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183 entries « 1 of 4 »

2021

Moore P B, Petrov A, Westhof E, Zirbel C L

Neocles B. Leontis (1955 - 2020) Journal Article

In: Rna, 2021, ISBN: 33452229, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: WESTHOF

Westhof E, Leontis N B

An RNA-centric historical narrative around the Protein Data Bank Journal Article

In: J Biol Chem, 296 , pp. 100555, 2021, ISBN: 33744291, (1083-351X (Electronic) 0021-9258 (Linking) Journal Article Review).

Abstract | Links | BibTeX | Tags: Computational Biology, Databases, modelling, Protein Data Bank, RNA, Structural biology, Unité ARN, WESTHOF

Marszalkowski M, Werner A, Feltens R, Helmecke D, Gossringer M, Westhof E, Hartmann R K

Comparative study on tertiary contacts and folding of RNase P RNAs from a psychrophilic, a mesophilic/radiation-resistant and a thermophilic bacterium Journal Article

In: Rna, 2021, ISBN: 34266994, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

2020

Li B, Cao Y, Westhof E, Miao Z

Advances in RNA 3D Structure Modeling Using Experimental Data Journal Article

In: Front Genet ., 11 (574485), 2020.

Abstract | Links | BibTeX | Tags: 3D shape, chemical probing, RNA structure, RNA-puzzles, structure prediction, Unité ARN, WESTHOF

Wolff P, Villette C, Zumsteg J, Heintz D, Antoine L, Chane-Woon-Ming B, Droogmans L, Grosjean H, Westhof E

Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea Journal Article

In: RNA, 26 (12), pp. 1957-1975, 2020.

Abstract | Links | BibTeX | Tags: (hyper)thermophiles Archaea mass spectrometry modifications tRNA, ARN-MS, ENNIFAR, Unité ARN, WESTHOF

Westhof E, Liang S, Tong X, Ding X, Zheng L, Dai F

Unusual tertiary pairs in eukaryotic tRNA-Ala Journal Article

In: RNA, 26 (11), pp. 1519-1529, 2020.

Abstract | Links | BibTeX | Tags: Ala Gly insects mammals tRNA, Unité ARN, WESTHOF

Trzaska C, Amand S, Bailly C, Leroy C, Marchand V, Duvernois-Berthet E, Saliou J M, Benhabiles H, Werkmeister E, Chassat T, Guilbert R, Hannebique D, Mouray A, Copin M C, Moreau P A, Adriaenssens E, Kulozik A, Westhof E, Tulasne D, Motorin Y, Rebuffat S, Lejeune F

2,6-Diaminopurine as a Highly Potent Corrector of UGA Nonsense Mutations Journal Article

In: Nat Commun, 11 (1), pp. 1509, 2020, ISBN: 32198346.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki J M, Westhof E, Szachniuk M, Miao Z

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools Journal Article

In: Nucleic Acids Res, 48 (2), pp. 576-588, 2020, ISBN: 31799609.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Pernod K, Schaeffer L, Chicher J, Hok E, Rick C, Geslain R, Eriani G, Westhof E, Ryckelynck M, Martin F

The Nature of the Purine at Position 34 in tRNAs of 4-codon Boxes Is Correlated With Nucleotides at Positions 32 and 38 to Maintain Decoding Fidelity Journal Article

In: Nucleic Acids Res, 48 (11), pp. 6170-6183, 2020, ISBN: 32266934.

Abstract | Links | BibTeX | Tags: ERIANI, PPSE, RYCKELYNCK, Unité ARN, WESTHOF

Miao Z, Adamiak R W, Antczak M, Boniecki M J, Bujnicki J M, Chen S J, Cheng C Y, Cheng Y, Chou F C, Das R, Dokholyan N V, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann T H, Piatkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Wang J, Watkins A M, Wiedemann J, Xiao Y, Xu X, Yesselman J D, Zhang D, Zhang Y, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Zyla A, Ren A, Batey R T, Golden B L, Huang L, Lilley D M, Liu Y, Patel D J, Westhof E

RNA-Puzzles Round IV: 3D Structure Predictions of Four Ribozymes and Two Aptamers Journal Article

In: RNA, 26 (8), pp. 982-995, 2020, ISBN: 32371455.

Abstract | Links | BibTeX | Tags: RNA structure aptamer modeing prediction ribozyme, Unité ARN, WESTHOF

2019

Rozov A, Khusainov I, Omari K El, Duman R, Mykhaylyk V, Yusupov M, Westhof E, Wagner A, Yusupova G

Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction Journal Article

In: Nat Commun, 10 (1), pp. 2519, 2019, ISBN: 31175275.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Westhof E, Yusupov M, Yusupova G

The multiple flavors of GoU pairs in RNA Journal Article

In: J Mol Recognit, pp. e2782, 2019, ISBN: 31033092.

Abstract | Links | BibTeX | Tags: GoU pair anticodon codon mRNA miscoding ribosome tRNA tautomer, Unité ARN, WESTHOF

Westhof E

Pseudouridines or how to draw on weak energy differences Journal Article

In: Biochem Biophys Res Commun, 520 (4), pp. 702-704, 2019, ISBN: 31761086.

Abstract | Links | BibTeX | Tags: RNA, Unité ARN, WESTHOF

Shcherbakov D, Teo Y, Boukari H, Cortes-Sanchon A, Mantovani M, Osinnii I, Moore J, Juskeviciene R, Brilkova M, Duscha S, Kumar H S, Laczko E, Rehrauer H, Westhof E, Akbergenov R, Böttger E C

Ribosomal mistranslation leads to silencing of the unfolded protein response and increased mitochondrial biogenesis Journal Article

In: Commun Biol, 2 , pp. 381, 2019, ISBN: 31637312.

Abstract | Links | BibTeX | Tags: Protein folding Protein transport Transcriptomics, Unité ARN, WESTHOF

Antoine L, Wolff P, Westhof E, Romby P, Marzi S

Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS Journal Article

In: Biochimie, 164 , pp. 60-69, 2019, ISBN: 31295507.

Abstract | Links | BibTeX | Tags: 2D gel isolation Staphylococcus aureus nanoLC/MSMS post-transcriptional tRNA modifications, ARN-MS, ENNIFAR, ROMBY, Unité ARN, WESTHOF

2018

Tosar J P, Gámbaro F, Darré L, Pantano S, Westhof E, Cayota A

Dimerization confers increased stability to nucleases in 5' halves from glycine and glutamic acid tRNAs Journal Article

In: Nucleic Acids Res, 46 (17), pp. 9081-9093, 2018, ISBN: 29893896.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Reinharz V, Soulé A, Westhof E, Waldispühl J, Denise A

Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families Journal Article

In: Nucleic Acids Res, 46 (8), pp. 3841-3851, 2018, ISBN: 29608773.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Patel D, Westhof E

Editorial overview: Protein nucleic acid interactions: order, ambiguities and disorder in recognition and complex formation between proteins and nucleic acids Journal Article

In: Curr Opin Struct Biol, 53 , pp. vi-viii, 2018, ISBN: 30553297.

Links | BibTeX | Tags: Unité ARN, WESTHOF

Hoernes T P, Faserl K, Juen M A, Kremser J, