Works by Merkl, Rainer

Results: 62

Artificial Light Regulation of an Allosteric Bienzyme Complex by a Photosensitive Ligand.

Published in:

ChemBioChem, 2018, v. 19, n. 16, p. 1750, doi. 10.1002/cbic.201800219

By:

Kneuttinger, Andrea C.;
Winter, Martin;
Simeth, Nadja A.;
Heyn, Kristina;
Merkl, Rainer;
König, Burkhard;
Sterner, Reinhard

Publication type:

Article

The genome sequence of the extreme thermophile Thermus thermophilus.

Published in:

Nature Biotechnology, 2004, v. 22, n. 5, p. 547, doi. 10.1038/nbt956

By:

Henne, Anke;
Brüggemann, Holger;
Raasch, Carsten;
Wiezer, Arnim;
Hartsch, Thomas;
Liesegang, Heiko;
Johann, Andre;
Lienard, Tanja;
Gohl, Olivia;
Martinez-Arias, Rosa;
Jacobi, Carsten;
Starkuviene, Vytaute;
Schlenczeck, Silke;
Dencker, Silke;
Huber, Robert;
Klend, Hans-Peter;
Kramer, Wilfried;
Merkl, Rainer;
Gottschalk, Gerhard;
Fritz, Hans-Joachim

Publication type:

Article

Towards Photochromic Azobenzene‐Based Inhibitors for Tryptophan Synthase.

Published in:

Chemistry - A European Journal, 2021, v. 27, n. 7, p. 2439, doi. 10.1002/chem.202004061

By:

Simeth, Nadja A.;
Kinateder, Thomas;
Rajendran, Chitra;
Nazet, Julian;
Merkl, Rainer;
Sterner, Reinhard;
König, Burkhard;
Kneuttinger, Andrea C.

Publication type:

Article

GO4genome: A Prokaryotic Phylogeny Based on Genome Organization.

Published in:

Journal of Molecular Evolution, 2009, v. 68, n. 5, p. 550, doi. 10.1007/s00239-009-9233-6

By:

Merkl, Rainer;
Wiezer, Arnim

Publication type:

Article

A Comparative Categorization of Protein Function Encoded in Bacterial or Archeal Genomic Islands.

Published in:

Journal of Molecular Evolution, 2006, v. 62, n. 1, p. 1, doi. 10.1007/s00239-004-0311-5

By:

Merkl, Rainer

Publication type:

Article

A Survey of Codon and Amino Acid Frequency Bias in Microbial Genomes Focusing on Translational Efficiency.

Published in:

Journal of Molecular Evolution, 2003, v. 57, n. 4, p. 453, doi. 10.1007/s00239-003-2499-1

By:

Merkl, Rainer

Publication type:

Article

DNA sequence encoded repression of rRNA gene transcription in chromatin.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 16, p. 5304, doi. 10.1093/nar/gkq263

By:

Felle, Max;
Exler, Josef H.;
Merkl, Rainer;
Dachauer, Karoline;
Brehm, Alexander;
Grummt, Ingrid;
Längst, Gernot

Publication type:

Article

Protein design on computers. Five new proteins: Shpilka, grendel, fingerclasp, leather, and aida.

Published in:

Proteins, 1992, v. 12, n. 2, p. 105, doi. 10.1002/prot.340120203

By:

Sander, Chris;
Vriend, Gerrit;
Bazan, Fernando;
Horovitz, Amnon;
Nakamura, Haruki;
Ribas, Luis;
Finkelstein, Alexei V.;
Lockhart, Andrew;
Merkl, Rainer;
Perry, L. Jeanne;
Emery, Stephen C.;
Gaboriaud, Christine;
Marks, Cara;
Moult, John;
Verlinde, Christophe;
Eberhard, Marc;
Elofsson, Arne;
Hubbard, Tim J. P.;
Regan, Lynne;
Banks, Jay

Publication type:

Article

Rosetta:MSF: a modular framework for multi-state computational protein design.

Published in:

2017

By:

Löffler, Patrick;
Schmitz, Samuel;
Hupfeld, Enrico;
Sterner, Reinhard;
Merkl, Rainer

Publication type:

Product Review

Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase.

Published in:

Biological Chemistry, 2019, v. 400, n. 3, p. 367, doi. 10.1515/hsz-2018-0344

By:

Straub, Kristina;
Linde, Mona;
Kropp, Cosimo;
Blanquart, Samuel;
Babinger, Patrick;
Merkl, Rainer

Publication type:

Article

Ancestral protein reconstruction: techniques and applications.

Published in:

Biological Chemistry, 2016, v. 397, n. 1, p. 1, doi. 10.1515/hsz-2015-0158

By:

Merkl, Rainer;
Sterner, Reinhard

Publication type:

Article

Maize EMBRYO SAC family peptides interact differentially with pollen tubes and fungal cells.

