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BioSolveIT
The Premier Scientific Solution Provider
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On this page you can find a compilation of successful applications of FlexX (FlexS, FTrees and other BioSolveIT tools will follow) published in all major journals sorted reverse chronologically.
FlexX
  1. Dessalew, N. and Bharatam, P. V. (2007).
    3D-QSAR and molecular docking study on bisarylmaleimide series as glycogen synthase kinase 3, cyclin dependent kinase 2 and cyclin dependent kinase 4 inhibitors: An insight into the criteria for selectivity.
    European Journal of Medicinal Chemistry. (Online First)
  2. Kumar, R., Ramachandran, U., Khanna, S., Bharatam, P. V., Raichur. S. Chakrabarti, R. (2007).
    Synthesis, in vitro and in silico evaluation of l-tyrosine containing PPARalpha/gamma dual agonists.
    Bioorganic & Medicinal Chemistry. 15(3): 1547-55.
  3. Price, S., Bordogna, W., Bull, R. J., Clark, D. E., Crackett, P. H., Dyke, H. J., Gill, M., Harris, N. V., Gorski, J., Lloyd, J., Lockey, P. M., Mullett, J., Roach, A. G., Roussel, F., White, A. B. (2007).
    Identification and optimisation of a series of substituted 5-(1H-pyrazol-3-yl)-thiophene-2-hydroxamic acids as potent histone deacetylase (HDAC) inhibitors.
    Bioorganic & Medicinal Chemistry Letters. 17(2): 370-5.
  4. Schellhammer, I. and Rarey, M. (2007).
    TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time.
    Journal Of Computer-Aided Molecular Design. (Online First)
  5. Xue, C., Zhang, L., Luo, W., Xie, X., Jiang, L. and Xiao, T. (2007).
    3D-QSAR and molecular docking studies of benzaldehyde thiosemicarbazone, benzaldehyde, benzoic acid, and their derivatives as phenoloxidase inhibitors.
    Bioorganic & Medicinal Chemistry 15(5): 2006-2015
  6. Bharatam, P. V. and Khanna, S. (2006).
    Molecular docking studies on pyridine derivatives of glitazones as PPAR gamma agonists.
    Indian Journal Of Chemistry Section A-Inorganic Bio-Inorganic Physical Theoretical & Analytical Chemistry 45(1): 188-193.
  7. Dessalew, N. and Bharatam, P. V. (2006).
    Investigation of potential glycogen synthase kinase 3 inhibitors using pharmacophore mapping and virtual screening.
    Chemical Biology and Drug Design. 68(3): 154-65.
  8. Jacobsson, M. and Karlen, A. (2006).
    Ligand bias of scoring functions in structure-based virtual screening.
    Journal Of Chemical Information And Modeling 46(3): 1334-1343.
  9. Kämper, A., Apostolakis, J., Rarey, M., Marian, C. M. and Lengauer, T. (2006).
    Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies.
    Journal Of Chemical Information And Modeling 46(2): 903-911.
  10. Oda, A., Tsuchida, K., Takakura, T., Yamaotsu, N. and Hirono, S. (2006).
    Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes.
    Journal Of Chemical Information And Modeling 46(1): 380-391.
  11. Patel, D. S. and Bharatam, P. V. (2006).
    New leads for selective GSK-3 inhibition: pharmacophore mapping and virtual screening studies.
    Journal Of Computer-Aided Molecular Design 20(1): 55-66.
  12. Rummey, C., Nordhoff, S., Thiemann, M. and Metz, G. (2006).
    In silico fragment-based discovery of DPP-IV S1 pocket binders.
    Bioorganic & Medicinal Chemistry Letters 16(5): 1405-1409.
  13. Stiefl, N. and Zaliani, A. (2006).
    A knowledge-based weighting approach to ligand-based virtual screening.
    Journal Of Chemical Information And Modeling 46(2): 587-596.
