Jens Meiler, Ph.D.

Associate Professor

jens.meiler@vanderbilt.edu

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Faculty Appointments
Associate Professor of Chemistry Associate Professor of Pharmacology
Education
Ph.D., Chemistry, Computational Structural Biochemistry, Universität Frankfurt, FrankfurtDiploma, Universität Leipzig, LeipzigVorDiplom, Universität Leipzig, Leipzig
Office Address
5144B BIOSCI/MRBIII
Vanderbilt University 372332-8725
TN
Research Description
The Meiler laboratory is recognized for methods developed for the structure determination of proteins, in particular using sparse experimental data. The Meiler laboratory pioneers usage of EPR spectroscopic information (Alexander, N.; et al. "De Novo High-Resolution Protein Structure Determination from Sparse Spin-Labeling EPR Data" Structure 2008, 16, 181) and cryo Electron Microscopy (Lindert, S.; et al. "EM-Fold: De Novo Atomic-Detail Protein Structure Determination from Medium-Resolution Density Maps"; Structure, 2012, 20, 464). These methods enable structure-based drug design for proteins that cannot be analyzed using the traditional structure determination techniques NMR Spectroscopy and X-ray crystallography. Such methods are in particular crucial for determining the structure of membrane proteins which are targets for half of our therapeutics: Weiner, B. E.; et al. "BCL::MP-fold: folding membrane proteins through assembly of transmembrane helices" Structure, 2013, 27, 7. One particular focus in our work is structure, dynamics, and interactions of G-Protein Coupled Receptors (Wu, H.; et al. "Structure of a class C GPCR metabotropic glutamate receptor 1 bound to an allosteric modulator"; Science; 2014; 58 or Alexander, N.; et al. "Energetic analysis of the rhodopsin-G-protein complex links the alpha5 helix to GDP release"; Nat Struct Mol Biol; 2014; 56).

Jens Meiler is a co-creator of the ROSETTA program. The Meiler laboratory leads the further development of ROSETTALIGAND (Meiler, J.; Baker, D. "ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility"; Proteins 2006; 65; 538-548). Through ROSETTACOMMONS the Meiler laboratory disseminates additions to the Rosetta program developed and has immediate access to novel ROSETTA technologies. Specifically we seek to de novo design proteins to bind small molecule ligands with high selectivity. Further the Meiler laboratory develops a structure-based drug design module for ROSETTA and docking protocols particularly suited for docking small molecules into comparative models. The PI of the proposal has also experience in cheminformatics method development for chemical biology and therapeutic development (Mueller, R., et al.; "Discovery of 2-(2-Benzoxazoyl amino)-4-Aryl-5-Cyanopyrimidine as Negative Allosteric Modulators (NAMs) of Metabotropic Glutamate Receptor 5 (mGlu5): From an Artificial Neural Network Virtual Screen to an In Vivo Tool Compound"; ChemMedChem; 2012; 7; 406). The Meiler laboratory develops pharmacophore mapping and virtual screening algorithms and applies those often in conjunction with ROSETTALIGAND to therapeutic development.

The Meiler laboratory develops technologies to engineer protein, for example through assembly of large protein scaffolds from fragments (Fortenberry, C.; et al.; "Exploring symmetry as an avenue to the computational design of large protein domains"; JACS 2011; 133; 18026 & Eisenbeis, S.; et al.; "Potential of Fragment Recombination for Rational Design of Proteins"; JACS 2012; 134; 4019). We currently build on these results developing methods for the computational design of protein-ligand interfaces as a therapeutic strategy. Further, we have a keen interest in developing innovative methods for antibody modeling and design (Willis, J.; et al.; "Human germline antibody gene segments encode polyspecific antibodies"; PLoS Comput Biol; 2013; 9; 100304). We apply these technologies to engineer broadly neutralizing antibodies (Willis, J.; et al.; "Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth"; J Clin Invest; 2015; 125; 2523) and mine novel antibodies from next generation sequencing data (Willis, J.; et al.; "Long Antibody HCDR3s from HIV-Naïve Donors Mediate HIV Neutralization"; pending).

Current application projects include drug and probe development for neurological diseases including Schizophrenia, Alzheimer's, and Parkinson’s, fundamentals of G-protein-coupled receptor signaling, cardiac arrhythmia as caused by the complex interplay of potassium channel regulation and drug interactions, multidrug resistance in cancer and bacterial cells related to multidrug transporter proteins, and f) structural basis of viral infections and antibody activity among others.
Research Keywords
computation, chemistry, biology, membrane, protein, C++, programming, GPCR, vaccine, antibody, drug discovery, therapeutic, folding, design
Publications
Li B, Mendenhall J, Nguyen ED, Weiner BE, Fischer AW, Meiler J. Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins. J Chem Inf Model [print-electronic]. 2016 Feb 2/5/2016; PMID: 26804342, DOI: 10.1021/acs.jcim.5b00517, ISSN: 1549-960X.

Dastvan R, Fischer AW, Mishra S, Meiler J, Mchaourab HS. Protonation-dependent conformational dynamics of the multidrug transporter EmrE. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2016 Feb 2/2/2016; 113(5): 1220-5. PMID: 26787875, PII: 1520431113, DOI: 10.1073/pnas.1520431113, ISSN: 1091-6490.

Mendenhall J, Meiler J. Improving quantitative structure-activity relationship models using Artificial Neural Networks trained with dropout. J. Comput. Aided Mol. Des [print-electronic]. 2016 Feb 2/1/2016; PMID: 26830599, PII: 10.1007/s10822-016-9895-2, DOI: 10.1007/s10822-016-9895-2, ISSN: 1573-4951.

Krug U, Alexander NS, Stein RA, Keim A, Mchaourab HS, Sträter N, Meiler J. Characterization of the Domain Orientations of E. coli 5'-Nucleotidase by Fitting an Ensemble of Conformers to DEER Distance Distributions. Structure [print-electronic]. 2016 Jan 1/5/2016; 24(1): 43-56. PMID: 26724996, PMCID: PMC4706771, PII: S0969-2126(15)00496-7, DOI: 10.1016/j.str.2015.11.007, ISSN: 1878-4186.

Vandavasi VG, Putnam DK, Zhang Q, Petridis L, Heller WT, Nixon BT, Haigler CH, Kalluri U, Coates L, Langan P, Smith JC, Meiler J, O'Neill H. A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers. Plant Physiol [print-electronic]. 2016 Jan; 170(1): 123-35. PMID: 26556795, PMCID: PMC4704586, PII: pp.15.01356, DOI: 10.1104/pp.15.01356, ISSN: 1532-2548.

Vandavasi VG, Putnam DK, Zhang Q, Petridis L, Heller WT, Nixon BT, Haigler CH, Kalluri U, Coates L, Langan P, Smith JC, Meiler J, O'Neill H. A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers. Plant Physiol [print-electronic]. 2016 Jan; 170(1): 123-35. PMID: 26556795, PMCID: PMC4704586, PII: pp.15.01356, DOI: 10.1104/pp.15.01356, ISSN: 1532-2548.

Sliwoski G, Mendenhall J, Meiler J. Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign. J. Comput. Aided Mol. Des [print-electronic]. 2015 Dec 12/31/2015; PMID: 26721261, PII: 10.1007/s10822-015-9893-9, DOI: 10.1007/s10822-015-9893-9, ISSN: 1573-4951.

Sliwoski G, Mendenhall J, Meiler J. Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign. J. Comput. Aided Mol. Des [print-electronic]. 2015 Dec 12/31/2015; PMID: 26721261, PII: 10.1007/s10822-015-9893-9, DOI: 10.1007/s10822-015-9893-9, ISSN: 1573-4951.