Published in:

Journal of Experimental Botany, 2015, v. 66, n. 17, p. 5205, doi. 10.1093/jxb/erv268

By:

Woriedh, Mayada;
Merkl, Rainer;
Dresselhaus, Thomas

Publication type:

Article

Light-Regulation of Tryptophan Synthase by Combining Protein Design and Enzymology.

Published in:

International Journal of Molecular Sciences, 2019, v. 20, n. 20, p. 5106, doi. 10.3390/ijms20205106

By:

Kneuttinger, Andrea C.;
Zwisele, Stefanie;
Straub, Kristina;
Bruckmann, Astrid;
Busch, Florian;
Kinateder, Thomas;
Gaim, Barbara;
Wysocki, Vicki H.;
Merkl, Rainer;
Sterner, Reinhard

Publication type:

Article

Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism.

Published in:

BMC Evolutionary Biology, 2017, v. 17, p. 1, doi. 10.1186/s12862-017-0886-2

By:

Veprinskiy, Valery;
Heizinger, Leonhard;
Plach, Maximilian G.;
Merkl, Rainer

Publication type:

Article

Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products.

Published in:

BMC Bioinformatics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12859-019-3200-z

By:

Esch, Robert;
Merkl, Rainer

Publication type:

Article

Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis.

Published in:

Protein Science: A Publication of the Protein Society, 2023, v. 32, n. 1, p. 1, doi. 10.1002/pro.4536

By:

Kinateder, Thomas;
Drexler, Lukas;
Straub, Kristina;
Merkl, Rainer;
Sterner, Reinhard

Publication type:

Article

Modelling the evolution of the archaeal tryptophan synthase.

Published in:

BMC Evolutionary Biology, 2007, v. 7, p. 1, doi. 10.1186/1471-2148-7-59

By:

Merkl, Rainer

Publication type:

Article

AGeNNT: annotation of enzyme families by means of refined neighborhood networks.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1689-6

By:

Kandlinger, Florian;
Plach, Maximilian G.;
Merkl, Rainer

Publication type:

Article

Long-Term Persistence of Bi-functionality Contributes to the Robustness of Microbial Life through Exaptation.

Published in:

PLoS Genetics, 2016, v. 12, n. 1, p. 1, doi. 10.1371/journal.pgen.1005836

By:

Plach, Maximilian G.;
Reisinger, Bernd;
Sterner, Reinhard;
Merkl, Rainer

Publication type:

Article

CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data.

Published in:

Bioinformatics, 2013, v. 29, n. 23, p. 3029, doi. 10.1093/bioinformatics/btt519

By:

Janda, Jan-Oliver;
Meier, Andreas;
Merkl, Rainer

Publication type:

Article

Statistical Evidence for a Biochemical Pathway of Natural, Sequence-Targeted G/C to C/G Transversion Mutagenesis in Haemophilus Influenzae Rd.

Published in:

Nucleic Acids Research, 1996, v. 24, n. 21, p. 4146, doi. 10.1093/nar/24.21.4146

By:

Merkl, Rainer;
Fritz, Hans-Joachim

Publication type:

Article

PROCOS: Computational analysis of protein-protein complexes.

Published in:

Journal of Computational Chemistry, 2011, v. 32, n. 12, p. 2575, doi. 10.1002/jcc.21837

By:

Fink, Florian;
Hochrein, Jochen;
Wolowski, Vincent;
Merkl, Rainer;
Gronwald, Wolfram

Publication type:

Article

Evidence for the preferential reuse of sub‐domain motifs in primordial protein folds.

Published in:

Proteins, 2021, v. 89, n. 9, p. 1167, doi. 10.1002/prot.26089

By:

Heizinger, Leonhard;
Merkl, Rainer

Publication type:

Article

Prediction of quaternary structure by analysis of hot spot residues in protein‐protein interfaces: the case of anthranilate phosphoribosyltransferases.

Published in:

Proteins, 2019, v. 87, n. 10, p. 815, doi. 10.1002/prot.25744

By:

Schlee, Sandra;
Straub, Kristina;
Schwab, Thomas;
Kinateder, Thomas;
Merkl, Rainer;
Sterner, Reinhard

Publication type:

Article

Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex.

Published in:

Proteins, 2017, v. 85, n. 2, p. 312, doi. 10.1002/prot.25225

By:

Holinski, Alexandra;
Heyn, Kristina;
Merkl, Rainer;
Sterner, Reinhard

Publication type:

Article

Prescont: Predicting protein-protein interfaces utilizing four residue properties.

