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Vieth, Michal
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Vieth, Michal

Graduate Student
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Positions

  • 1998 - Senior Research Advisor, Eli Lilly & Company

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  • Doctoral Dissertation
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Publications

recent publications
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  • Publications without PubMed PMIDs

  • academic article

    • Wang, J., Varin, T., Vieth, M., Elkins, J. M. Crystal structure of human RIOK2 bound to a specific inhibitor Open Biology  2019 9  DOI:10.1098/rsob.190037  PMID:30991936  PMCID:PMC6501643
    • Meng, Y. L., Gao, C., Clawson, D. K., Atwell, S., Russell, M., Vieth, M., Roux, B. Predicting the conformational variability of Abl tyrosine kinase using molecular dynamics simulations and Markov state models Journal of Chemical Theory and Computation  2018 14:2721-2732  DOI:10.1021/acs.jctc.7b01170  PMID:29474075
    • Bagchi, A., Haidar, J. N., Eastman, S. W., Vieth, M., Topper, M., Iacolina, M. D., Walker, J. M., Forest, A., Shen, Y., Novosiadly, R. D., Ferguson, K. M. Molecular basis for necitumumab inhibition of EGFR variants associated with acquired cetuximab resistance Molecular Cancer Therapeutics  2018 17:521-531  DOI:10.1158/1535-7163.mct-17-0575  PMID:29158469  PMCID:PMC5925748
    • Gao, C., Desaphy, J., Vieth, M. Are induced fit protein conformational changes caused by ligand-binding predictable? A molecular dynamics investigation Journal of Computational Chemistry  2017 38:1229-1237  DOI:10.1002/jcc.24714  PMID:28419481
    • Chen, Q., Vieth, M., Timm, D. E., Humblet, C., Schneidman-Duhovny, D., Chemmama, I. E., Sali, A., Zeng, W., Lu, J., Liu, L. Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages PLoS One  2017 12  DOI:10.1371/journal.pone.0175758  PMID:28406969  PMCID:PMC5391116
    • Early, J. V., Casey, A., Martinez-Grau, M. A., Valcarcel, I. C. G., Vieth, M., Ollinger, J., Bailey, M. A., Alling, T., Files, M., Ovechkina, Y., Parish, T. Oxadiazoles have butyrate-specific conditional activity against mycobacterium tuberculosis Antimicrobial Agents and Chemotherapy  2016 60:3608-3616  DOI:10.1128/aac.02896-15  PMID:27044545  PMCID:PMC4879361
    • Varin, T., Godfrey, A. G., Masquelin, T., Nicolaou, C. A., Evans, D. A., Vieth, M. Discovery of selective RIO2 kinase small molecule ligand Biochimica Et Biophysica Acta-Proteins and Proteomics  2015 1854:1630-1636  DOI:10.1016/j.bbapap.2015.04.006  PMID:25891899
    • Martin, E., Knapp, S., Engh, R. A., Moebitz, H., Varin, T., Roux, B., Meiler, J., Berdini, V., Baumann, A., Vieth, M. Perspective on computational and structural aspects of kinase discovery from IPK2014 Biochimica Et Biophysica Acta-Proteins and Proteomics  2015 1854:1595-1604  DOI:10.1016/j.bbapap.2015.03.014  PMID:25861861  PMCID:PMC5105597
    • Kumar, A., Casey, A., Odingo, J., Kesicki, E. A., Abrahams, G., Vieth, M., Masquelin, T., Mizrahi, V., Hipskind, P. A., Sherman, D. R., Parish, T. A high-throughput screen against pantothenate synthetase (PanC) identifies 3-biphenyl-4-cyanopyrrole-2-carboxylic acids as a new class of inhibitor with activity against Mycobacterium tuberculosis PLoS One  2013 8  DOI:10.1371/journal.pone.0072786  PMID:24244263  PMCID:PMC3820577
    • Gao, C., Cahya, S., Nicolaou, C. A., Wang, J., Watson, I. A., Cummins, D. J., Iversen, P. W., Vieth, M. Selectivity data: assessment, predictions, concordance, and implications Journal of Medicinal Chemistry  2013 56:6991-7002  DOI:10.1021/jm400798j  PMID:23937569
    • Sutherland, J. J., Gao, C., Cahya, S., Vieth, M. What general conclusions can we draw from kinase profiling data sets? Biochimica et Biophysica Acta-Proteins and Proteomics  2013 1834:1425-1433  DOI:10.1016/j.bbapap.2012.12.023  PMID:23333421
    • Erickson, J. A., Mader, M. M., Watson, I. A., Webster, Y. W., Higgs, R. E., Bell, M. A., Vieth, M. Structure-guided expansion of kinase fragment libraries driven by support vector machine models Biochimica Et Biophysica Acta-Proteins and Proteomics  2010 1804:642-652  DOI:10.1016/j.bbapap.2009.12.002  PMID:20005305