Gallant JN, Sheehan JH, Shaver TM, Bailey M, Lipson D, Chandramohan R, Red Brewer M, York SJ, Kris MG, Pietenpol JA, Ladanyi M, Miller VA, Ali SM, Meiler J, Lovly CM. EGFR Kinase Domain Duplication (EGFR-KDD) Is a Novel Oncogenic Driver in Lung Cancer That Is Clinically Responsive to Afatinib. Cancer Discov [print-electronic]. 2015 Nov; 5(11): 1155-63. PMID: 26286086, PMCID: PMC4631701, PII: 2159-8290.CD-15-0654, DOI: 10.1158/2159-8290.CD-15-0654, ISSN: 2159-8290.

Hofmann T, Fischer AW, Meiler J, Kalkhof S. Protein structure prediction guided by crosslinking restraints - A systematic evaluation of the impact of the crosslinking spacer length. Methods [print-electronic]. 2015 Nov 11/1/2015; 89: 79-90. PMID: 25986934, PII: S1046-2023(15)00207-8, DOI: 10.1016/j.ymeth.2015.05.014, ISSN: 1095-9130.

Fischer AW, Alexander NS, Woetzel N, Karakas M, Weiner BE, Meiler J. BCL::MP-fold: Membrane protein structure prediction guided by EPR restraints. Proteins [print-electronic]. 2015 Nov; 83(11): 1947-62. PMID: 25820805, DOI: 10.1002/prot.24801, ISSN: 1097-0134.

Gallant JN, Sheehan JH, Shaver TM, Bailey M, Lipson D, Chandramohan R, Red Brewer M, York SJ, Kris MG, Pietenpol JA, Ladanyi M, Miller VA, Ali SM, Meiler J, Lovly CM. EGFR Kinase Domain Duplication (EGFR-KDD) Is a Novel Oncogenic Driver in Lung Cancer That Is Clinically Responsive to Afatinib. Cancer Discov [print-electronic]. 2015 Nov; 5(11): 1155-63. PMID: 26286086, PMCID: PMC4631701, PII: 2159-8290.CD-15-0654, DOI: 10.1158/2159-8290.CD-15-0654, ISSN: 2159-8290.

Hofmann T, Fischer AW, Meiler J, Kalkhof S. Protein structure prediction guided by crosslinking restraints--A systematic evaluation of the impact of the crosslinking spacer length. Methods [print-electronic]. 2015 Nov 11/1/2015; 89: 79-90. PMID: 25986934, PII: S1046-2023(15)00207-8, DOI: 10.1016/j.ymeth.2015.05.014, ISSN: 1095-9130.

Fischer AW, Alexander NS, Woetzel N, Karakas M, Weiner BE, Meiler J. BCL::MP-fold: Membrane protein structure prediction guided by EPR restraints. Proteins [print-electronic]. 2015 Nov; 83(11): 1947-62. PMID: 25820805, DOI: 10.1002/prot.24801, ISSN: 1097-0134.

Martin E, Knapp S, Engh RA, 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. Biochim. Biophys. Acta [print-electronic]. 2015 Oct; 1854(10 Pt B): 1595-604. PMID: 25861861, PII: S1570-9639(15)00096-5, DOI: 10.1016/j.bbapap.2015.03.014, ISSN: 0006-3002.

Martin E, Knapp S, Engh RA, 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. Biochim. Biophys. Acta [print-electronic]. 2015 Oct; 1854(10 Pt B): 1595-604. PMID: 25861861, PII: S1570-9639(15)00096-5, DOI: 10.1016/j.bbapap.2015.03.014, ISSN: 0006-3002.

Putnam DK, Weiner BE, Woetzel N, Lowe EW, Meiler J. BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles. Proteins [print-electronic]. 2015 Aug; 83(8): 1500-12. PMID: 26018949, DOI: 10.1002/prot.24838, ISSN: 1097-0134.

Putnam DK, Weiner BE, Woetzel N, Lowe EW, Meiler J. BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles. Proteins [print-electronic]. 2015 Aug; 83(8): 1500-12. PMID: 26018949, DOI: 10.1002/prot.24838, ISSN: 1097-0134.

Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure [print-electronic]. 2015 Jul 7/7/2015; 23(7): 1156-67. PMID: 26095030, PII: S0969-2126(15)00194-X, DOI: 10.1016/j.str.2015.05.013, ISSN: 1878-4186.

Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure [print-electronic]. 2015 Jul 7/7/2015; 23(7): 1156-67. PMID: 26095030, PII: S0969-2126(15)00194-X, DOI: 10.1016/j.str.2015.05.013, ISSN: 1878-4186.

Sevy AM, Jacobs TM, Crowe JE, Meiler J. Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences. PLoS Comput. Biol. 2015 Jul; 11(7): e1004300. PMID: 26147100, PMCID: PMC4493036, PII: PCOMPBIOL-D-15-00033, DOI: 10.1371/journal.pcbi.1004300, ISSN: 1553-7358.

Sevy AM, Jacobs TM, Crowe JE, Meiler J. Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences. PLoS Comput. Biol. 2015 Jul; 11(7): e1004300. PMID: 26147100, PMCID: PMC4493036, PII: PCOMPBIOL-D-15-00033, DOI: 10.1371/journal.pcbi.1004300, ISSN: 1553-7358.

Kaiser A, Müller P, Zellmann T, Scheidt HA, Thomas L, Bosse M, Meier R, Meiler J, Huster D, Beck-Sickinger AG, Schmidt P. Unwinding of the C-Terminal Residues of Neuropeptide Y is critical for Y2 Receptor Binding and Activation. Angew. Chem. Int. Ed. Engl [print-electronic]. 2015 Jun 6/15/2015; 54(25): 7446-9. PMID: 25924821, DOI: 10.1002/anie.201411688, ISSN: 1521-3773.

Kaiser A, Müller P, Zellmann T, Scheidt HA, Thomas L, Bosse M, Meier R, Meiler J, Huster D, Beck-Sickinger AG, Schmidt P. Unwinding of the C-Terminal Residues of Neuropeptide Y is critical for Y2 Receptor Binding and Activation. Angew. Chem. Int. Ed. Engl [print-electronic]. 2015 Jun 6/15/2015; 54(25): 7446-9. PMID: 25924821, DOI: 10.1002/anie.201411688, ISSN: 1521-3773.

Kroncke BM, Vanoye CG, Meiler J, George AL, Sanders CR. Personalized biochemistry and biophysics. Biochemistry [print-electronic]. 2015 Apr 4/28/2015; 54(16): 2551-9. PMID: 25856502, PMCID: PMC4415889, DOI: 10.1021/acs.biochem.5b00189, ISSN: 1520-4995.

Kroncke BM, Vanoye CG, Meiler J, George AL, Sanders CR. Personalized biochemistry and biophysics. Biochemistry [print-electronic]. 2015 Apr 4/28/2015; 54(16): 2551-9. PMID: 25856502, PMCID: PMC4415889, DOI: 10.1021/acs.biochem.5b00189, ISSN: 1520-4995.

Swale DR, Sheehan JH, Banerjee S, Husni AS, Nguyen TT, Meiler J, Denton JS. Computational and functional analyses of a small-molecule binding site in ROMK. Biophys. J. 2015 Mar 3/10/2015; 108(5): 1094-103. PMID: 25762321, PMCID: PMC4375722, PII: S0006-3495(15)00116-2, DOI: 10.1016/j.bpj.2015.01.022, ISSN: 1542-0086.

Swale DR, Sheehan JH, Banerjee S, Husni AS, Nguyen TT, Meiler J, Denton JS. Computational and functional analyses of a small-molecule binding site in ROMK. Biophys. J. 2015 Mar 3/10/2015; 108(5): 1094-103. PMID: 25762321, PMCID: PMC4375722, PII: S0006-3495(15)00116-2, DOI: 10.1016/j.bpj.2015.01.022, ISSN: 1542-0086.

Heinze S, Putnam DK, Fischer AW, Kohlmann T, Weiner BE, Meiler J. CASP10-BCL::Fold efficiently samples topologies of large proteins. Proteins. 2015 Mar; 83(3): 547-63. PMID: 25581562, DOI: 10.1002/prot.24733, ISSN: 1097-0134.

