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Genomes and Genes | Jens MeilerSummaryCountry: Germany Publications
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Publications
Genius: a genetic algorithm for automated structure elucidation from 13C NMR spectraJens Meiler
University of Washington, Box 357350, Seattle, Washington 98195 7350, USA
J Am Chem Soc 124:1868-70. 2002..The method is implemented and tested successfully for organic molecules with up to 18 non-hydrogen atoms...- ROSETTALIGAND: protein-small molecule docking with full side-chain flexibilityJens Meiler
Vanderbilt University, Department of Chemistry, Center for Structural Biology, Nashville, TN 37235 8725, USA
Proteins 65:538-48. 2006..In cross-docking calculations in which both protein side-chain and small molecule internal degrees of freedom were varied the lowest energy predictions had RMSDs less than 2 A in 14 of 20 test cases... - The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopyJens Meiler
Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195, USA
J Magn Reson 173:310-6. 2005..8 angstrom could rapidly be built. The ability to generate moderate resolution models within days of NMR data collection should facilitate large scale NMR structure determination efforts... - PROSHIFT: protein chemical shift prediction using artificial neural networksJens Meiler
University of Washington, Department of Biochemistry, Box 357350, Seattle, Washington 98195 7350, USA
J Biomol NMR 26:25-37. 2003..It is freely available for academic users at the PROSHIFT server: www.jens-meiler.de/proshift.html.. - EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density mapsSteffen Lindert
Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA
Structure 17:990-1003. 2009..We report the first topological model for the alpha-helical 400 residue N-terminal region of protein IIIa. EM-Fold also has the potential to interpret medium-resolution density maps in X-ray crystallography... - Free modeling with Rosetta in CASP6Philip Bradley
University of Washington, Seattle, Washington 98195, USA
Proteins 61:128-34. 2005..Highlights include improved performance on larger proteins (100-200 residues) and the prediction of a 70-residue alpha-beta protein to near-atomic resolution... - Computational design of an endo-1,4-beta-xylanase ligand binding siteAndrew Morin
Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
Protein Eng Des Sel 24:503-16. 2011..These findings offer new insight into the dynamic and structural determinants of the ?-xylanase proteins... - A unified hydrophobicity scale for multispan membrane proteinsJULIA KOEHLER
Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232 8725, USA
Proteins 76:13-29. 2009..The accuracy of the present hydrophobicity scale profits from the doubling of the number of integral MPs in the PDB over the past four years. The UHS paves the way for an increased accuracy in the prediction of trans-membrane spans... - The Kir channel immunoglobulin domain is essential for Kir1.1 (ROMK) thermodynamic stability, trafficking and gatingKatherine Fallen
Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
Channels (Austin) 3:57-68. 2009..Our study sheds new light on the pathogenesis of ABS and establishes the IgLD as an essential structure within the Kir channel family... - BCL::contact-low confidence fold recognition hits boost protein contact prediction and de novo structure determinationMert Karakaş
Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
J Comput Biol 17:153-68. 2010..3 A on average root mean square deviation (RMSD), when driven by the predicted contacts. Further, filtering Rosetta models by agreement with the predicted contacts enriches for native-like fold topologies... - Hybrid approaches: applying computational methods in cryo-electron microscopySteffen Lindert
Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA
Curr Opin Struct Biol 19:218-25. 2009..It is these hybrid approaches between cryoEM and computational protein structure prediction algorithms that will shape protein structure elucidation from density maps... - BCL::Align-sequence alignment and fold recognition with a custom scoring function onlineElizabeth Dong
Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
Gene 422:41-6. 2008..g. membrane proteins) or fold families (e.g. TIM-barrel proteins). BCL::Align is free for academic use and available online at http://www.meilerlab.org/... - Rosetta predictions in CASP5: successes, failures, and prospects for complete automationPhilip Bradley