    • Vieth, M., Erickson, J., Wang, J. B., Webster, Y., Mader, M., Higgs, R., Watson, I. Kinase inhibitor data modeling and de novo inhibitor design with fragment approaches Journal of Medicinal Chemistry  2009 52:6456-6466  DOI:10.1021/jm901147e  PMID:19791746
    • Sutherland, J. J., Higgs, R. E., Watson, I., Vieth, M. Chemical fragments as foundations for understanding target space and activity prediction Journal of Medicinal Chemistry  2008 51:2689-2700  DOI:10.1021/jm701399f  PMID:18386916
    • Sutherland, J. J., Nandigam, R. K., Erickson, J. A., Vieth, M. Lessons in molecular recognition. 2. Assessing and improving cross-docking accuracy Journal of Chemical Information and Modeling  2007 47:2293-2302  DOI:10.1021/ci700253h  PMID:17956084
    • Siegel, M. G., Vieth, M. Drugs in other drugs: a new look at drugs as fragments Drug Discovery Today  2007 12:71-79  DOI:10.1016/j.drudis.2006.11.011  PMID:17198975
    • Chen, Q., Higgs, R. E., Vieth, M. Geometric accuracy of three-dimensional molecular overlays Journal of Chemical Information and Modeling  2006 46:1996-2002  DOI:10.1021/ci060134h  PMID:16995730
    • Vieth, M., Sutherland, J. J. Dependence of molecular properties on proteomic family for marketed oral drugs Journal of Medicinal Chemistry  2006 49:3451-3453  DOI:10.1021/jm0603825  PMID:16759087
    • Zhong, B., Al-Awar, R. S., Shih, C., Grimes, J. H., Vieth, M., Hamdouchi, C. Novel route to the synthesis of 4-quinolyl isothiocyanates Tetrahedron Letters  2006 47:2161-2164  DOI:10.1016/j.tetlet.2006.01.119
    • Vieth, M., Sutherland, J. J., Robertson, D. H., Campbell, R. M. Kinomics: Characterizing the therapeutically validated kinase space Drug Discovery Today  2005 10:839-846  DOI:10.1016/s1359-6446(05)03477-x  PMID:15970266
    • de Dios, A., Shih, C., de Uralde, B. L., Sanchez, C., Del Prado, M., Cabrejas, L. M. M., Pleite, S., Blanco-Urgoiti, J., Lorite, M. J., Nevill, C. R., Bonjouklian, R., York, J., et al. Design of potent and selective 2-aminobenzimidazole-based p38 alpha MAP kinase inhibitors with excellent in vivo efficacy Journal of Medicinal Chemistry  2005 48:2270-2273  DOI:10.1021/jm048978k  PMID:15801819
    • Jaramillo, C., de Diego, J. E., Hamdouchi, C., Collins, E., Keyser, H., Sanchez-Martinez, C., del Prado, M., Norman, B., Brooks, H. B., Watkins, S. A., Spencer, C. D., Dempsey, J. A., et al. Aminoimidazo[1,2-a]pyridines as a new structural class of cyclin-dependent kinase inhibitors. Part 1: Design, synthesis, and biological evaluation Bioorganic & Medicinal Chemistry Letters  2004 14:6095-6099  DOI:10.1016/j.bmcl.2004.09.053  PMID:15546737
    • Lajiness, M. S., Vieth, M., Erickson, J. Molecular properties that influence oral drug-like behavior Current Opinion in Drug Discovery & Development  2004 7:470-477  PMID:15338956
    • Wu, G. S., Vieth, M. SDOCKER: A method utilizing existing X-ray structures to improve docking accuracy Journal of Medicinal Chemistry  2004 47:3142-3148  DOI:10.1021/jm040015y  PMID:15163194
    • Vieth, M., Higgs, R. E., Robertson, D. H., Shapiro, M., Gragg, E. A., Hemmerle, H. Kinomics-structural biology and chemogenomics of kinase inhibitors and targets Biochimica Et Biophysica Acta-Proteins and Proteomics  2004 1697:243-257  DOI:10.1016/j.bbapap.2003.11.028  PMID:15023365
    • Vieth, M., Siegel, M. G., Higgs, R. E., Watson, I. A., Robertson, D. H., Savin, K. A., Durst, G. L., Hipskind, P. A. Characteristic physical properties and structural fragments of marketed oral drugs Journal of Medicinal Chemistry  2004 47:224-232  DOI:10.1021/jm030267j  PMID:14695836
    • Erickson, J. A., Jalaie, M., Robertson, D. H., Lewis, R. A., Vieth, M. Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy Journal of Medicinal Chemistry  2004 47:45-55  DOI:10.1021/jm030209y  PMID:14695819
    • Hamdouchi, C., Keyser, H., Collins, E., Jaramillo, C., De Diego, J. E., Spencer, C. D., Dempsey, J. A., Anderson, B. D., Leggett, T., Stamm, N. B., Schultz, R. M., Watkins, S. A., et al. The discovery of a new structural class of cyclin-dependent kinase inhibitors, aminoimidazo[1,2-a]pyridines Molecular Cancer Therapeutics  2004 3:1-9  PMID:14749470
