publications

Selected Publications

Download	Reference	Publication Number
2010
	Kaufmann, K., Lemmon, G,, DeLuca, S., Sheehan, J., Meiler J. Practically Useful: What the ROSETTA Protein Modeling Suite Can Do for You Biochemistry ; 2010	63
2009
	Lindert, S., Stewart, P. L., Meiler, J. Hybrid approaches: applying computational methods in cryo-electron microscopy Curr Opin Struct Biol ; 2009	62
	Koehler, J., Mueller, R., Meiler, J. Improved prediction of trans-membrane spans in proteins using an Artificial Neural Network (best overall student paper in IEEE symposium) In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology; Wiese, K. C., Ed.: Nashville, ; 2009	61
	Durham, E., Dorr, B., Woetzel, N., Staritzbichler, R., Meiler, J. Solvent accessible surface area approximations for rapid and accurate protein structure prediction J Mol Model ; 2009	60
	Butkiewicz, M., Mueller, R., Selic, D., Dawson, E., Meiler, J. Application of Machine Learning Approaches on Quantitative Structure Activity Relationships (best student paper in IEEE symposium in CIBCB) In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology; Wiese, K. C., Ed.: Nashville ; 2009	59
2008
	Kaufmann, K. W., Dawson, E. S., Henry, L. K., Field, J. R., Blakely, R. D., Meiler, J. Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies Proteins ; 2008	58
	Kaufmann, K., Glab, K., Mueller, R., Meiler, J. Small Molecule Rotamers Enable Simultaneous Optimization of Small Molecule and Protein Degrees of Freedom in ROSETTALIGAND Docking German Conference on Bioinformatics, Beyer, A., Schroeder, M., Eds.: Dresden, pp 148-157 ; 2008	57
	Lange, O. F., Lakomek, N. A., Fares, C., Schroder, G. F., Walter, K. F., Becker, S., Meiler, J., Grubmuller, H., Griesinger, C., de Groot, B. L. Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution Science, 320, 1471-5 ; 2008	56
	Lakomek, N. A., Walter, K. F., Fares, C., Lange, O. F., de Groot, B. L., Grubmuller, H., Bruschweiler, R., Munk, A., Becker, S., Meiler, J., Griesinger, C. Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics J Biomol NMR, 41, 139-55. ; 2008	55
	Kang, C., Tian, C., Sonnichsen, F. D., Smith, J. A., Meiler, J., George, A. L., Jr., Vanoye, C. G., Kim, H. J., Sanders, C. R. Structure of KCNE1 and implications for how it modulates the KCNQ1 potassium channel Biochemistry, 47, 7999-8006 ; 2008	54
	Hanson, S. M., Dawson, E. S., Francis, D. J., Van Eps, N., Klug, C. S., Hubbell, W. L., Meiler, J., Gurevich, V. V. A model for the solution structure of the rod arrestin tetramer Structure, 16, 924-34 ; 2008	53
	Dong, E., Smith, J., Heinze, S., Alexander, N., Meiler, J. BCL::Align-Sequence alignment and fold recognition with a custom scoring function online Gene 2008 ; 2008	52
	Alexander, N., Al-Mestarihi, A., Bortolus, M., McHaourab, H., Meiler, J. De Novo High-Resolution Protein Structure Determination from Sparse Spin-Labeling EPR Data Structure, 16, 181-95 ; 2008	51
2007
	Smith, J. A., Vanoye, C. G., Jr, A. L., Meiler, J., Sanders, C. R. Structural Models for the KCNQ1 Voltage-Gated Potassium Channel Biochemistry ; 2007	50
