Awards


  1. 2007 National Innovation Award , Yen-Fu Chen, Yu-Ju Chen, and Jinn-Moon Yang, "GEMDOCK: An Integrated Environment for Computer-aided Drug Design and Its Applications", (Web site of National Innovation Award)


Publications

Primary References:
  1. J.-M. Yang and C.-C. Chen, "GEMDOCK: A generic evolutionary method for molecular docking", Proteins: Structure, Function and Bioinformatics, vol. 55, pp. 288-304, 2004. (IF: 3.354; Times Cited: 37 ). (PDF)


  2. J.-M. Yang, "Development and evaluation of a generic evolutionary method for protein-ligand docking", Journal of Computational Chemistry, vol. 25, pp. 843-857, 2004. (IF: 4.297; Times Cited: 5) (PDF)


  3. J.-M. Yang and T.-W. Shen, "A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators", Proteins: Structure, Function and Bioinformatics,vol. 59, pp. 205-220, 2005. (IF: 3.354; Times Cited: 19). (PDF)


  4. J.-M. Yang, Y.-F. Chen, T.-W. Shen, B. S. Kristal, and D. F. Hsu, "Consensus Scoring Criteria for Improving Enrichment in Virtual Screening ", Journal of Chemical Information and Modeling 2005. (IF: 2.986; Times Cited: 34). (PDF)


Selected Applications:
  1. K.-H. Chin, Y.-C. Lee, Z.-L. Tu, C.-H. Chen, Y.-H. Tseng, J.-M. Yang, R. P. Ryan, Y. McCarthy, J. M. Dow, A. H.-J. Wang, and S.-H. Chou "The c-AMP receptor-like protein CLP is a novel c-di-GMP receptor linking cell-cell signaling to virulence gene expression in xanthomonas campestris," Journal of Molecular Biology, vol.396, pp. 646-662, 2010. (PDF)


  2. H.-C. Hung, C.-P. Tseng, J.-M. Yang, Y.-W Ju, S.-N. Tseng, Y.-F. Chen, Y.-S. Chao, H.-P. Hsieh, S.-R. Shih, John T.-A. Hsu, "Aurintricarboxylic acid inhibits influenza virus neuraminidase,"Antiviral Research, vol.81, pp. 123-131, 2009. (PDF)


  3. M.-C. Yang, H.-H. Guan, J.-M. Yang, C.-N. Ko, M.-Y. Liu, Y.-H. Lin, C.-J. Chen, and Simon JT Mao*, "Rational Design for crystallization of b-Lactoglobulin and vitamin D3 complex: reveal of a secondary binding site,"Crystal Growth & Design, vol. 8, pp. 4268-4276, 2008. (One of cover stories) (PDF)


  4. M.-C. Yang, H.-H. Guan, M.-Y. Liu, Y.-H. Lin, J.-M. Yang, W.-L. Chen, C.-J. Chen, and Simon J. T. Mao*, "Crystal structure of a secondary vitamin D3 binding site of milk s-lactoglobulin," Proteins: Structure, Function, and Bioinformatics, vol. 71, pp. 1197-1210, 2008. (PDF)


  5. J.-M. Yang, Y.-F. Chen, Y.-Y. Tu, K.-R. Yen, and Y.-L. Yang*, ˇ§Combinatorial computation approaches identifying tetracycline derivates as flaviviruses inhibitorsˇ¨, PLoS ONE, pp. e428.1- e428.12, 2007. (PDF)


  6. E.-S. Lin, J.-M. Yang, and Y.-S. Yang, "Modeling the binding and inhibition mechanism of nucleotide and sulfotransferase using molecular docking", Journal of the Chinese Chemical Society, vol. 50, pp. 655-663, 2003. (SCI) (PDF)


Selected citations

Virtual screening:
  1. R. Jia, LJ. Yang, SY. Yang, "Binding energy contributions of the conserved bridging water molecules in CDK2-inhibitor complexes: A combined QM/MM study", Chemical Physics Letters, vol. 460, pp. 300-305, 2008.