Heinze S, Putnam DK, Fischer AW, Kohlmann T, Weiner BE, Meiler J. CASP10-BCL::Fold efficiently samples topologies of large proteins. Proteins. 2015 Mar; 83(3): 547-63. PMID: 25581562, DOI: 10.1002/prot.24733, ISSN: 1097-0134.

Donahue JP, Levinson RT, Sheehan JH, Sutton L, Taylor HE, Meiler J, D'Aquila RT, Song C. Genetic analysis of the localization of APOBEC3F to human immunodeficiency virus type 1 virion cores. J. Virol [print-electronic]. 2015 Feb; 89(4): 2415-24. PMID: 25505075, PMCID: PMC4338907, PII: JVI.01981-14, DOI: 10.1128/JVI.01981-14, ISSN: 1098-5514.

Kothiwale S, Borza CM, Lowe EW, Pozzi A, Meiler J. Discoidin domain receptor 1 (DDR1) kinase as target for structure-based drug discovery. Drug Discov. Today [print-electronic]. 2015 Feb; 20(2): 255-61. PMID: 25284748, PMCID: PMC4336622, PII: S1359-6446(14)00391-2, DOI: 10.1016/j.drudis.2014.09.025, ISSN: 1878-5832.

Donahue JP, Levinson RT, Sheehan JH, Sutton L, Taylor HE, Meiler J, D'Aquila RT, Song C. Genetic analysis of the localization of APOBEC3F to human immunodeficiency virus type 1 virion cores. J. Virol [print-electronic]. 2015 Feb; 89(4): 2415-24. PMID: 25505075, PMCID: PMC4338907, PII: JVI.01981-14, DOI: 10.1128/JVI.01981-14, ISSN: 1098-5514.

Kothiwale S, Borza CM, Lowe EW, Pozzi A, Meiler J. Discoidin domain receptor 1 (DDR1) kinase as target for structure-based drug discovery. Drug Discov. Today [print-electronic]. 2015 Feb; 20(2): 255-61. PMID: 25284748, PMCID: PMC4336622, PII: S1359-6446(14)00391-2, DOI: 10.1016/j.drudis.2014.09.025, ISSN: 1878-5832.

Kothiwale S, Mendenhall JL, Meiler J. BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library. J Cheminform. 2015; 7: 47. PMID: 26473018, PMCID: PMC4607025, PII: 95, DOI: 10.1186/s13321-015-0095-1, ISSN: 1758-2946.

DeLuca S, Khar K, Meiler J. Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand. PLoS ONE. 2015; 10(7): e0132508. PMID: 26207742, PMCID: PMC4514752, PII: PONE-D-15-06401, DOI: 10.1371/journal.pone.0132508, ISSN: 1932-6203.

Vortmeier G, DeLuca SH, Els-Heindl S, Chollet C, Scheidt HA, Beck-Sickinger AG, Meiler J, Huster D. Integrating solid-state NMR and computational modeling to investigate the structure and dynamics of membrane-associated ghrelin. PLoS ONE. 2015; 10(3): e0122444. PMID: 25803439, PMCID: PMC4372444, PII: PONE-D-14-38674, DOI: 10.1371/journal.pone.0122444, ISSN: 1932-6203.

Kothiwale S, Mendenhall JL, Meiler J. BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library. J Cheminform. 2015; 7: 47. PMID: 26473018, PMCID: PMC4607025, PII: 95, DOI: 10.1186/s13321-015-0095-1, ISSN: 1758-2946.

DeLuca S, Khar K, Meiler J. Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand. PLoS ONE. 2015; 10(7): e0132508. PMID: 26207742, PMCID: PMC4514752, PII: PONE-D-15-06401, DOI: 10.1371/journal.pone.0132508, ISSN: 1932-6203.

Vortmeier G, DeLuca SH, Els-Heindl S, Chollet C, Scheidt HA, Beck-Sickinger AG, Meiler J, Huster D. Integrating solid-state NMR and computational modeling to investigate the structure and dynamics of membrane-associated ghrelin. PLoS ONE. 2015; 10(3): e0122444. PMID: 25803439, PMCID: PMC4372444, PII: PONE-D-14-38674, DOI: 10.1371/journal.pone.0122444, ISSN: 1932-6203.

Margetic A, Nannemann D, Meiler J, Huster D, Theisgen S. Guanylate Cyclase-Activating Protein-2 Undergoes Structural Changes upon Binding to Detergent Micelles and Bicelles. Biochim. Biophys. Acta [print-electronic]. 2014 Nov; 1838(11): 2767-77. PMID: 25051529, PII: S0005-2736(14)00256-9, DOI: 10.1016/j.bbamem.2014.07.012, ISSN: 0006-3002.

Margetic A, Nannemann D, Meiler J, Huster D, Theisgen S. Guanylate Cyclase-Activating Protein-2 Undergoes Structural Changes upon Binding to Detergent Micelles and Bicelles. Biochim. Biophys. Acta [print-electronic]. 2014 Nov; 1838(11): 2767-77. PMID: 25051529, PII: S0005-2736(14)00256-9, DOI: 10.1016/j.bbamem.2014.07.012, ISSN: 0006-3002.

Mittendorf KF, Kroncke BM, Meiler J, Sanders CR. The homology model of PMP22 suggests mutations resulting in peripheral neuropathy disrupt transmembrane helix packing. Biochemistry [print-electronic]. 2014 Oct 10/7/2014; 53(39): 6139-41. PMID: 25243937, PMCID: PMC4188248, DOI: 10.1021/bi500809t, ISSN: 1520-4995.

Mittendorf KF, Kroncke BM, Meiler J, Sanders CR. The homology model of PMP22 suggests mutations resulting in peripheral neuropathy disrupt transmembrane helix packing. Biochemistry [print-electronic]. 2014 Oct 10/7/2014; 53(39): 6139-41. PMID: 25243937, PMCID: PMC4188248, DOI: 10.1021/bi500809t, ISSN: 1520-4995.

Jaeschke H, Schaarschmidt J, Eszlinger M, Huth S, Puttinger R, Rittinger O, Meiler J, Paschke R. A newly discovered TSHR variant (L665F) associated with nonautoimmune hyperthyroidism in an Austrian family induces constitutive TSHR activation by steric repulsion between TM1 and TM7. J. Clin. Endocrinol. Metab [print-electronic]. 2014 Oct; 99(10): E2051-9. PMID: 24947036, DOI: 10.1210/jc.2014-1436, ISSN: 1945-7197.

Jaeschke H, Schaarschmidt J, Eszlinger M, Huth S, Puttinger R, Rittinger O, Meiler J, Paschke R. A newly discovered TSHR variant (L665F) associated with nonautoimmune hyperthyroidism in an Austrian family induces constitutive TSHR activation by steric repulsion between TM1 and TM7. J. Clin. Endocrinol. Metab [print-electronic]. 2014 Oct; 99(10): E2051-9. PMID: 24947036, DOI: 10.1210/jc.2014-1436, ISSN: 1945-7197.

Conn PJ, Lindsley CW, Meiler J, Niswender CM. Opportunities and challenges in the discovery of allosteric modulators of GPCRs for treating CNS disorders. Nat Rev Drug Discov. 2014 Sep; 13(9): 692-708. PMID: 25176435, PMCID: PMC4208620, PII: nrd4308, DOI: 10.1038/nrd4308, ISSN: 1474-1784.

Conn PJ, Lindsley CW, Meiler J, Niswender CM. Opportunities and challenges in the discovery of allosteric modulators of GPCRs for treating CNS disorders. Nat Rev Drug Discov. 2014 Sep; 13(9): 692-708. PMID: 25176435, PMCID: PMC4208620, PII: nrd4308, DOI: 10.1038/nrd4308, ISSN: 1474-1784.

Kaya AI, Lokits AD, Gilbert JA, Iverson TM, Meiler J, Hamm HE. A conserved phenylalanine as a relay between the a5 helix and the GDP binding region of heterotrimeric Gi protein a subunit. J. Biol. Chem [print-electronic]. 2014 Aug 8/29/2014; 289(35): 24475-87. PMID: 25037222, PMCID: PMC4148873, PII: M114.572875, DOI: 10.1074/jbc.M114.572875, ISSN: 1083-351X.

