839.
Böhm HJ. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. Journal of Computer-Aided Molecular Design. Jun 1994, 8 (3): 243–56. Bibcode:1994JCAMD...8..243B. PMID 7964925. S2CID 2491616. doi:10.1007/BF00126743.
Shirai H, Prades C, Vita R, Marcatili P, Popovic B, Xu J, Overington JP, Hirayama K, Soga S, Tsunoyama K, Clark D, Lefranc MP, Ikeda K. Antibody informatics for drug discovery. Biochimica et Biophysica Acta. Nov 2014, 1844 (11): 2002–2015. PMID 25110827. doi:10.1016/j.bbapap.2014.07.006.
Tollenaere JP. The role of structure-based ligand design and molecular modelling in drug discovery. Pharmacy World & Science. Apr 1996, 18 (2): 56–62. PMID 8739258. S2CID 21550508. doi:10.1007/BF00579706.
Waring MJ, Arrowsmith J, Leach AR, Leeson PD, Mandrell S, Owen RM, Pairaudeau G, Pennie WD, Pickett SD, Wang J, Wallace O, Weir A. An analysis of the attrition of drug candidates from four major pharmaceutical companies. Nature Reviews Drug Discovery. 2015, 14 (7): 475–86. PMID 26091267. S2CID 25292436. doi:10.1038/nrd4609.
Yu H, Adedoyin A. ADME-Tox in drug discovery: integration of experimental and computational technologies. Drug Discovery Today. Sep 2003, 8 (18): 852–61. PMID 12963322. doi:10.1016/S1359-6446(03)02828-9.
Imming P, Sinning C, Meyer A. Drugs, their targets and the nature and number of drug targets. Nature Reviews. Drug Discovery. Oct 2006, 5 (10): 821–34. PMID 17016423. S2CID 8872470. doi:10.1038/nrd2132.
Recanatini M, Bottegoni G, Cavalli A. In silico antitarget screening. Drug Discovery Today: Technologies. Dec 2004, 1 (3): 209–15. PMID 24981487. doi:10.1016/j.ddtec.2004.10.004.
Scomparin A, Polyak D, Krivitsky A, Satchi-Fainaro R. Achieving successful delivery of oligonucleotides - From physico-chemical characterization to in vivo evaluation. Biotechnology Advances. Apr 2015, 33 (6): 1294–309. PMID 25916823. doi:10.1016/j.biotechadv.2015.04.008.
Yuan Y, Pei J, Lai L. Binding site detection and druggability prediction of protein targets for structure-based drug design. Current Pharmaceutical Design. Dec 2013, 19 (12): 2326–33. PMID 23082974. doi:10.2174/1381612811319120019.
Rajamani R, Good AC. Ranking poses in structure-based lead discovery and optimization: current trends in scoring function development. Current Opinion in Drug Discovery & Development. May 2007, 10 (3): 308–15. PMID 17554857.
de Azevedo WF, Dias R. Computational methods for calculation of ligand-binding affinity. Current Drug Targets. Dec 2008, 9 (12): 1031–9. PMID 19128212. doi:10.2174/138945008786949405.
Singh J, Chuaqui CE, Boriack-Sjodin PA, Lee WC, Pontz T, Corbley MJ, Cheung HK, Arduini RM, Mead JN, Newman MN, Papadatos JL, Bowes S, Josiah S, Ling LE. Successful shape-based virtual screening: the discovery of a potent inhibitor of the type I TGFbeta receptor kinase (TbetaRI). Bioorganic & Medicinal Chemistry Letters. Dec 2003, 13 (24): 4355–9. PMID 14643325. doi:10.1016/j.bmcl.2003.09.028.
Becker OM, Dhanoa DS, Marantz Y, Chen D, Shacham S, Cheruku S, Heifetz A, Mohanty P, Fichman M, Sharadendu A, Nudelman R, Kauffman M, Noiman S. An integrated in silico 3D model-driven discovery of a novel, potent, and selective amidosulfonamide 5-HT1A agonist (PRX-00023) for the treatment of anxiety and depression. Journal of Medicinal Chemistry. Jun 2006, 49 (11): 3116–35. PMID 16722631. doi:10.1021/jm0508641.
Oda A, Tsuchida K, Takakura T, Yamaotsu N, Hirono S. Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes. Journal of Chemical Information and Modeling. 2006, 46 (1): 380–91. PMID 16426072. doi:10.1021/ci050283k.
Deng Z, Chuaqui C, Singh J. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. Journal of Medicinal Chemistry. Jan 2004, 47 (2): 337–44. PMID 14711306. doi:10.1021/jm030331x.
Amari S, Aizawa M, Zhang J, Fukuzawa K, Mochizuki Y, Iwasawa Y, Nakata K, Chuman H, Nakano T. VISCANA: visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening. Journal of Chemical Information and Modeling. 2006, 46 (1): 221–30. PMID 16426058. doi:10.1021/ci050262q.
Mauser H, Guba W. Recent developments in de novo design and scaffold hopping. Current Opinion in Drug Discovery & Development. May 2008, 11 (3): 365–74. PMID 18428090.