  14. Sun, J., Chen, H. F., Xia, H. R., Yao, J. H. and Fan, B. T. (2006).
    Comparative study of Factor Xa inhibitors using molecular docking/SVM/HQSAR/3D-QSAR methods.
    QSAR & Combinatorial Science 25(1): 25-45.
  15. Wang, M. H. and Hampson, D. R. (2006).
    An evaluation of automated in silico ligand docking of amino acid ligands to Family C G-protein coupled receptors.
    Bioorganic & Medicinal Chemistry 14(6): 2032-2039.
  16. Alonso, H., Gillies, M. B., Cummins, P. L., Bliznyuk, A. A. and Gready, J. E. (2005).
    Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase.
    Journal of Computer-Aided Molecular Design 19(3): 165-187.
  17. Antes, I., Merkwirth, C. and Lengauer, T. (2005).
    POEM: Parameter optimization using ensemble methods: Application to target specific scoring functions.
    Journal Of Chemical Information And Modeling 45(5): 1291-1302.
  18. Brautigan, D. L., Brown, M., Grindrod, S., Chinigo, G., Kruszewski, A., Lukasik, S. M., Bushweller, J. H., Horal, M., Keller, S., Tamura, S., Heimark, D. B., Price, J., Larner, A. N. and Larner, J. (2005).
    Allosteric activation of protein phosphatase 2C by D-chiro-inositol-galactosamine, a putative mediator mimetic of insulin action.
    Biochemistry 44(33): 11067-11073.
  19. Cross, S. S. J. (2005).
    Improved FlexX docking using FlexS-determined base fragment placement.
    Journal Of Chemical Information And Modeling 45(4): 993-1001.
  20. da Silva, G. M. S., Lima, L. M., Fraga, C. A. M., Sant'Anna, C. M. R. and Barreiro, E. J. (2005).
    The molecular basis for coxib inhibition of p38 alpha MAP kinase.
    Bioorganic & Medicinal Chemistry Letters 15(15): 3506-3509.
  21. Forino, M., Jung, D., Easton, J. B., Houghton, P. J. and Pellecchia, M. (2005).
    Virtual docking approaches to protein kinase B inhibition.
    Journal Of Medicinal Chemistry 48(7): 2278-2281.
  22. Johnsamuel, J., Eriksson, S., Oliveira, M. and Tjarks, W. (2005).
    Docking simulation with a purine nucleoside specific homology model of deoxycytidine kinase, a target enzyme for anticancer and antiviral therapy.
    Bioorganic & Medicinal Chemistry 13(13): 4160-4167.
  23. Khanna, S., Sobhia, M. E. and Bharatam, P. V. (2005).
    Additivity of molecular fields: CoMFA study on dual activators of PPAR alpha and PPAR gamma.
    Journal Of Medicinal Chemistry 48(8): 3015-3025.
  24. Kontoyianni, M., Sokol, G. S. and McClellan, L. M. (2005).
    Evaluation of library ranking efficacy in virtual screening.
    Journal Of Computational Chemistry 26(1): 11-22.
  25. Krier, M., de Araujo-Junior, J. X., Schmitt, M., Duranton, J., Justiano-Basaran, H., Lugnier, C., Bourguignon, J. J. and Rognan, D. (2005).
    Design of small-sized libraries by combinatorial assembly of linkers and functional groups to a given scaffold: Application to the structure-based optimization of a phosphodiesterase 4 inhibitor.
    Journal Of Medicinal Chemistry 48(11): 3816-3822.
  26. Pan, W. L., Tan, N. H., Zeng, G. Z., Zhang, Y. M. and Jia, R. R. (2005).
    Amentoflavone and its derivatives as novel natural inhibitors of human Cathepsin B.
    Bioorganic & Medicinal Chemistry 13(20): 5819-5825.
  27. Polgar, T., Baki, A., Szendrei, G. I. and Keseru, G. M. (2005).
    Comparative virtual and experimental high-throughput screening for glycogen synthase kinase-3 beta inhibitors.
    Journal Of Medicinal Chemistry 48(25): 7946-7959.