Kaya AI, Lokits AD, Gilbert JA, Iverson TM, Meiler J, Hamm HE. A conserved phenylalanine as a relay between the a5 helix and the GDP binding region of heterotrimeric Gi protein a subunit. J. Biol. Chem [print-electronic]. 2014 Aug 8/29/2014; 289(35): 24475-87. PMID: 25037222, PMCID: PMC4148873, PII: M114.572875, DOI: 10.1074/jbc.M114.572875, ISSN: 1083-351X.

Doberenz C, Zorn M, Falke D, Nannemann D, Hunger D, Beyer L, Ihling CH, Meiler J, Sinz A, Sawers RG. Pyruvate formate-lyase interacts directly with the formate channel FocA to regulate formate translocation. J. Mol. Biol [print-electronic]. 2014 Jul 7/29/2014; 426(15): 2827-39. PMID: 24887098, PII: S0022-2836(14)00273-3, DOI: 10.1016/j.jmb.2014.05.023, ISSN: 1089-8638.

Doberenz C, Zorn M, Falke D, Nannemann D, Hunger D, Beyer L, Ihling CH, Meiler J, Sinz A, Sawers RG. Pyruvate formate-lyase interacts directly with the formate channel FocA to regulate formate translocation. J. Mol. Biol [print-electronic]. 2014 Jul 7/29/2014; 426(15): 2827-39. PMID: 24887098, PII: S0022-2836(14)00273-3, DOI: 10.1016/j.jmb.2014.05.023, ISSN: 1089-8638.

Austin TM, Nannemann DP, Deluca SL, Meiler J, Delpire E. In silico analysis and experimental verification of OSR1 kinase - Peptide interaction. J. Struct. Biol [print-electronic]. 2014 Jul; 187(1): 58-65. PMID: 24821279, PMCID: PMC4082687, PII: S1047-8477(14)00107-5, DOI: 10.1016/j.jsb.2014.05.001, ISSN: 1095-8657.

Austin TM, Nannemann DP, Deluca SL, Meiler J, Delpire E. In silico analysis and experimental verification of OSR1 kinase - Peptide interaction. J. Struct. Biol [print-electronic]. 2014 Jul; 187(1): 58-65. PMID: 24821279, PMCID: PMC4082687, PII: S1047-8477(14)00107-5, DOI: 10.1016/j.jsb.2014.05.001, ISSN: 1095-8657.

Gregory KJ, Nguyen ED, Malosh C, Mendenhall JL, Zic JZ, Bates BS, Noetzel MJ, Squire EF, Turner EM, Rook JM, Emmitte KA, Stauffer SR, Lindsley CW, Meiler J, Conn PJ. Identification of specific ligand-receptor interactions that govern binding and cooperativity of diverse modulators to a common metabotropic glutamate receptor 5 allosteric site. ACS Chem Neurosci [print-electronic]. 2014 Apr 4/16/2014; 5(4): 282-95. PMID: 24528109, PMCID: PMC3990945, DOI: 10.1021/cn400225x, ISSN: 1948-7193.

Weiner BE, Alexander N, Akin LR, Woetzel N, Karakas M, Meiler J. BCL::Fold--protein topology determination from limited NMR restraints. Proteins [print-electronic]. 2014 Apr; 82(4): 587-95. PMID: 24123100, PMCID: PMC3949166, DOI: 10.1002/prot.24427, ISSN: 1097-0134.

Lössl P, Kölbel K, Tänzler D, Nannemann D, Ihling CH, Keller MV, Schneider M, Zaucke F, Meiler J, Sinz A. Analysis of nidogen-1/laminin ¿1 interaction by cross-linking, mass spectrometry, and computational modeling reveals multiple binding modes. PLoS ONE. 2014; 9(11): e112886. PMID: 25387007, PMCID: PMC4227867, PII: PONE-D-14-34166, DOI: 10.1371/journal.pone.0112886, ISSN: 1932-6203.

Kumar KK, Lowe EW, Aboud AA, Neely MD, Redha R, Bauer JA, Odak M, Weaver CD, Meiler J, Aschner M, Bowman AB. Cellular manganese content is developmentally regulated in human dopaminergic neurons. Sci Rep. 2014; 4: 6801. PMID: 25348053, PMCID: PMC4210885, PII: srep06801, DOI: 10.1038/srep06801, ISSN: 2045-2322.

Sliwoski G, Kothiwale S, Meiler J, Lowe EW. Computational methods in drug discovery. Pharmacol. Rev [electronic-print]. 2014; 66(1): 334-95. PMID: 24381236, PMCID: PMC3880464, PII: 66/1/334, DOI: 10.1124/pr.112.007336, ISSN: 1521-0081.

Alexander NS, Preininger AM, Kaya AI, Stein RA, Hamm HE, Meiler J. Energetic analysis of the rhodopsin-G-protein complex links the a5 helix to GDP release. Nat. Struct. Mol. Biol [print-electronic]. 2014 Jan; 21(1): 56-63. PMID: 24292645, PMCID: PMC3947367, PII: nsmb.2705, DOI: 10.1038/nsmb.2705, ISSN: 1545-9985.

Lössl P, Kölbel K, Tänzler D, Nannemann D, Ihling CH, Keller MV, Schneider M, Zaucke F, Meiler J, Sinz A. Analysis of nidogen-1/laminin ¿1 interaction by cross-linking, mass spectrometry, and computational modeling reveals multiple binding modes. PLoS ONE. 2014; 9(11): e112886. PMID: 25387007, PMCID: PMC4227867, PII: PONE-D-14-34166, DOI: 10.1371/journal.pone.0112886, ISSN: 1932-6203.

Kumar KK, Lowe EW, Aboud AA, Neely MD, Redha R, Bauer JA, Odak M, Weaver CD, Meiler J, Aschner M, Bowman AB. Cellular manganese content is developmentally regulated in human dopaminergic neurons. Sci Rep. 2014; 4: 6801. PMID: 25348053, PMCID: PMC4210885, PII: srep06801, DOI: 10.1038/srep06801, ISSN: 2045-2322.

Crivelli JJ, Lemmon G, Kaufmann KW, Meiler J. Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions. J. Comput. Aided Mol. Des [print-electronic]. 2013 Dec; 27(12): 1051-65. PMID: 24305904, PMCID: PMC3909503, DOI: 10.1007/s10822-013-9696-9, ISSN: 1573-4951.

Turlington M, Noetzel MJ, Chun A, Zhou Y, Gogliotti RD, Nguyen ED, Gregory KJ, Vinson PN, Rook JM, Gogi KK, Xiang Z, Bridges TM, Daniels JS, Jones C, Niswender CM, Meiler J, Conn PJ, Lindsley CW, Stauffer SR. Exploration of allosteric agonism structure-activity relationships within an acetylene series of metabotropic glutamate receptor 5 (mGlu5) positive allosteric modulators (PAMs): discovery of 5-((3-fluorophenyl)ethynyl)-N-(3-methyloxetan-3-yl)picolinamide (ML254). J. Med. Chem [print-electronic]. 2013 Oct 10/24/2013; 56(20): 7976-96. PMID: 24050755, PMCID: PMC3908770, DOI: 10.1021/jm401028t, ISSN: 1520-4804.

Preininger AM, Meiler J, Hamm HE. Conformational flexibility and structural dynamics in GPCR-mediated G protein activation: a perspective. J. Mol. Biol [print-electronic]. 2013 Jul 7/10/2013; 425(13): 2288-98. PMID: 23602809, PMCID: PMC3686903, PII: S0022-2836(13)00242-8, DOI: 10.1016/j.jmb.2013.04.011, ISSN: 1089-8638.

Weiner BE, Woetzel N, Karakas M, Alexander N, Meiler J. BCL::MP-fold: folding membrane proteins through assembly of transmembrane helices. Structure [print-electronic]. 2013 Jul 7/2/2013; 21(7): 1107-17. PMID: 23727232, PMCID: PMC3738745, PII: S0969-2126(13)00152-4, DOI: 10.1016/j.str.2013.04.022, ISSN: 1878-4186.