Schneider G, Fechner U. Computer-based de novo design of drug-like molecules. Nature Reviews. Drug Discovery. Aug 2005, 4 (8): 649–63. PMID 16056391. S2CID 2549851. doi:10.1038/nrd1799.
Yuan Y, Pei J, Lai L. Binding site detection and druggability prediction of protein targets for structure-based drug design. Current Pharmaceutical Design. Dec 2013, 19 (12): 2326–33. PMID 23082974. doi:10.2174/1381612811319120019.Yuan Y, Pei J, Lai L (Dec 2013). "Binding site detection and druggability prediction of protein targets for structure-based drug design". Current Pharmaceutical Design. 19 (12): 2326–33. doi:10.2174/1381612811319120019. PMID23082974 (页面存档备份,存于互联网档案馆).
Leis S, Schneider S, Zacharias M. In silico prediction of binding sites on proteins. Current Medicinal Chemistry. 2010, 17 (15): 1550–62. PMID 20166931. doi:10.2174/092986710790979944.
Böhm HJ. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. Journal of Computer-Aided Molecular Design. Jun 1994, 8 (3): 243–56. Bibcode:1994JCAMD...8..243B. PMID 7964925. S2CID 2491616. doi:10.1007/BF00126743.
Liu J, Wang R. Classification of Current Scoring Functions. Journal of Chemical Information and Modeling. 23 March 2015, 55 (3): 475–482. PMID 25647463. doi:10.1021/ci500731a.
Ajay, Murcko MA. Computational methods to predict binding free energy in ligand-receptor complexes. J. Med. Chem. 1995, 38 (26): 4953–67. PMID 8544170. doi:10.1021/jm00026a001.
Greer J, Erickson JW, Baldwin JJ, Varney MD. Application of the three-dimensional structures of protein target molecules in structure-based drug design. Journal of Medicinal Chemistry. Apr 1994, 37 (8): 1035–54. PMID 8164249. doi:10.1021/jm00034a001.
Capdeville R, Buchdunger E, Zimmermann J, Matter A. Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug. Nature Reviews. Drug Discovery. Jul 2002, 1 (7): 493–502. PMID 12120256. S2CID 2728341. doi:10.1038/nrd839.
Yuan Y, Pei J, Lai L. Binding site detection and druggability prediction of protein targets for structure-based drug design. Current Pharmaceutical Design. Dec 2013, 19 (12): 2326–33. PMID 23082974. doi:10.2174/1381612811319120019.Yuan Y, Pei J, Lai L (Dec 2013). "Binding site detection and druggability prediction of protein targets for structure-based drug design". Current Pharmaceutical Design. 19 (12): 2326–33. doi:10.2174/1381612811319120019. PMID23082974 (页面存档备份,存于互联网档案馆).
Tollenaere JP. The role of structure-based ligand design and molecular modelling in drug discovery. Pharmacy World & Science. Apr 1996, 18 (2): 56–62. PMID 8739258. S2CID 21550508. doi:10.1007/BF00579706.
Waring MJ, Arrowsmith J, Leach AR, Leeson PD, Mandrell S, Owen RM, Pairaudeau G, Pennie WD, Pickett SD, Wang J, Wallace O, Weir A. An analysis of the attrition of drug candidates from four major pharmaceutical companies. Nature Reviews Drug Discovery. 2015, 14 (7): 475–86. PMID 26091267. S2CID 25292436. doi:10.1038/nrd4609.
Imming P, Sinning C, Meyer A. Drugs, their targets and the nature and number of drug targets. Nature Reviews. Drug Discovery. Oct 2006, 5 (10): 821–34. PMID 17016423. S2CID 8872470. doi:10.1038/nrd2132.
Wang R, Gao Y, Lai L. LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design. Journal of Molecular Modeling. 2000, 6 (7–8): 498–516. S2CID 59482623. doi:10.1007/s0089400060498.
Schneider G, Fechner U. Computer-based de novo design of drug-like molecules. Nature Reviews. Drug Discovery. Aug 2005, 4 (8): 649–63. PMID 16056391. S2CID 2549851. doi:10.1038/nrd1799.
Böhm HJ. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. Journal of Computer-Aided Molecular Design. Jun 1994, 8 (3): 243–56. Bibcode:1994JCAMD...8..243B. PMID 7964925. S2CID 2491616. doi:10.1007/BF00126743.
Capdeville R, Buchdunger E, Zimmermann J, Matter A. Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug. Nature Reviews. Drug Discovery. Jul 2002, 1 (7): 493–502. PMID 12120256. S2CID 2728341. doi:10.1038/nrd839.
Yuan Y, Pei J, Lai L. Binding site detection and druggability prediction of protein targets for structure-based drug design. Current Pharmaceutical Design. Dec 2013, 19 (12): 2326–33. PMID 23082974. doi:10.2174/1381612811319120019.Yuan Y, Pei J, Lai L (Dec 2013). "Binding site detection and druggability prediction of protein targets for structure-based drug design". Current Pharmaceutical Design. 19 (12): 2326–33. doi:10.2174/1381612811319120019. PMID23082974 (页面存档备份,存于互联网档案馆).