  28. Polgar, T. and Keseru, G. M. (2005).
    Virtual screening for beta-secretase (BACE1) inhibitors reveals the importance of protonation states at Asp32 and Asp228.
    Journal Of Medicinal Chemistry 48(11): 3749-3755.
  29. Virag, I., Polgar, T. and Keseru, G. M. (2005).
    Functional virtual screening of estrogen receptor alpha modulators by FlexX-Pharm.
    Journal Of Molecular Structure-Theochem 725(1-3): 239-242.
  30. von Langen, J., Fritzemeier, K. H., Diekmann, S. and Hillisch, A. (2005).
    Molecular basis of the interaction specificity between the human glucocorticoid receptor and its endogenous steroid ligand cortisol.
    Chembiochem 6(6): 1110-1118.
  31. Zhou, M., Zhang, W., Cheng, Y. H., Ji, M. J. and Xu, X. J. (2005).
    Molecular docking and 3D-QSAR studies on protein tyrosine phosphatase 1B inhibitors.
    Acta Chimica Sinica 63(23): 2131-2136.
  32. Andras, B. A., Kovdari, Z. and Keseru, G. A. (2004).
    Optimization of virtual screening protocols: FlexX based virtual screening for COX-2 inhibitors reveals the importance of tailoring screen parameters.
    Journal Of Molecular Structure-Theochem 676(1-3): 1-5.
  33. Chema, D., Eren, D., Yayon, A., Goldblum, A. and Zaliani, A. (2004).
    Identifying the binding mode of a molecular scaffold.
    Journal Of Computer-Aided Molecular Design 18(1): 23-40.
  34. Kraemer, O., Hazemann, I., Podjarny, A. D. and Klebe, G. (2004).
    Virtual screening for inhibitors of human aldose reductase.
    Proteins-Structure Function And Bioinformatics 55(4): 814-823.
  35. Lyne, P. D., Kenny, P. W., Cosgrove, D. A., Deng, C., Zabludoff, S., Wendoloski, J. J. and Ashwell, S. (2004).
    Identification of compounds with nanomolar binding affinity for checkpoint kinase-1 using knowledge-based virtual screening.
    Journal Of Medicinal Chemistry 47(8): 1962-1968.
  36. Schellhammer, I. and Rarey, M. (2004).
    FlexX-Scan: Fast, structure-based virtual screening.
    Proteins-Structure Function And Bioinformatics 57(3): 504-517.
  37. Xing, L., Hodgkin, E., Liu, Q. and Sedlock, D. (2004).
    Evaluation and application of multiple scoring functions for a virtual screening experiment.
    Journal Of Computer-Aided Molecular Design 18(5): 333-344.
  38. Bissantz, C., Bernard, P., Hibert, M. and Rognan, D. (2003).
    Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets?
    Proteins-Structure Function And Genetics 50(1): 5-25.
  39. Chakraborti, A. K. and Thilagavathi, R. (2003).
    Computer-aided design of non sulphonyl COX-2 inhibitors: An improved comparative molecular field analysis incorporating additional descriptors and comparative molecular similarity indices analysis of 1,3-diarylisoindole derivatives.
    Bioorganic & Medicinal Chemistry 11(18): 3989-3996.
  40. Frimurer, T. M., Peters, G. H., Iversen, L. F., Andersen, H. S., Moller, N. P. H. and Olsen, O. H. (2003).
    Ligand-induced conformational changes: Improved predictions of ligand binding conformations and affinities.
    Biophysical Journal 84(4): 2273-2281.
  41. Johnsamuel, J., Byun, Y. J., Jones, T. P., Endo, Y. and Tjarks, W. (2003).
    A convenient method for the computer-aided molecular design of carborane containing compounds.
    Bioorganic & Medicinal Chemistry Letters 13(19): 3213-3216.
