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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

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  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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

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

Contact

full name

• Michal Vieth

geographic location

• Scripps California