  2. R. Kim, J. Skolnick, "Assessment of programs for ligand binding affinity prediction", Journal of Computational Chemistry, vol. 29, pp. 1316-1331, 2008.


  3. BC. Robeits, RL. Mancera, "Ligand-protein docking with water molecules", Journal of Chemical Information and Modeling, vol. 48, pp. 397-408, 2008.


  4. N. Moitessier, P. Englebienne, D. Lee, J. Lawandi, CR. Corbeil, "Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go", British Journal of Pharmacology, vol. 153, pp. S7-S26, 2008.


  5. P. Taylor, E. Blackburn, YG. Sheng,S. Harding,KY. Hsin,D. Kan,S. Shave, M. Walkinshaw, "Ligand discovery and virtual screening using the program LIDAEUS", British Journal of Pharmacology, vol. 153, pp. S55-S67, 2008.


  6. NS. Sapre, S. Gupta, N. Pancholi, N. Sapre, "Molecular docking studies on tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepinone (TIBO) derivatives as HIV-1NNRT inhibitors", Journal of Computer-Aided Molecular Design, vol. 22, pp. 69-80, 2008.


  7. AJS. Knox, MJ. Meegan,V. Sobolev, D. Frost, DM. Zisterer, DC. Williams, DG. Lloyd, "Target specific virtual screening: Optimization of an estrogen receptor screening platform", Journal of Medicinal Chemistry, vol. 50, pp. 5301-5310, 2007.


  8. SJ. Zhong, AT. Macias, AD. MacKerell, "Computational identification of inhibitors of protein-protein interactions", Current Topics in Medicinal Chemistry, vol. 7, pp. 63-82, 2007.


  9. Z. Li, T. Lazaridis, "Water at biomolecular binding interfaces", Physical Chemistry Chemical Physics, vol. 9, pp. 573-581, 2007.


  10. ADJ. van Dijk, AMJJ. Bonvin, Solvated docking: introducing water into the modelling of biomolecular complexes", Bioinformatics, vol. 22, pp. 2340-2347, 2006.


  11. O. Sperandio, MA. Miteva, F. Delfaud, BO. Villoutreix, "Receptor-based computational screening of compound databases: The main docking-scoring engines", Current Protein & Peptide Science, vol. 7, pp. 369-393, 2006.


  12. S. Mitra, Y. Hayashi, "Bioinformatics with soft computing", Ieee Transactions on Systems Man and Cybernetics Part C-Applications and Reviews, vol. 36, pp. 616-635, 2006.


  13. R. Thomsen, MH. Christensen, "MolDock: A new technique for high-accuracy molecular docking", Journal of Medicinal Chemistry, vol. 49, pp. 3315-3321, 2006.


  14. AJS. Knox, MJ. Meegan, DG. Lloyd, "Estrogen receptors: Molecular interactions, virtual screening and future prospects", Current Topics in Medicinal Chemistry, vol. 6, pp. 217-243, 2006.


  15. K. Chen, TH. Li, TC. Cao, "Tribe-PSO: A novel global optimization algorithm and its application in molecular docking", Chemometrics and Intelligent Laboratory Systems, vol. 82, pp. 248-259, 2006.


  16. S. Amari, M. Aizawa, JW. Zhang, K. Fukuzawa, Y. Mochizuki, Y. Iwasawa, K. Nakata, H. Chuman, T. Nakano, "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, vol. 46, pp. 221-230, 2006.


  17. ML. Verdonk, G. Chessari, JC. Cole, MJ. Hartshorn, CW. Murray, JWM. Nissink, RD. Taylor, R. Taylor, "Modeling water molecules in protein-ligand docking using GOLD", Journal of Medicinal Chemistry, vol. 48, pp. 6504-6515, 2005.


  18. S. Radestock, M. Bohm, H. Gohlke, "Improving binding mode predictions by docking into protein-specifically adapted potential fields", Journal of Medicinal Chemistry, vol. 48, pp. 5466-5479, 2005.


  19. DTH. Chang, YJ. Oyang, JH. Lin, "MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm", Nucleic Acids Research, vol. 33, pp. W233-W238, 2005.


  20. DS. Wishart, "Bioinformatics in drug development and assessment", Drug Metabolism Reviews, vol. 37, pp. 279-310, 2005.


  21. YH. Duan, BVB. Reddy, YN. Kaznessis, "Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions", Protein Science, vol. 14, pp. 316-328, 2005.


Scoring function:
  1. B. Fischer, K. Fukuzawa, W. Wenzel, "Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery", Proteins: Structure Function and Bioinformatics, vol. 70, pp. 1264-1273, 2008.


  2. R. Teramoto, H. Fukunishi, "Supervised scoring models with docked ligand conformations for structure-based virtual screening", Journal of Chemical Information and Modeling, vol. 47, pp. 1858-1867, 2007.


  3. AS. Reddy, SP. Pati, PP. Kumar, HN. Pradeep, GN. Sastry, "Virtual screening in drug discovery - A computational perspective", Current Protein & Peptide Science, vol. 8, pp. 329-351, 2007.


  4. YH. Shi, "Orphan nuclear receptors in drug discovery", Drug Discovery Today, vol. 12, pp. 440-445, 2007.


  5. YH. Shi, "Orphan nuclear receptors, excellent targets of drug discovery", Combinatorial Chemistry & High Throughput Screening, vol. 9, pp. 683-689, 2006.


  6. SJ. Zhong, AT. Macias, AD. MacKerell, "Computational identification of inhibitors of protein-protein interactions", Current Topics in Medicinal Chemistry, vol. 7, pp. 63-82, 2007.


  7. N. Huang, BK. Shoichet, JJ. Irwin, "Benchmarking sets for molecular docking", Journal of Medicinal Chemistry, vol. 49, pp. 6789-6801, 2006.


  8. A. Koike, "Comparison of methods for chemical-compound affinity prediction", SAR and QSAR in Environmental Research, vol. 17, pp. 497-514, 2006.


  9. AJS. Knox, MJ. Meegan, DG. Lloyd, "Estrogen receptors: Molecular interactions, virtual screening and future prospects", Current Topics in Medicinal Chemistry, vol. 6, pp. 217-243, 2006.


  10. S. Amari, M. Aizawa, JW. Zhang, K. Fukuzawa, Y. Mochizuki, Y. Iwasawa, K. Nakata, H. Chuman, T. Nakano, "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, vol. 46, pp. 221-230, 2006.


  11. XC. Kretschmer, WS. Baldwin, "CAR and PXR: Xenosensors of endocrine disrupters?", Chemico-Biological Interactions, vol. 155, pp. 111-128, 2005.


Post-analysis:
  1. H. Fukunishi, R. Teramoto, T. Takada, J. Shimada, "Bootstrap-based consensus scoring method for protein-ligand docking", Journal of Chemical Information and Modeling, vol. 48, pp. 988 - 996, 2008.


  2. SG. Rohrer, K. Baumann, "Impact of benchmark data set topology on the validation of virtual screening methods: Exploration and quantification by spatial statistics", Journal of Chemical Information and Modeling, vol. 48, pp. 704 - 718, 2008.


  3. H. Fukunishi, R. Teramoto, J. Shimada, "Hidden active. information in a random compound library: Extraction using a pseudo-structure-activity relationship model", Journal of Chemical Information and Modeling, vol. 48, pp. 575 - 582, 2008.


  4. L. Celik, S. Sinning, K. Severinsen, CG. Hansen, MS. Moller, M. Bols, O. Wiborg, B. Schiott, "Binding of serotonin to the human serotonin transporter. Molecular modeling and experimental validation", Journal of the American Chemical Society , vol. 130, pp. 3853 - 3865, 2008.


  5. R. Teramoto, H. Fukunishi, "Consensus scoring with feature selection for structure-based virtual screening", Journal of Chemical Information and Modeling, vol. 48, pp. 288 - 295, 2008.