Published in:

Proteins, 2012, v. 80, n. 1, p. 154, doi. 10.1002/prot.23172

By:

Zellner, Hermann;
Staudigel, Martin;
Trenner, Thomas;
Bittkowski, Meik;
Wolowski, Vincent;
Icking, Christian;
Merkl, Rainer

Publication type:

Article

Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes.

Published in:

BMC Genomics, 2012, v. 13, n. 1, p. 144, doi. 10.1186/1471-2164-13-144

By:

Hain, Torsten;
Ghai, Rohit;
Billion, Andrï¿½;
Tobias Kuenne, Carsten;
Steinweg, Christiane;
Izar, Benjamin;
Mohamed, Walid;
Abu Mraheil, Mobarak;
Domann, Eugen;
Schaffrath, Silke;
Kï¿½rst, Uwe;
Goesmann, Alexander;
Oehm, Sebastian;
Pï¿½hler, Alfred;
Merkl, Rainer;
Vorwerk, Sonja;
Glaser, Philippe;
Garrido, Patricia;
Rusniok, Christophe;
Buchrieser, Carmen

Publication type:

Article

An assessment of catalytic residue 3D ensembles for the prediction of enzyme function.

Published in:

BMC Bioinformatics, 2015, v. 16, p. 1, doi. 10.1186/s12859-015-0807-6

By:

Žváček, Clemens;
Friedrichs, Gerald;
Heizinger, Leonhard;
Merkl, Rainer

Publication type:

Article

Rosetta design with co-evolutionary information retains protein function.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 1, p. 1, doi. 10.1371/journal.pcbi.1008568

By:

Schmitz, Samuel;
Ertelt, Moritz;
Merkl, Rainer;
Meiler, Jens

Publication type:

Article

Corrigendum: Dimerization Determines Substrate Specificity of a Bacterial Prenyltransferase.

Published in:

ChemBioChem, 2012, v. 13, n. 12, p. 1710, doi. 10.1002/cbic.201200473

By:

Peterhoff, David;
Zellner, Hermann;
Guldan, Harald;
Merkl, Rainer;
Sterner, Reinhard;
Babinger, Patrick

Publication type:

Article

Dimerization Determines Substrate Specificity of a Bacterial Prenyltransferase.

Published in:

ChemBioChem, 2012, v. 13, n. 9, p. 1297, doi. 10.1002/cbic.201200127

By:

Peterhoff, David;
Zellner, Hermann;
Guldan, Harald;
Merkl, Rainer;
Sterner, Reinhard;
Babinger, Patrick

Publication type:

Article

A Fast and Precise Approach for Computational Saturation Mutagenesis and its Experimental Validation by Using an Artificial (βα).

Published in:

ChemBioChem, 2011, v. 12, n. 10, p. 1544, doi. 10.1002/cbic.201100051

By:

Fischer, Andre;
Seitz, Tobias;
Lochner, Adriane;
Sterner, Reinhard;
Merkl, Rainer;
Bocola, Marco

Publication type:

Article

Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y.

Published in:

Journal of Cell Biology, 2010, v. 190, n. 5, p. 777, doi. 10.1083/jcb.201002043

By:

Wiedemann, Sonja M.;
Mildner, Silke N.;
Bönisch, Clemens;
Israel, Lars;
Maiser, Andreas;
Matheisl, Sarah;
Straub, Tobias;
Merkl, Rainer;
Leonhardt, Heinrich;
Kremmer, Elisabeth;
Schermelleh, Lothar;
Hake, Sandra B.

Publication type:

Article

Identification of the retinoschisin-binding site on the retinal Na/K-ATPase.

Published in:

PLoS ONE, 2019, v. 14, n. 5, p. 1, doi. 10.1371/journal.pone.0216320

By:

Plössl, Karolina;
Straub, Kristina;
Schmid, Verena;
Strunz, Franziska;
Wild, Jens;
Merkl, Rainer;
Weber, Bernhard H. F.;
Friedrich, Ulrike

Publication type:

Article

H2rs: Deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments.

Published in:

BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2105-15-118

By:

Janda, Jan-Oliver;
Popal, Ajmal;
Bauer, Jochen;
Busch, Markus;
Klocke, Michael;
Spitzer, Wolfgang;
Keller, Jörg;
Merkl, Rainer

Publication type:

Article

TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-54

By:

Fischer, André;
Enkler, Nils;
Neudert, Gerd;
Bocola, Marco;
Sterner, Reinhard;
Merkl, Rainer

Publication type:

Article

H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-151

By:

Merkl, Rainer;
Zwick, Matthias

Publication type:

Article

Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites.

Published in:

2004

By:

Meinicke, Peter;
Tech, Maike;
Morgenstern, Burkhard;
Merkl, Rainer

Publication type:

Case Study

SIGI: score-based identification of genomic islands.