Leman JK, Mueller R, Karakas M, Woetzel N, Meiler J. Simultaneous prediction of protein secondary structure and transmembrane spans. Proteins [print-electronic]. 2013 Jul; 81(7): 1127-40. PMID: 23349002, DOI: 10.1002/prot.24258, ISSN: 1097-0134.

Gregory KJ, Nguyen ED, Reiff SD, Squire EF, Stauffer SR, Lindsley CW, Meiler J, Conn PJ. Probing the metabotropic glutamate receptor 5 (mGlu5) positive allosteric modulator (PAM) binding pocket: discovery of point mutations that engender a "molecular switch" in PAM pharmacology. Mol. Pharmacol [print-electronic]. 2013 May; 83(5): 991-1006. PMID: 23444015, PMCID: PMC3629835, PII: mol.112.083949, DOI: 10.1124/mol.112.083949, ISSN: 1521-0111.

Deluca SH, Rathmann D, Beck-Sickinger AG, Meiler J. The activity of prolactin releasing peptide correlates with its helicity. Biopolymers. 2013 May; 99(5): 314-25. PMID: 23426574, PMCID: PMC3580954, DOI: 10.1002/bip.22162, ISSN: 1097-0282.

Willis JR, Briney BS, DeLuca SL, Crowe JE, Meiler J. Human germline antibody gene segments encode polyspecific antibodies. PLoS Comput. Biol [print-electronic]. 2013 Apr; 9(4): e1003045. PMID: 23637590, PMCID: PMC3636087, PII: PCOMPBIOL-D-12-01934, DOI: 10.1371/journal.pcbi.1003045, ISSN: 1553-7358.

Lindert S, Stewart PL, Meiler J. Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. Comput Biol Chem [print-electronic]. 2013 Feb; 42: 1-4. PMID: 23246775, PMCID: PMC3540162, PII: S1476-9271(12)00079-5, DOI: 10.1016/j.compbiolchem.2012.11.001, ISSN: 1476-928X.

Yang T, Smith JA, Leake BF, Sanders CR, Meiler J, Roden DM. An allosteric mechanism for drug block of the human cardiac potassium channel KCNQ1. Mol. Pharmacol [print-electronic]. 2013 Feb; 83(2): 481-9. PMID: 23193163, PMCID: PMC3558809, PII: mol.112.081513, DOI: 10.1124/mol.112.081513, ISSN: 1521-0111.

Alexander NS, Stein RA, Koteiche HA, Kaufmann KW, McHaourab HS, Meiler J. RosettaEPR: rotamer library for spin label structure and dynamics. PLoS ONE. 2013; 8(9): e72851. PMID: 24039810, PMCID: PMC3764097, PII: PONE-D-13-07728, DOI: 10.1371/journal.pone.0072851, ISSN: 1932-6203.

Nguyen ED, Norn C, Frimurer TM, Meiler J. Assessment and challenges of ligand docking into comparative models of G-protein coupled receptors. PLoS ONE [electronic-print]. 2013; 8(7): e67302. PMID: 23844000, PMCID: PMC3699586, PII: PONE-D-13-08245, DOI: 10.1371/journal.pone.0067302, ISSN: 1932-6203.

Lemmon G, Meiler J. Towards ligand docking including explicit interface water molecules. PLoS ONE [electronic-print]. 2013; 8(6): e67536. PMID: 23840735, PMCID: PMC3695863, PII: PONE-D-13-08760, DOI: 10.1371/journal.pone.0067536, ISSN: 1932-6203.

Combs SA, Deluca SL, Deluca SH, Lemmon GH, Nannemann DP, Nguyen ED, Willis JR, Sheehan JH, Meiler J. Small-molecule ligand docking into comparative models with Rosetta. Nat Protoc [print-electronic]. 2013; 8(7): 1277-98. PMID: 23744289, PII: nprot.2013.074, DOI: 10.1038/nprot.2013.074, ISSN: 1750-2799.

Aiyegbo MS, Sapparapu G, Spiller BW, Eli IM, Williams DR, Kim R, Lee DE, Liu T, Li S, Woods VL, Nannemann DP, Meiler J, Stewart PL, Crowe JE. Human rotavirus VP6-specific antibodies mediate intracellular neutralization by binding to a quaternary structure in the transcriptional pore. PLoS ONE [electronic-print]. 2013; 8(5): e61101. PMID: 23671563, PMCID: PMC3650007, PII: PONE-D-13-06430, DOI: 10.1371/journal.pone.0061101, ISSN: 1932-6203.

Butkiewicz M, Lowe EW, Mueller R, Mendenhall JL, Teixeira PL, Weaver CD, Meiler J. Benchmarking ligand-based virtual High-Throughput Screening with the PubChem database. Molecules. 2013; 18(1): 735-56. PMID: 23299552, PMCID: PMC3759399, PII: molecules18010735, DOI: 10.3390/molecules18010735, ISSN: 1420-3049.

Putnam DK, Lowe EW, Meiler J. Reconstruction of SAXS Profiles from Protein Structures. Comput Struct Biotechnol J. 2013; 8: e201308006. PMID: 24688746, PMCID: PMC3962079, PII: CSBJ-8-e201308006, DOI: 10.5936/csbj.201308006, ISSN: 2001-0370.

Duran AM, Meiler J. Inverted topologies in membrane proteins: a mini-review. Comput Struct Biotechnol J. 2013; 8: e201308004. PMID: 24688744, PMCID: PMC3962082, PII: CSBJ-8-e201308004, DOI: 10.5936/csbj.201308004, ISSN: 2001-0370.

Mueller R, Dawson ES, Niswender CM, Butkiewicz M, Hopkins CR, Weaver CD, Lindsley CW, Conn PJ, Meiler J. Iterative experimental and virtual high-throughput screening identifies metabotropic glutamate receptor subtype 4 positive allosteric modulators. J Mol Model [print-electronic]. 2012 Sep; 18(9): 4437-46. PMID: 22592386, PMCID: PMC3766737, DOI: 10.1007/s00894-012-1441-0, ISSN: 0948-5023.

Lindert S, Hofmann T, Wötzel N, Karakas M, Stewart PL, Meiler J. Ab initio protein modeling into CryoEM density maps using EM-Fold. Biopolymers [print-electronic]. 2012 Sep; 97(9): 669-77. PMID: 22302372, PMCID: PMC3375387, DOI: 10.1002/bip.22027, ISSN: 0006-3525.

Lemmon G, Kaufmann K, Meiler J. Prediction of HIV-1 protease/inhibitor affinity using RosettaLigand. Chem Biol Drug Des [print-electronic]. 2012 Jun; 79(6): 888-96. PMID: 22321894, PMCID: PMC3342459, DOI: 10.1111/j.1747-0285.2012.01356.x, ISSN: 1747-0285.

Lindert S, Alexander N, Wötzel N, Karakas M, Stewart PL, Meiler J. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps. Structure. 2012 Mar 3/7/2012; 20(3): 464-78. PMID: 22405005, PMCID: PMC3304577, PII: S0969-2126(12)00054-8, DOI: 10.1016/j.str.2012.01.023, ISSN: 1878-4186.

Mueller R, Dawson ES, Meiler J, Rodriguez AL, Chauder BA, Bates BS, Felts AS, Lamb JP, Menon UN, Jadhav SB, Kane AS, Jones CK, Gregory KJ, Niswender CM, Conn PJ, Olsen CM, Winder DG, Emmitte KA, Lindsley CW. Discovery of 2-(2-benzoxazoyl amino)-4-aryl-5-cyanopyrimidine as negative allosteric modulators (NAMs) of metabotropic glutamate receptor 5 (mGlu5): from an artificial neural network virtual screen to an in vivo tool compound. ChemMedChem [print-electronic]. 2012 Mar 3/5/2012; 7(3): 406-14. PMID: 22267125, PMCID: PMC3517057, DOI: 10.1002/cmdc.201100510, ISSN: 1860-7187.