Department of Biochemistry, University of Washington, Seattle 98195-7350, USA
Proteins 53:457-68. 2003..For the three targets where the human-assisted predictions were significantly closer to the native structure, we identify the steps that remain to be automated... - Rapid protein fold determination using unassigned NMR dataJens Meiler
Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, PO Box 357350, Seattle, WA 98195-7350, USA
Proc Natl Acad Sci U S A 100:15404-9. 2003..6-1.8 A) by repeated cycles of structure generation guided by the partial assignments, followed by reassignment using the newly generated models... - Exploring symmetry as an avenue to the computational design of large protein domainsCarie Fortenberry
Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
J Am Chem Soc 133:18026-9. 2011.... - BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinementNils Woetzel
Department of Chemistry, Vanderbilt University, TN 37212, USA
J Struct Biol 175:264-76. 2011..The BCL::EM-Fit algorithm offers an alternative to the established Fourier/Real space fitting programs. BCL::EM-Fit is free for academic use and available from a web server or as downloadable binary file at http://www.meilerlab.org... - Algorithm for selection of optimized EPR distance restraints for de novo protein structure determinationKelli Kazmier
Chemical and Physical Biology Program, 340 Light Hall, Vanderbilt University, Nashville, TN 37232, USA
J Struct Biol 173:549-57. 2011.... - RosettaEPR: an integrated tool for protein structure determination from sparse EPR dataStephanie J Hirst
Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USA
J Struct Biol 173:506-14. 2011..In order to affirm the method's general performance, it must be tested on a larger and more versatile dataset of proteins... - Practically useful: what the Rosetta protein modeling suite can do for youKRISTIAN W KAUFMANN
Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, USA
Biochemistry 49:2987-98. 2010..Most recently, Rosetta has been used to solve the X-ray crystallographic phase problem... - A conserved asparagine residue in transmembrane segment 1 (TM1) of serotonin transporter dictates chloride-coupled neurotransmitter transportL Keith Henry
Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 8548, USA
J Biol Chem 286:30823-36. 2011.... - Computational design of protein-ligand interfaces: potential in therapeutic developmentAndrew Morin
Departments of Chemistry, Pharmacology, and Biomedical Informatics, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
Trends Biotechnol 29:159-66. 2011..Future prospects for applications in drug development are discussed, including limitations that will need to be overcome to achieve computational design of protein therapeutics with novel modes of action... - A physical model for PDZ-domain/peptide interactionsKRISTIAN KAUFMANN
Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
J Mol Model 17:315-24. 2011..60 and R?=?0.17, respectively. The computational method improves prediction of PDZ domain specificity from sequence and allows design of novel PDZ domain/peptide interactions... - EM-fold: de novo atomic-detail protein structure determination from medium-resolution density mapsSteffen Lindert
Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USA
Structure 20:464-78. 2012..The EM-Fold algorithm assembles the SSEs de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins, the protocol consistently and reproducibly achieves models with root mean square deviation values <3 Å... - Development of a selective small-molecule inhibitor of Kir1.1, the renal outer medullary potassium channelGautam Bhave
Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
Mol Pharmacol 79:42-50. 2011..1 and more than 65 other potential off-targets. VU591 seems to block the intracellular pore of the channel. The development of VU591 may enable studies to explore the viability of ROMK as a diuretic target... - Solvent accessible surface area approximations for rapid and accurate protein structure predictionElizabeth Durham
Department of Chemistry, Center for Structural Biology, Vanderbilt University, 465 21st Ave South, Nashville, TN 37232 8725, USA
J Mol Model 15:1093-108. 2009..We find the newly developed "Neighbor Vector" algorithm provides the most optimal balance of accurate yet rapid exposure measures... - New algorithms and an in silico benchmark for computational enzyme designAlexandre Zanghellini