Published in:

BMC Bioinformatics, 2004, v. 5, p. 22, doi. 10.1186/1471-2105-5-22

By:

Merkl, Rainer

Publication type:

Article

Umwandlung einer Anthranilatsynthase in eine Isochorismatsynthase: Implikationen für die Evolution von Chorismat-umsetzenden Enzymen.

Published in:

Angewandte Chemie, 2015, v. 127, n. 38, p. 11423, doi. 10.1002/ange.201505063

By:

Plach, Maximilian G.;
Löffler, Patrick;
Merkl, Rainer;
Sterner, Reinhard

Publication type:

Article

Nutzung natürlicher Proteinsymmetrie zum Design lichtschaltbarer Enzyminhibitoren.

Published in:

Angewandte Chemie, 2014, v. 126, n. 2, p. 606, doi. 10.1002/ange.201307207

By:

Reisinger, Bernd;
Kuzmanovic, Natascha;
Löffler, Patrick;
Merkl, Rainer;
König, Burkhard;
Sterner, Reinhard

Publication type:

Article

Chorismate mutase of Thermus thermophilus is a monofunctional AroH class enzyme inhibited by tyrosine.

Published in:

Archives of Microbiology, 2004, v. 181, n. 3, p. 195, doi. 10.1007/s00203-003-0639-z

By:

Helmstaedt, Kerstin;
Heinrich, Gabriele;
Merkl, Rainer;
Braus, Gerhard H.

Publication type:

Article

Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 3, p. 1239, doi. 10.1093/nar/gky1203

By:

Schwartz, Uwe;
Németh, Attila;
Diermeier, Sarah;
Exler, Josef H;
Hansch, Stefan;
Maldonado, Rodrigo;
Heizinger, Leonhard;
Merkl, Rainer;
Längst, Gernot

Publication type:

Article

TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning.

Published in:

Genome Biology, 2014, v. 15, n. 12, p. 536, doi. 10.1186/s13059-014-0536-6

By:

Diermeier, Sarah;
Kolovos, Petros;
Heizinger, Leonhard;
Schwartz, Uwe;
Georgomanolis, Theodore;
Zirkel, Anne;
Wedemann, Gero;
Grosveld, Frank;
Knoch, Tobias A;
Merkl, Rainer;
Cook, Peter R;
Längst, Gernot;
Papantonis, Argyris

Publication type:

Article

Turning catalytically inactive human Argonaute proteins into active slicer enzymes.

Published in:

Nature Structural & Molecular Biology, 2013, v. 20, n. 7, p. 814, doi. 10.1038/nsmb.2577

By:

Hauptmann, Judith;
Dueck, Anne;
Harlander, Simone;
Pfaff, Janina;
Merkl, Rainer;
Meister, Gunter

Publication type:

Article

The extended AT-hook is a novel RNA binding motif.

Published in:

RNA Biology, 2015, v. 12, n. 8, p. 864, doi. 10.1080/15476286.2015.1060394

By:

Filarsky, Michael;
Zillner, Karina;
Araya, Ingrid;
Villar-Garea, Ana;
Merkl, Rainer;
Längst, Gernot;
Németh, Attila

Publication type:

Article

Rosetta:MSF:NN: Boosting performance of multi-state computational protein design with a neural network.

Published in:

PLoS ONE, 2021, v. 16, n. 8, p. 1, doi. 10.1371/journal.pone.0256691

By:

Nazet, Julian;
Lang, Elmar;
Merkl, Rainer

Publication type:

Article

Conversion of Anthranilate Synthase into Isochorismate Synthase: Implications for the Evolution of Chorismate-Utilizing Enzymes.

Published in:

Angewandte Chemie International Edition, 2015, v. 54, n. 38, p. 11270, doi. 10.1002/anie.201505063

By:

Plach, Maximilian G.;
Löffler, Patrick;
Merkl, Rainer;
Sterner, Reinhard

Publication type:

Article

Exploiting Protein Symmetry To Design Light-Controllable Enzyme Inhibitors.

Published in:

Angewandte Chemie International Edition, 2014, v. 53, n. 2, p. 595, doi. 10.1002/anie.201307207

By:

Reisinger, Bernd;
Kuzmanovic, Natascha;
Löffler, Patrick;
Merkl, Rainer;
König, Burkhard;
Sterner, Reinhard

Publication type:

Article

Improving thermal and detergent stability of Bacillus stearothermophilus neopullulanase by rational enzyme design.

Published in:

PEDS: Protein Engineering, Design & Selection, 2015, v. 28, p. 147, doi. 10.1093/protein/gzv001

By:

Ece, Selin;
Evran, Serap;
Janda, Jan-Oliver;
Merkl, Rainer;
Sterner, Reinhard

Publication type:

Article