	Reese, M., Sanchez-Pedregal, V. M., Kubicek, K., Meiler, J., Blommers, M. J., Griesinger, C., Carlomagno, T. Structural Basis of the Activity of the Microtubule-Stabilizing Agent Epothilone A Studied by NMR Spectroscopy in Solution Angew Chem Int Ed Engl, 46, 1864-1868 ; 2007	49
	McKinney, B. A., Kallewaard, N. L., Crowe, J. E., Jr., Meiler, J. Using the natural evolution of a rotavirus-specific human monoclonal antibody to predict the complex topography of a viral antigenic site Immunome Res, 3, 8 ; 2007	48
	Henry, L. K., Meiler, J., Blakely, R. D. Bound to Be Different: Neurotransmitter Transporters Meet Their Bacterial Cousins Mol. Interv., 7, 306-309 ; 2007	47
not available request reprint	Field, J. R., Kaufmann, K. W., Meiler, J., Blakely, R. D. Model-guided exploration of the serotonin transporter: Evaluation of residues engaged in substrate binding and selectivity Journal of Neurochemistry, 102, 45-45 ; 2007	46
2006
	Meiler J., Baker D. ROSETTALIGAND: Protein–Small Molecule Docking ROSETTALIGAND: Protein–Small Molecule Docking with Full Side-Chain Flexibility Proteins, 65, (3), 538-548. ; 2006	45
	Lakomek, N. A.; Carlomagno, T.; Becker, S.; Griesinger, C.; Meiler, J., A thorough dynamic interpretation of residual dipolar couplings in ubiquitin. J Biomol NMR, 34, (2), 101-15. ; 2006	44
	Zanghellini, A., Jiang, L., Wollacott, A. M., Cheng, G., Meiler, J., Althoff, E. A., Rothlisberger, D., Baker, D. New algorithms and an in silico benchmark for computational enzyme design Protein Sci 2006, 15, Protein Sci, 15, 2785-94 ; 2006	43
	Sanchez-Pedregal, V. M., Kubicek, K., Meiler, J., Lyothier, I., Paterson, I., Carlomagno, T. The tubulin-bound conformation of discodermolide derived by NMR studies in solution supports a common pharmacophore model for epothilone and discodermolide Angew Chem Int Ed Engl, 45, 7388-94 ; 2006	42
2005
	Staritzbichler R., Gu W., Helms V. Are Solvation Free Energies of Homogeneous Helical Peptides Additive? Journal of Physical Chemistry B, Vol. 109 (140), p. 19000-19007. ; 2005	41
	Lakomek N. A., Fares C., Becker S., Carlomagno T., Meiler J., Griesinger C. Side-chain orientation and hydrogen-bonding imprint supra-tauc motion on the protein backbone of ubiquitin. Angew Chem Int Ed, Engl, 44, (47), 7776-8. ; 2005	40
	Sanchez-Pedregal V. M., Reese M., Meiler J., Blommers M. J., Griesinger C., Carlomagno T. The INPHARMA Method: Protein-Mediated Interligand NOEs for Pharmacophore Mapping. Angew Chem Int Ed Engl, 44, (27), 4172-4175. ; 2005	39
	Meiler J., Baker D. The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy. J Magn Reson, 173, (2), 310-6. ; 2005	38
	Bradley, P., Malmstrom, L., Qian, B., Schonbrun, J., Chivian, D., Kim, D. E., Meiler J., Misura, K. M., Baker, D. Free modeling with Rosetta in CASP6. Proteins, 54, (2):282-8. ; 2005	37
	Grana O., Baker D., MacCallum R. M., Meiler J., Punta M., Rost B., Tress M. L., Valencia A. CASP6 assessment of contact prediction. Proteins, 61 Suppl 7, 214-24. ; 2005	36
2004
	Park Y., Elsner M.,Staritzbichler R., Helms V. Novel scoring function for modeling structures of oligomers of transmembrane alpha-helices. Proteins, 57(3):577-85. ; 2004	35
	Kuhn M., Meiler J., Baker D. Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins, 54, (2), 282-8.0 ; 2004	34