Yang R, Shi J, Byeon IJ, Ahn J, Sheehan JH, Meiler J, Gronenborn AM, Aiken C. Second-site suppressors of HIV-1 capsid mutations: restoration of intracellular activities without correction of intrinsic capsid stability defects. Retrovirology. 2012; 9: 30. PMID: 22515365, PMCID: PMC3351742, PII: 1742-4690-9-30, DOI: 10.1186/1742-4690-9-30, ISSN: 1742-4690.

Lemmon G, Meiler J. Rosetta Ligand docking with flexible XML protocols. Methods Mol. Biol. 2012; 819: 143-55. PMID: 22183535, PMCID: PMC3749076, DOI: 10.1007/978-1-61779-465-0_10, ISSN: 1940-6029.

Kaufmann KW, Meiler J. Using RosettaLigand for small molecule docking into comparative models. PLoS ONE [print-electronic]. 2012; 7(12): e50769. PMID: 23239984, PMCID: PMC3519832, PII: PONE-D-12-23247, DOI: 10.1371/journal.pone.0050769, ISSN: 1932-6203.

Woetzel N, Karakas M, Staritzbichler R, Müller R, Weiner BE, Meiler J. BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure elements. PLoS ONE [print-electronic]. 2012; 7(11): e49242. PMID: 23173051, PMCID: PMC3500277, PII: PONE-D-12-09706, DOI: 10.1371/journal.pone.0049242, ISSN: 1932-6203.

Karakas M, Woetzel N, Staritzbichler R, Alexander N, Weiner BE, Meiler J. BCL::Fold--de novo prediction of complex and large protein topologies by assembly of secondary structure elements. PLoS ONE [print-electronic]. 2012; 7(11): e49240. PMID: 23173050, PMCID: PMC3500284, PII: PONE-D-12-09707, DOI: 10.1371/journal.pone.0049240, ISSN: 1932-6203.

Sliwoski G, Lowe EW, Butkiewicz M, Meiler J. BCL::EMAS--enantioselective molecular asymmetry descriptor for 3D-QSAR. Molecules. 2012; 17(8): 9971-89. PMID: 22907158, PMCID: PMC3805266, PII: molecules17089971, DOI: 10.3390/molecules17089971, ISSN: 1420-3049.

Fortenberry C, Bowman EA, Proffitt W, Dorr B, Combs S, Harp J, Mizoue L, Meiler J. Exploring symmetry as an avenue to the computational design of large protein domains. J. Am. Chem. Soc [print-electronic]. 2011 Nov 11/16/2011; 133(45): 18026-9. PMID: 21978247, PMCID: PMC3781211, DOI: 10.1021/ja2051217, ISSN: 1520-5126.

Koehler J, Meiler J. Expanding the utility of NMR restraints with paramagnetic compounds: background and practical aspects. Prog Nucl Magn Reson Spectrosc [print-electronic]. 2011 Nov; 59(4): 360-89. PMID: 22027343, PMCID: PMC3202700, PII: S0079-6565(11)00041-0, DOI: 10.1016/j.pnmrs.2011.05.001, ISSN: 1873-3301.

DeLuca S, Dorr B, Meiler J. Design of native-like proteins through an exposure-dependent environment potential. Biochemistry [print-electronic]. 2011 Oct 10/11/2011; 50(40): 8521-8. PMID: 21905701, PMCID: PMC3752783, DOI: 10.1021/bi200664b, ISSN: 1520-4995.

Henry LK, Iwamoto H, Field JR, Kaufmann K, Dawson ES, Jacobs MT, Adams C, Felts B, Zdravkovic I, Armstrong V, Combs S, Solis E, Rudnick G, Noskov SY, DeFelice LJ, Meiler J, Blakely RD. A conserved asparagine residue in transmembrane segment 1 (TM1) of serotonin transporter dictates chloride-coupled neurotransmitter transport. J. Biol. Chem [print-electronic]. 2011 Sep 9/2/2011; 286(35): 30823-36. PMID: 21730057, PMCID: PMC3162443, PII: M111.250308, DOI: 10.1074/jbc.M111.250308, ISSN: 1083-351X.

Woetzel N, Lindert S, Stewart PL, Meiler J. BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement. J. Struct. Biol [print-electronic]. 2011 Sep; 175(3): 264-76. PMID: 21565271, PMCID: PMC3150432, PII: S1047-8477(11)00131-6, DOI: 10.1016/j.jsb.2011.04.016, ISSN: 1095-8657.

Morin A, Kaufmann KW, Fortenberry C, Harp JM, Mizoue LS, Meiler J. Computational design of an endo-1,4-beta-xylanase ligand binding site. Protein Eng. Des. Sel [print-electronic]. 2011 Jun; 24(6): 503-16. PMID: 21349882, PMCID: PMC3092692, PII: gzr006, DOI: 10.1093/protein/gzr006, ISSN: 1741-0134.

Ganguly S, Weiner BE, Meiler J. Membrane protein structure determination using paramagnetic tags. Structure. 2011 Apr 4/13/2011; 19(4): 441-3. PMID: 21481766, PMCID: PMC3754786, PII: S0969-2126(11)00110-9, DOI: 10.1016/j.str.2011.03.008, ISSN: 1878-4186.

Morin A, Meiler J, Mizoue LS. Computational design of protein-ligand interfaces: potential in therapeutic development. Trends Biotechnol [print-electronic]. 2011 Apr; 29(4): 159-66. PMID: 21295366, PMCID: PMC3749302, PII: S0167-7799(11)00003-5, DOI: 10.1016/j.tibtech.2011.01.002, ISSN: 1879-3096.

Kazmier K, Alexander NS, Meiler J, McHaourab HS. Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination. J. Struct. Biol [print-electronic]. 2011 Mar; 173(3): 549-57. PMID: 21074624, PMCID: PMC3073550, PII: S1047-8477(10)00340-0, DOI: 10.1016/j.jsb.2010.11.003, ISSN: 1095-8657.

Hirst SJ, Alexander N, McHaourab HS, Meiler J. RosettaEPR: an integrated tool for protein structure determination from sparse EPR data. J. Struct. Biol [print-electronic]. 2011 Mar; 173(3): 506-14. PMID: 21029778, PMCID: PMC3040274, PII: S1047-8477(10)00333-3, DOI: 10.1016/j.jsb.2010.10.013, ISSN: 1095-8657.

Combs S, Kaufmann K, Field JR, Blakely RD, Meiler J. Y95 and E444 interaction required for high-affinity S-citalopram binding in the human serotonin transporter. ACS Chem Neurosci [print-electronic]. 2011 Feb 2/16/2011; 2(2): 75-81. PMID: 22778858, PMCID: PMC3369724, DOI: 10.1021/cn100066p, ISSN: 1948-7193.

Kaufmann K, Shen N, Mizoue L, Meiler J. A physical model for PDZ-domain/peptide interactions. J Mol Model [print-electronic]. 2011 Feb; 17(2): 315-24. PMID: 20461427, PMCID: PMC3029681, DOI: 10.1007/s00894-010-0725-5, ISSN: 0948-5023.

Bhave G, Chauder BA, Liu W, Dawson ES, Kadakia R, Nguyen TT, Lewis LM, Meiler J, Weaver CD, Satlin LM, Lindsley CW, Denton JS. Development of a selective small-molecule inhibitor of Kir1.1, the renal outer medullary potassium channel. Mol. Pharmacol [print-electronic]. 2011 Jan; 79(1): 42-50. PMID: 20926757, PMCID: PMC3014278, PII: mol.110.066928, DOI: 10.1124/mol.110.066928, ISSN: 1521-0111.

Gregory KJ, Dong EN, Meiler J, Conn PJ. Allosteric modulation of metabotropic glutamate receptors: structural insights and therapeutic potential. Neuropharmacology [print-electronic]. 2011 Jan; 60(1): 66-81. PMID: 20637216, PMCID: PMC2981682, PII: S0028-3908(10)00168-1, DOI: 10.1016/j.neuropharm.2010.07.007, ISSN: 1873-7064.