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Protein Sci 15:2785-94. 2006..The new methods can be directly applied to the design of new enzymes, and the benchmark provides a powerful in silico test for guiding improvements in computational enzyme design... - Design and directed evolution of a dideoxy purine nucleoside phosphorylaseDavid P Nannemann
Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
Protein Eng Des Sel 23:607-16. 2010..The engineered PNP may form the basis for catalysts and pathways for the biosynthesis of ddI... - Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studiesKRISTIAN W KAUFMANN
Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235 1822, USA
Proteins 74:630-42. 2009..Our studies identify a number of potential contacts whose contribution to substrate binding and transport was previously unsuspected... - A model for the solution structure of the rod arrestin tetramerSusan M Hanson
Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
Structure 16:924-34. 2008..The structure of the solution tetramer explains its inability to bind rhodopsin and paves the way for experimental studies of the physiological role of rod arrestin self-association... - RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suiteSarel J Fleishman
Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
PLoS ONE 6:e20161. 2011.... - Design of native-like proteins through an exposure-dependent environment potentialSamuel Deluca
Departments of Chemistry, Pharmacology, and Biomedical Informatics, Center for Structural Biology, Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37212, United States
Biochemistry 50:8521-8. 2011..et al. (2009) J. Mol. Model. 15, 1093-1108]. Benchmarking of this potential in protein design displays a 3.2% improvement in the overall sequence recovery and an 8.5% improvement in recovery of amino acid types tolerated in evolution... - Discovery of 2-(2-Benzoxazoyl amino)-4-Aryl-5-Cyanopyrimidine as Negative Allosteric Modulators (NAMs) of Metabotropic Glutamate Receptor?5 (mGlu(5) ): From an Artificial Neural Network Virtual Screen to an In Vivo Tool CompoundRalf Mueller
Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37232 6600 USA
ChemMedChem 7:406-14. 2012..This effort identified two potent mGlu(5) NAMs with a unique chemotype. Optimization afforded a tool compound (shown), active in mouse models of anxiety and addiction... - Structure of KCNE1 and implications for how it modulates the KCNQ1 potassium channelCongbao Kang
Department of Biochemitry, Vanderbilt University, Nashville, Tennessee 37232, USA
Biochemistry 47:7999-8006. 2008..These working models for the KCNE1-KCNQ1 complexes may be used to formulate testable hypotheses for the molecular bases of disease phenotypes associated with the dozens of known inherited mutations in KCNE1 and KCNQ1... - The evolutionarily conserved residue A653 plays a key role in HERG channel closingSvetlana Z Stepanovic
Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
J Physiol 587:2555-66. 2009..Our study suggests that A653 plays an important functional role in the outwardly rectifying gating behaviour of HERG, supporting channel closure at membrane potentials negative to the channel activation threshold... - Novel methods of automated structure elucidation based on 13C NMR spectroscopyJens Meiler
University of Washington, Box 357350, Seattle, Washington 98195, USA
Magn Reson Chem 42:1042-5. 2004..These three existing implementations are compared using realistic example molecules. The applicability and reliability of such approaches is addressed... - De novo high-resolution protein structure determination from sparse spin-labeling EPR dataNathan Alexander
Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USA
Structure 16:181-95. 2008..The approach can be extended to other experimental techniques such as fluorescence spectroscopy, substituted cysteine accessibility method, or mutational studies... - Coupled prediction of protein secondary and tertiary structureJens Meiler
Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195-7350, USA
Proc Natl Acad Sci U S A 100:12105-10. 2003..Analysis of proteins with particularly large improvements in secondary structure prediction using tertiary structure information provides insight into the feedback from tertiary to secondary structure... - ROSETTA3: an object-oriented software suite for the simulation and design of macromoleculesAndrew Leaver-Fay
Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, USA