    • Wu, G., Robertson, D. H., Brooks III, C. L., Vieth, M. Detailed analysis of grid-based molecular docking: a case study of CDOCKER - A CHARMm-based MD docking algorithm Journal of Computational Chemistry  2003 24:1549-1562  DOI:10.1002/jcc.10306  PMID:12925999
    • Sawyer, J. S., Anderson, B. D., Beight, D. W., Campbell, R. M., Jones, M. L., Herron, D. K., Lampe, J. W., McCowan, J. R., McMillen, W. T., Mort, N., Parsons, S., Smith, E. C. R., et al. Synthesis and activity of new aryl- and heteroaryl- substituted pyrazole inhibitors of the transforming growth factor-βtype I receptor kinase domain Journal of Medicinal Chemistry  2003 46:3953-3956  DOI:10.1021/jm0205705  PMID:12954047
    • Vieth, M., Cummins, D. J. DoMCoSAR: A novel approach for establishing the docking mode that is consistent with the structure-activity relationship. Application to HIV-1 protease inhibitors and VEGF receptor tyrosine kinase inhibitors Journal of Medicinal Chemistry  2000 43:3020-3032  DOI:10.1021/jm990609e  PMID:10956210
    • Vieth, M., Hirst, J. D., Kolinski, A., Brooks III, C. L. Assessing energy functions for flexible docking Journal of Computational Chemistry  1998 19:1612-1622
    • Vieth, M., Hirst, J. D., Dominy, B. N., Daigler, H., Brooks III, C. L. Assessing search strategies for flexible docking Journal of Computational Chemistry  1998 19:1623-1631
    • Vieth, M., Hirst, J. D., Brooks III, C. L. Do active site conformations of small ligands correspond to low free-energy solution structures? Journal of Computer-Aided Molecular Design  1998 12:563-572  DOI:10.1023/A:1008055202136  PMID:9879504
    • Severin, K., Lee, D. H., Martinez, J. A., Vieth, M., Ghadiri, M. R. Dynamic error correction in autocatalytic peptide networks Angewandte Chemie-International Edition  1998 37:126-128  DOI:10.1002/(sici)1521-3773(19980202)37:1/2<126::aid-anie126>3.0.co;2-4
    • degree-related publication Hirst, J. D., Vieth, M., Skolnick, J., Brooks III, C. L. Predicting leucine zipper structures from sequence Protein Engineering  1996 9:657-662  PMID:8875642
    • degree-related publication Vieth, M., Kolinski, A., Skolnick, J. Method for predicting the state of association of discretized protein models. Application to leucine zippers Biochemistry  1996 35:955-967  DOI:10.1021/bi9520702
    • degree-related publication Vieth, M., Kolinski, A., Brooks III, C. L., Skolnick, J. Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper Journal of Molecular Biology  1995 251:448-467  DOI:10.1006/jmbi.1995.0447  PMID:7650742
    • degree-related publication Vieth, M., Kolinski, A., Skolnick, J. A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations Journal of Chemical Physics  1995 102:6189-6193  DOI:10.1063/1.469063
    • degree-related publication Vieth, M., Kolinski, A., Brooks III, C. L., Skolnick, J. Prediction of the folding pathways and structure of the GCN4 leucine zipper. Journal of Molecular Biology  1994 237:361-367  DOI:10.1006/jmbi.1994.1239  PMID:8151697
    • degree-related publication Vieth, M., Kolinski, A., Skolnick, J., Sikorski, A. Prediction of protein secondary structure by neural networks: encoding short and long range patterns of amino acid packing Acta Biochimica Polonica  1992 39:369-392  PMID:1293893
    • Kolinski, A.*, Vieth, M.*, Sikorski, A. Collapse of semiflexible polymers in two dimensions. Monte Carlo simulations Acta Physica Polonica A  1991 79:601-612 (* = equal contribution)
    • Vieth, M., Kolinski, A. Prediction of protein secondary structure by an enhanced neural network Acta Biochimica Polonica  1991 38:335-351  PMID:1799113
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Background

education and training

  • Ph.D. in Chemistry, Scripps Research 1991 - 1995
  • M.Sc. in Chemistry, University of Warsaw 1986 - 1991

advisee of

  • graduate advising relationship

    • Skolnick, Jeffrey, Ph.D.  candidacy, 1992 - 1995
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Contact

full name

  • Michal Vieth

geographic location

  • Scripps California 

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