  42. Sun, W. S., Park, Y. S., Yoo, J., Park, K. D., Kim, S. H., Kim, J. H. and Park, H. J. (2003).
    Rational design of an indolebutanoic acid derivative as a novel aldose reductase inhibitor based on docking and 3D QSAR studies of phenethylamine derivatives.
    Journal Of Medicinal Chemistry 46(26): 5619-5627.
  43. Wolf, K. and Dormeyer, M. (2003).
    Information-based methods in the development of antiparasitic drugs.
    Parasitology Research 90: S91-S96.
  44. Xu, X. Y., Cheng, F., Shen, J. H., Luo, X. M., Chen, L. L., Yue, L. D., Du, Y., Ye, F., Jiang, S. H., Zhu, D. Y., Jiang, H. L. and Chen, K. X. (2003).
    Agonist-PPAR gamma interactions: Molecular modeling study with docking approach.
    International Journal Of Quantum Chemistry 93(6): 405-410.
  45. Buolamwini, J. K. and Assefa, H. (2002).
    CoMFA and CoMSIA 3D QSAR and docking studies on conformationally-restrained cinnamoyl HIV-1 integrase inhibitors: Exploration of a binding mode at the active site.
    Journal Of Medicinal Chemistry 45(4): 841-852.
  46. Clark, R. D., Strizhev, A., Leonard, J. M., Blake, J. F. and Matthew, J. B. (2002).
    Consensus scoring for ligand/protein interactions.
    Journal Of Molecular Graphics & Modelling 20(4): 281-295.
  47. Hindle, S. A., Rarey, M., Buning, C. and Lengauer, T. (2002).
    Flexible docking under pharmacophore type constraints.
    Journal Of Computer-Aided Molecular Design 16(2): 129-149.
  48. Paul, N. and Rognan, D. (2002).
    ConsDock: A new program for the consensus analysis of protein-ligand interactions.
    Proteins-Structure Function And Genetics 47(4): 521-533.
  49. Siedle, B., Cisielski, S., Murillo, R., Loser, B., Castro, V., Klaas, C. A., Hucke, O., Labahn, A., Melzig, M. F. and Merfort, I. (2002).
    Sesquiterpene Lactones as inhibitors of human neutrophil elastase.
    Bioorganic & Medicinal Chemistry 10(9): 2855-2861.
  50. Keseru, G. M. (2001).
    A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism.
    Journal Of Computer-Aided Molecular Design 15(7): 649-657.
  51. Marhefka, C. A., Moore, B. M., Bishop, T. C., Kirkovsky, L., Mukherjee, A., Dalton, J. T. and Miller, D. D. (2001).
    Homology modeling using multiple molecular dynamics simulations and docking studies of the human androgen receptor ligand binding domain bound to testosterone and nonsteroidal ligands.
    Journal Of Medicinal Chemistry 44(11) 1729-1740.
  52. Sadowski, J., Böhm, M., Sattler, I., Dahse, H. M. and Schlitzer, M. (2001).
    Synthesis, molecular modeling, and structure-activity relationship of benzophenone-based CAAX-peptidomimetic farnesyltransferase inhibitors.
    Journal Of Medicinal Chemistry 44(18): 2886-2899.
  53. Stahl, M. and Rarey, M. (2001).
    Detailed analysis of scoring functions for virtual screening.
    Journal Of Medicinal Chemistry 44(7): 1035-1042.
  54. Gohlke, H., Hendlich, M. and Klebe, G. (2000).
    Predicting binding modes, binding affinities and 'hot spots' for protein-ligand complexes using a knowledge-based scoring function.
    Perspectives In Drug Discovery And Design 20(1): 115-144.
  55. Rarey, M. and Lengauer, T. (2000).
    A recursive algorithm for efficient combinatorial library docking.
    Perspectives In Drug Discovery And Design 20(1): 63-81.
  56. Stahl, M. (2000).
    Modifications of the scoring function in FlexX for virtual screening applications.
    Perspectives In Drug Discovery And Design 20(1): 83-98.
Last modified Wednesday, 02. Dec 2009 15:52 CET by WebMaster