not available request reprint	Griesinger C., Peti W., Meiler J., Bruschweiler R. Projection angle restraints for studying structure and dynamics of biomolecules. Methods Mol Biol, 278, 107-21. ; 2004	33
	Meiler J., Kock M. Novel methods of automated structure elucidation based on 13C NMR spectroscopy. Magn Reson Chem, 42, (12), 1042-5. ; 2004	32
2003
	Bradley P., Chivian D., Meiler J., Misura K., Wedemeyer W., Rohl C., Schief B., Baker D. Rosetta in CASP5: Successes, failures, and prospects for complete automation. Proteins: Struct., Funct., Genet., 53, (Suppl 6), 457-468. ; 2003	31
	Meiler J., Baker D. Rapid Protein Structure Elucidation Utilizing Unassigned NMR Data. PNAS, 100, (26), 15404-15409. ; 2003	30
not available request reprint	Griesinger C., Meiler J., Peti W. In Protein NMR for the Millennium. In Biological Magnetic Resonance, Krishna, N. R., Berliner, L. J., Eds. Kluwer Academic / Plenum Press: New York, pp 163-229. ; 2003	29
	Meiler J. PROSHIFT: Protein Chemical Shift Prediction Using Artificial Neural Networks. J. Biomol. NMR, 26, 25-37. ; 2003	28
	Carlomagno T., Blommers M. J., Meiler J., Jahnke W., Schupp T., Petersen F., Schinzer D., Altmann K. H., Griesinger C. The high-resolution solution structure of epothilone A bound to tubulin: an understanding of the structure-activity relationships for a powerful class of antitumor agents. Angew Chem Int Ed Engl, 42, (22), 2511-5. ; 2003	27
	Bleckmann A., Meiler J. Epothilones: Quantitative Structure Activity Relations Studied by Support Vector Machines and Artificial Neural Networks. QSAR Comb. Sci., 22, (7), 719-721. ; 2003	26
	Meiler J., Peti W., Griesinger C. Dipolar Couplings in Multiple Alignments suggest a helical Motion in Ubiquitin. J. Am. Chem. Soc., 125, 8072-8073. ; 2003	25
	Meiler J., Baker D. Coupled Prediction of Protein Secondary and Tertiary Structure. PNAS, 100, (21), 12105-12110. ; 2003	24
2002
	Will M., Meiler J. Genius: A genetic algorithm for automated structure elucidation from 13 C-NMR spectra. J. Am. Chem. Soc. 124 (9): 1868-1870. ; 2002	23
	Meiler J., Sanli E., Junker, J., Meusinger R., Lindel T., Will M., Maier W., K�ck M. Validation of Structural Proposals by Substructure Analysis and 13C NMR Chemical Shift Prediction. J. Chem. Inf. Comput. Sci., 42, 241-248. ; 2002	22
	Meiler J., Maier W., Will M., Meusinger R. Using Neural Networks for 13C NMR Chemical Shift Prediction-Comparison with Traditional Methods. J. Magn. Res., 157, 242-252. ; 2002	21
	Hutter M. C., Krebs J., Meiler J., Griesinger C., Carafoli E., Helms V. A Structural Model of the Complex Formed by Phospholamban and the Calcium Pump of Sarcoplasmic Reticulum Obtained by Molecular Mechanics. ChemBioChem, 3, (12), 1200-1208. ; 2002	20
not available request reprint	Meiler J., Meringer M. Ranking MOLGEN Structure Proposals by 13C NMR Chemical Shift Prediction with ANALYZE. MATCH, 45, 85-108. ; 2002	19
	Peti W., Meiler J., Bruschweiler R., Griesinger C. Model-Free Analysis of Protein Backbone Motion from Residual Dipolar Couplings. J. Am. Chem. Soc., 124, 5822-5833. ; 2002	18
2001
	Neubauer H., Meiler J., Peti W., Griesinger C. NMR Structure Determination of Saccharose and Raffinose by Means of Homo- and Heteronuclear Dipolar Couplings. Hel. Chim. Acta, 84, 243-2858. ; 2001	17