  6. S. Renner, S. Derksen, S. Radestock, F. Morchen, "Maximum common binding modes (MCBM): Consensus docking scoring using multiple ligand information and interaction fingerprints", Journal of Chemical Information and Modeling, vol. 48, pp. 319 - 332, 2008.


  7. SR. Shave, P. Taylor, M. Walkinshaw, L. Smith, J. Hardy, A. Trew, "Ligand discovery on massively parallel systems", Ibm Journal of Research and Development , vol. 52, pp. 57 - 67, 2008.


  8. R. Teramoto, H. Fukunishi, "Supervised scoring models with docked ligand conformations for structure-based virtual screening", Journal of Chemical Information and Modeling, vol. 47, pp. 1858 - 1867, 2007.


  9. K. Onodera, K. Satou, H. Hirota, "Evaluations of molecular docking programs for virtual screening", Journal of Chemical Information and Modeling, vol. 47, pp. 1609 - 1618, 2007.


  10. X. Morelli, AC. Rigby, "Acceleration of the drug discovery process: A combinatorial approach using NMR spectroscopy and virtual screening", Current Computer-Aided Drug Design , vol. 3, pp. 33 - 49, 2007.


  11. KL. Lin, CY. Lin, CD. Huang, HM. Chang, CY. Yang, CT. Lin, CY. Tang, DF. Hsu, "Feature selection and combination criteria for improving accuracy in protein structure prediction", IEEE Transactions on Nanobioscience , vol. 6, pp. 186 - 196, 2007.


  12. D. Joseph-McCarthy, JC. Baber, E. Feyfant, DC. Thompson, C. Humblet, "Lead optimization via high-throughput molecular docking", Current Opinion in Drug Discovery & Development, vol. 10, pp. 264 - 274, 2007.


  13. MHJ. Seifert, J. Kraus, B. Kramer, "Virtual high-throughput screening of molecular databases", Current Opinion in Drug Discovery & Development, vol. 10, pp. 298 - 307, 2007.


  14. R. Teramoto, H. Fukunishi, "Supervised consensus scoring for docking and virtual screening", Journal of Chemical Information and Modeling, vol. 47, pp. 526 - 534, 2007.


  15. P. Willett, "Enhancing the effectiveness of ligand-based virtual screening using data fusion", QSAR & Combinatorial Science , vol. 25, pp. 1143 - 1152, 2006.


  16. CH. Peng, JT. Hsu, YS. Chung, YJ. Lin, WY. Chow, DF. Hsu, CY. Tang, "Identification of degenerate motifs using position restricted selection and hybrid ranking combination", Nucleic Acids Research , vol. 34, pp. 6379 - 6391, 2006.


  17. M. Whittle, VJ. Gillet, P. Willett, "Analysis of data fusion methods in virtual screening: Theoretical model", Journal of Chemical Information and Modeling, vol. 46, pp. 2193 - 2205, 2006.


  18. E. Stjernschantz, J. Marelius, C. Medina, M. Jacobsson, NPE. Vermeulen, C. Oostenbrink, "Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? An evaluation of the linear interaction energy (LIE) method", Journal of Chemical Information and Modeling, vol. 46, pp. 1972 - 1983, 2006.


  19. O. Sperandio, MA. Miteva, F. Delfaud, BO. Villoutreix, "Receptor-based computational screening of compound databases: The main docking-scoring engines", Current Protein & Peptide Science , vol. 7, pp. 369 - 393, 2006.


  20. B. Coupez, RA. Lewis, "Docking and scoring - Theoretically easy, practically impossible?", Current Medicinal Chemistry , vol. 13, pp. 2995 - 3003, 2006.


  21. S. Betzi, K. Suhre, B. Chetrit, F. Guerlesquin, X. Morelli, "GFscore: A general nonlinear consensus scoring function for high-throughput docking", Journal of Chemical Information and Modeling, vol. 46, pp. 1704 - 1712, 2006.


  22. M. Feher, "Consensus scoring for protein-ligand interactions", Drug Discovery Today , vol. 11, pp. 421 - 428, 2006.