Lowe EW, Ferrebee A, Rodriguez AL, Conn PJ, Meiler J. 3D-QSAR CoMFA study of benzoxazepine derivatives as mGluR5 positive allosteric modulators. Bioorg. Med. Chem. Lett [print-electronic]. 2010 Oct 10/1/2010; 20(19): 5922-4. PMID: 20732812, PMCID: PMC2943337, PII: S0960-894X(10)01017-6, DOI: 10.1016/j.bmcl.2010.07.061, ISSN: 1464-3405.

Nannemann DP, Kaufmann KW, Meiler J, Bachmann BO. Design and directed evolution of a dideoxy purine nucleoside phosphorylase. Protein Eng. Des. Sel [print-electronic]. 2010 Aug; 23(8): 607-16. PMID: 20525731, PMCID: PMC2898500, PII: gzq033, DOI: 10.1093/protein/gzq033, ISSN: 1741-0134.

Kaufmann KW, Lemmon GH, Deluca SL, Sheehan JH, Meiler J. Practically useful: what the Rosetta protein modeling suite can do for you. Biochemistry. 2010 Apr 4/13/2010; 49(14): 2987-98. PMID: 20235548, PMCID: PMC2850155, DOI: 10.1021/bi902153g, ISSN: 1520-4995.

Karakas M, Woetzel N, Meiler J. BCL::contact-low confidence fold recognition hits boost protein contact prediction and de novo structure determination. J. Comput. Biol. 2010 Feb; 17(2): 153-68. PMID: 19772383, PMCID: PMC3148831, DOI: 10.1089/cmb.2009.0030, ISSN: 1557-8666.

Lebois EP, Bridges TM, Lewis LM, Dawson ES, Kane AS, Xiang Z, Jadhav SB, Yin H, Kennedy JP, Meiler J, Niswender CM, Jones CK, Conn PJ, Weaver CD, Lindsley CW. Discovery and characterization of novel subtype-selective allosteric agonists for the investigation of M(1) receptor function in the central nervous system. ACS Chem Neurosci. 2010; 1(2): 104-21. PMID: 21961051, PMCID: PMC3180826, DOI: 10.1021/cn900003h, ISSN: 1948-7193.

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 [print-electronic]. 2009 Sep; 15(9): 1093-108. PMID: 19234730, PMCID: PMC2712621, DOI: 10.1007/s00894-009-0454-9, ISSN: 0948-5023.

Lindert S, Staritzbichler R, Wötzel N, Karakas M, Stewart PL, Meiler J. EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. Structure. 2009 Jul 7/15/2009; 17(7): 990-1003. PMID: 19604479, PMCID: PMC3760413, PII: S0969-2126(09)00223-8, DOI: 10.1016/j.str.2009.06.001, ISSN: 1878-4186.

Koehler J, Woetzel N, Staritzbichler R, Sanders CR, Meiler J. A unified hydrophobicity scale for multispan membrane proteins. Proteins. 2009 Jul; 76(1): 13-29. PMID: 19089980, PMCID: PMC2761718, DOI: 10.1002/prot.22315, ISSN: 1097-0134.

Stepanovic SZ, Potet F, Petersen CI, Smith JA, Meiler J, Balser JR, Kupershmidt S. The evolutionarily conserved residue A653 plays a key role in HERG channel closing. J. Physiol. (Lond.) [print-electronic]. 2009 Jun 6/1/2009; 587(Pt 11): 2555-66. PMID: 19406877, PMCID: PMC2714020, PII: jphysiol.2008.166694, DOI: 10.1113/jphysiol.2008.166694, ISSN: 1469-7793.

Lindert S, Stewart PL, Meiler J. Hybrid approaches: applying computational methods in cryo-electron microscopy. Curr. Opin. Struct. Biol [print-electronic]. 2009 Apr; 19(2): 218-25. PMID: 19339173, PMCID: PMC2726835, PII: S0959-440X(09)00026-8, DOI: 10.1016/j.sbi.2009.02.010, ISSN: 1879-033X.

Kaufmann KW, Dawson ES, Henry LK, Field JR, Blakely RD, Meiler J. Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies. Proteins. 2009 Feb 2/15/2009; 74(3): 630-42. PMID: 18704946, PMCID: PMC2782712, DOI: 10.1002/prot.22178, ISSN: 1097-0134.

Fallen K, Banerjee S, Sheehan J, Addison D, Lewis LM, Meiler J, Denton JS. The Kir channel immunoglobulin domain is essential for Kir1.1 (ROMK) thermodynamic stability, trafficking and gating. Channels (Austin) [print-electronic]. 2009 Jan; 3(1): 57-68. PMID: 19221509, PII: 7817, ISSN: 1933-6969.

Dong E, Smith J, Heinze S, Alexander N, Meiler J. BCL::Align-sequence alignment and fold recognition with a custom scoring function online. Gene [print-electronic]. 2008 Oct 10/1/2008; 422(1-2): 41-6. PMID: 18601985, PMCID: PMC2658673, PII: S0378-1119(08)00233-3, DOI: 10.1016/j.gene.2008.06.006, ISSN: 0378-1119.

Kang C, Tian C, Sönnichsen FD, Smith JA, Meiler J, George AL, Vanoye CG, Kim HJ, Sanders CR. Structure of KCNE1 and implications for how it modulates the KCNQ1 potassium channel. Biochemistry [print-electronic]. 2008 Aug 8/5/2008; 47(31): 7999-8006. PMID: 18611041, PMCID: PMC2580054, DOI: 10.1021/bi800875q, ISSN: 1520-4995.

Hanson SM, Dawson ES, Francis DJ, Van Eps N, Klug CS, Hubbell WL, Meiler J, Gurevich VV. A model for the solution structure of the rod arrestin tetramer. Structure. 2008 Jun; 16(6): 924-34. PMID: 18547524, PMCID: PMC2464289, PII: S0969-2126(08)00143-3, DOI: 10.1016/j.str.2008.03.006, ISSN: 0969-2126.

Alexander N, Bortolus M, Al-Mestarihi A, Mchaourab H, Meiler J. De novo high-resolution protein structure determination from sparse spin-labeling EPR data. Structure. 2008 Feb; 16(2): 181-95. PMID: 18275810, PMCID: PMC2390841, PII: S0969-2126(08)00012-9, DOI: 10.1016/j.str.2007.11.015, ISSN: 0969-2126.

Smith JA, Vanoye CG, George AL, Meiler J, Sanders CR. Structural models for the KCNQ1 voltage-gated potassium channel. Biochemistry [print-electronic]. 2007 Dec 12/11/2007; 46(49): 14141-52. PMID: 17999538, PMCID: PMC2565492, DOI: 10.1021/bi701597s, ISSN: 0006-2960.

Henry LK, Meiler J, Blakely RD. Bound to be different: neurotransmitter transporters meet their bacterial cousins. Mol. Interv. 2007 Dec; 7(6): 306-9. PMID: 18199851, PII: 7/6/306, DOI: 10.1124/mi.7.6.4, ISSN: 1534-0384.

Reese M, Sánchez-Pedregal VM, Kubicek K, Meiler J, Blommers MJ, 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. 2007; 46(11): 1864-8. PMID: 17274084, DOI: 10.1002/anie.200604505, ISSN: 1433-7851.

Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Röthlisberger D, Baker D. New algorithms and an in silico benchmark for computational enzyme design. Protein Sci. 2006 Dec; 15(12): 2785-94. PMID: 17132862, PMCID: PMC2242439, PII: 15/12/2785, DOI: 10.1110/ps.062353106, ISSN: 0961-8368.

Meiler J, Baker D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins. 2006 Nov 11/15/2006; 65(3): 538-48. PMID: 16972285, DOI: 10.1002/prot.21086, ISSN: 1097-0134.