Methods Enzymol 487:545-74. 2011..This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform... - 3D-QSAR CoMFA study of benzoxazepine derivatives as mGluR5 positive allosteric modulatorsEdward W Lowe
Center for Structural Biology, Vanderbilt University, Nashville, TN 37232 6600, USA
Bioorg Med Chem Lett 20:5922-4. 2010..58 (r(2) = 0.81) yielding a standard error of 0.20 in pEC(50) for this class of compounds. The subsequent contour maps highlight the structural features pertinent to the bioactivity values of benzoxazepines... - Allosteric modulation of metabotropic glutamate receptors: structural insights and therapeutic potentialKaren J Gregory
Department of Pharmacology, Vanderbilt Program in Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232 0697, USA
Neuropharmacology 60:66-81. 2011..In the absence of a class C GPCR crystal structure, this approach has shown promise with respect to the interpretation of mutagenesis data and understanding structure-activity relationships of allosteric modulator pharmacophores... - Rosetta Ligand docking with flexible XML protocolsGordon Lemmon
Department of Chemistry, Vanderbilt University, Nashville, TN, USA
Methods Mol Biol 819:143-55. 2012.... - Measurement of aptamer-protein interactions with back-scattering interferometryIan R Olmsted
Department of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, 7330 Stevenson Center, Nashville, Tennessee 37235, United States
Anal Chem 83:8867-70. 2011..Preliminary modeling efforts suggest evidence for allosteric linkage between the two exosites... - Projection angle restraints for studying structure and dynamics of biomoleculesChristian Griesinger
Max Planck Institute for Biophysical Chemistry, , Germany
Methods Mol Biol 278:107-21. 2004..This range of time-scales has been previously inaccessible by other nuclear magnetic resonance (NMR) techniques. In addition, information about the anisotropy of the motion is obtained... - Model-free analysis of protein backbone motion from residual dipolar couplingsWolfgang Peti
Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, , Germany
J Am Chem Soc 124:5822-33. 2002..Amplitudes and anisotropies of the motion can be derived from the model-free analysis. The method can be applied provided that at least five sufficiently different alignment media can be found for the biomolecule under investigation... - Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solutionOliver F Lange
Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
Science 320:1471-5. 2008..A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost... - Structural basis of the activity of the microtubule-stabilizing agent epothilone a studied by NMR spectroscopy in solutionMarcel Reese
, , Am Fassberg 11, , Germany
Angew Chem Int Ed Engl 46:1864-8. 2007 - A thorough dynamic interpretation of residual dipolar couplings in ubiquitinNils A Lakomek
NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Goettingen, Germany
J Biomol NMR 34:101-15. 2006..Amplitudes and anisotropies of the motion were derived. The effect of structural noise on the results was proven to be negligible... - The high-resolution solution structure of epothilone A bound to tubulin: an understanding of the structure-activity relationships for a powerful class of antitumor agentsTeresa Carlomagno
, Am Fassberg 11, , Germany
Angew Chem Int Ed Engl 42:2511-5. 2003 - Dipolar couplings in multiple alignments suggest alpha helical motion in ubiquitinJens Meiler
Max Planck Insitute for Biophysical Chemistry, , Germany
J Am Chem Soc 125:8072-3. 2003..Such motion contradicts neither NOE data nor molecular force-field calculations... - Side-chain orientation and hydrogen-bonding imprint supra-Tau(c) motion on the protein backbone of ubiquitinNils A Lakomek
, , Germany
Angew Chem Int Ed Engl 44:7776-8. 2005 - Bound to be different: neurotransmitter transporters meet their bacterial cousinsL Keith Henry
Department of Pharmacology, Vanderbilt University Nashville, TN 37232 8548, USA
Mol Interv 7:306-9. 2007.... - Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteinsMichael Kuhn
California Institute of Technology, Pasadena, USA
Proteins 54:282-8. 2004..The beta-hairpin/diverging turn classification from amino acid sequences is available online for academic use (Meiler and Kuhn, 2003; www.jens-meiler.de/turnpred.html)... - Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamicsNils Alexander Lakomek
Department for NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, Germany
J Biomol NMR 41:139-55. 2008....