	Meiler J., Peti W., Prompers J., Griesinger C., Bruschweiler R. Model-Free Approach to the Dynamic Interpretation of Residual Dipolar Couplings in Globular Proteins. J. Am. Chem. Soc., 123, (25), 6098-6107. ; 2001	16
	Meiler J. �K�nstliche Intelligenz� in Chemie und Biologie. Faszination Chemie, 7, 35-43. ; 2001	15
	Meiler J., Muller M., Zeidler A., Schmaschke F. Generation and Evaluation of Dimension Reduced Amino Acid Parameter Representations by Artificial Neural Networks. J. Mol. Model., 7, (9), 360-369. ; 2001	14
	Carlomagno T., Blommers M. J. J., Meiler J., Cuenoud B., Griesinger C. Determination of Aliphatic Side-Chain Conformation Using Cross-Correlated Relaxation: Application to an Extraordinairily Stable 2`-aminoethoxy-Modified Oligonucleotide Triplex. J. Am. Chem. Soc., 123, (30), 7364-7370. ; 2001	13
	Meiler J., Will M. Automated Structure Elucidation of Organic Molecules from 13C NMR Spectra using Genetic Algorithms and Neural Networks. J. Chem. Inf. Comput. Sci., 41, (6), 1535-1546. ; 2001	12
2000
	Bartels J., Ewerz C., Staritzbichler R. *Effect of the charm quark mass on the BFKL gammagamma* total cross section at LEP.** Physics Letters B. 492(1 2):56 62 ; 2000	11
	Meiler J., Blomberg N., Nilges M., Griesinger C. A new Approach for Applying Residual Dipolar Couplings as Restraints in Structure Elucidation. J. Biomol. NMR, 16, 245-252. ; 2000	10
	Meiler J., Will M., Meusinger R. Fast Determination of 13C-NMR Chemical Shifts Using Artificial Neural Networks. J. Chem. Inf. Comput. Sci., 40, 1169-1176. ; 2000	9
	Meiler J., Peti W., Griesinger C. DipoCoup: A versatile program for 3D-structure homology comparision based on residual dipolar couplings and pseudocontact shifts. J. Biomol. NMR, 17, 283-294. ; 2000	8
1999
not available request reprint	Meiler J., Meusinger R., Will M. Neural Network Prediction of 13C NMR Chemical Shifts of Substituted Benzenes. Monatshefte f�r Chemie, 130, 1089-1095. ; 1999	7
1998
	Wendt M. A., Meiler J., Weinhold F., Farrar T. C. Solvent And Concentration Dependence Of The Hydroxyl Chemical Shift Of Methanol. Molecular Physics, 93, (1), 145-151. ; 1998	6
1996
not available request reprint	Meiler J., Seidel P. Reaktionen in der Kerzenflamme. Junge Wissenschaft, 41, 10-22. ; 1996	5
not available request reprint	Meiler J., Meusinger R., Will M. Prediction of 13C-NMR Chemical Shifts of Substituted Benzenes by Means of a Neural Network. In Software - Entwicklung in der Chemie, Fels, G., Schubert, V., Eds. Gesellschaft Deutscher Chemiker: Frankfurt am Main; Vol. 11, pp 234-238. ; 1996	4
not available request reprint	Meiler J. K�nstliche Intelligenz zur Aufdeckung von Spektren-Eigenschafts-Beziehungen. Junge Wissenschaft, 43, 33-41. ; 1996	3
1995
not available request reprint	Meiler J., Meusinger R. Use of Neural Networks to Determine Properties of Alkanes from their 13C-NMR Spectra. In Software � Entwicklung in der Chemie, Gasteiger, J., Ed. Gesellschaft Deutscher Chemiker: Frankfurt am Main; Vol. 10, pp 259-263. ; 1995	2
1993
not available request reprint	Meiler J. Untersuchung von Reaktionsprodukten bei einigen Reaktionen von Derivaten der Abietins�ure. Junge Wissenschaft, 32, 40-45. ; 1993	1