Sánchez-Pedregal VM, 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. 2006 Nov 11/13/2006; 45(44): 7388-94. PMID: 17036370, DOI: 10.1002/anie.200602793, ISSN: 1433-7851.

Lakomek NA, Carlomagno T, Becker S, Griesinger C, Meiler J. A thorough dynamic interpretation of residual dipolar couplings in ubiquitin. J. Biomol. NMR. 2006 Feb; 34(2): 101-15. PMID: 16518697, DOI: 10.1007/s10858-005-5686-0, ISSN: 0925-2738.

Lakomek NA, Farès C, Becker S, Carlomagno T, Meiler J, Griesinger C. Side-chain orientation and hydrogen-bonding imprint supra-Tau(c) motion on the protein backbone of ubiquitin. Angew. Chem. Int. Ed. Engl. 2005 Dec 12/2/2005; 44(47): 7776-8. PMID: 16276548, DOI: 10.1002/anie.200502573, ISSN: 1433-7851.

Sánchez-Pedregal VM, Reese M, Meiler J, Blommers MJ, Griesinger C, Carlomagno T. The INPHARMA method: protein-mediated interligand NOEs for pharmacophore mapping. Angew. Chem. Int. Ed. Engl. 2005 Jul 7/4/2005; 44(27): 4172-5. PMID: 15929149, DOI: 10.1002/anie.200500503, ISSN: 1433-7851.

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. 2005 Apr; 173(2): 310-6. PMID: 15780923, PII: S1090-7807(04)00400-8, DOI: 10.1016/j.jmr.2004.11.031, ISSN: 1090-7807.

Graña O, Baker D, MacCallum RM, Meiler J, Punta M, Rost B, Tress ML, Valencia A. CASP6 assessment of contact prediction. Proteins. 2005; 61 Suppl 7: 214-24. PMID: 16187364, DOI: 10.1002/prot.20739, ISSN: 1097-0134.

Bradley P, Malmström L, Qian B, Schonbrun J, Chivian D, Kim DE, Meiler J, Misura KM, Baker D. Free modeling with Rosetta in CASP6. Proteins. 2005; 61 Suppl 7: 128-34. PMID: 16187354, DOI: 10.1002/prot.20729, ISSN: 1097-0134.

Meiler J, Köck M. Novel methods of automated structure elucidation based on 13C NMR spectroscopy. Magn Reson Chem. 2004 Dec; 42(12): 1042-5. PMID: 15470690, DOI: 10.1002/mrc.1424, ISSN: 0749-1581.

Kuhn M, Meiler J, Baker D. Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins. 2004 Feb 2/1/2004; 54(2): 282-8. PMID: 14696190, DOI: 10.1002/prot.10589, ISSN: 1097-0134.

Griesinger C, Peti W, Meiler J, Brüschweiler R. Projection angle restraints for studying structure and dynamics of biomolecules. Methods Mol. Biol. 2004; 278: 107-21. PMID: 15317994, PII: 1-59259-809-9:107, DOI: 10.1385/1-59259-809-9:107, ISSN: 1064-3745.

Meiler J, Baker D. Rapid protein fold determination using unassigned NMR data. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2003 Dec 12/23/2003; 100(26): 15404-9. PMID: 14668443, PMCID: PMC307580, PII: 2434121100, DOI: 10.1073/pnas.2434121100, ISSN: 0027-8424.

Meiler J, Baker D. Coupled prediction of protein secondary and tertiary structure. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2003 Oct 10/14/2003; 100(21): 12105-10. PMID: 14528006, PMCID: PMC218720, PII: 1831973100, DOI: 10.1073/pnas.1831973100, ISSN: 0027-8424.

Meiler J, Peti W, Griesinger C. Dipolar couplings in multiple alignments suggest alpha helical motion in ubiquitin. J. Am. Chem. Soc. 2003 Jul 7/9/2003; 125(27): 8072-3. PMID: 12837055, DOI: 10.1021/ja029816l, ISSN: 0002-7863.

Carlomagno T, Blommers MJ, Meiler J, Jahnke W, Schupp T, Petersen F, Schinzer D, Altmann KH, 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. 2003 Jun 6/6/2003; 42(22): 2511-5. PMID: 12800173, DOI: 10.1002/anie.200351276, ISSN: 1433-7851.

Meiler J. PROSHIFT: protein chemical shift prediction using artificial neural networks. J. Biomol. NMR. 2003 May; 26(1): 25-37. PMID: 12766400, PII: 5121785, ISSN: 0925-2738.

Bradley P, Chivian D, Meiler J, Misura KM, Rohl CA, Schief WR, Wedemeyer WJ, Schueler-Furman O, Murphy P, Schonbrun J, Strauss CE, Baker D. Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins. 2003; 53 Suppl 6: 457-68. PMID: 14579334, DOI: 10.1002/prot.10552, ISSN: 1097-0134.

Hutter MC, 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. 2002 Dec 12/2/2002; 3(12): 1200-8. PMID: 12465028, DOI: 10.1002/1439-7633(20021202)3:12<1200::AID-CBIC1200>3.0.CO;2-H, ISSN: 1439-4227.

Meiler J, Maier W, Will M, Meusinger R. Using neural networks for (13)c NMR chemical shift prediction-comparison with traditional methods. J. Magn. Reson. 2002 Aug; 157(2): 242-52. PMID: 12323143, PII: S1090780702925991, ISSN: 1090-7807.

Peti W, Meiler J, Brüschweiler R, Griesinger C. Model-free analysis of protein backbone motion from residual dipolar couplings. J. Am. Chem. Soc. 2002 May 5/22/2002; 124(20): 5822-33. PMID: 12010057, PII: ja011883c, ISSN: 0002-7863.

Meiler J, Will M. Genius: a genetic algorithm for automated structure elucidation from 13C NMR spectra. J. Am. Chem. Soc. 2002 Mar 3/6/2002; 124(9): 1868-70. PMID: 11866596, PII: ja0109388, ISSN: 0002-7863.

Meiler J, Sanli E, Junker J, Meusinger R, Lindel T, Will M, Maier W, Köck M. Validation of structural proposals by substructure analysis and 13C NMR chemical shift prediction. J Chem Inf Comput Sci. 2002 Mar; 42(2): 241-8. PMID: 11911693, PII: ci010294n, ISSN: 0095-2338.

Meiler J, Will M. Automated structure elucidation of organic molecules from (13)c NMR spectra using genetic algorithms and neural networks. J Chem Inf Comput Sci. 2001 Nov; 41(6): 1535-46. PMID: 11749580, PII: ci0102970, ISSN: 0095-2338.

Carlomagno T, Blommers MJ, Meiler J, Cuenoud B, Griesinger C. Determination of aliphatic side-chain conformation using cross-correlated relaxation: application to an extraordinarily stable 2'-aminoethoxy-modified oligonucleotide triplex. J. Am. Chem. Soc. 2001 Aug 8/1/2001; 123(30): 7364-70. PMID: 11472167, PII: ja002592r, ISSN: 0002-7863.

Meiler J, Prompers JJ, Peti W, Griesinger C, Brüschweiler R. Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. J. Am. Chem. Soc. 2001 Jun 6/27/2001; 123(25): 6098-107. PMID: 11414844, PII: ja010002z, ISSN: 0002-7863.

Meiler J, Meusinger R, Will M. Fast determination of 13C NMR chemical shifts using artificial neural networks. J Chem Inf Comput Sci. 2000 Sep; 40(5): 1169-76. PMID: 11045810, ISSN: 0095-2338.

Meiler J, Peti W, Griesinger C. DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts. J. Biomol. NMR. 2000 Aug; 17(4): 283-94. PMID: 11014592, ISSN: 0925-2738.

Meiler J, Blomberg N, Nilges M, Griesinger C. A new approach for applying residual dipolar couplings as restraints in structure elucidation. J. Biomol. NMR. 2000 Mar; 16(3): 245-52. PMID: 10805131, ISSN: 0925-2738.

Available Postdoctoral Position Details
positions in computational and experimental structural biology available. please contact jens.meiler@vanderbilt.edu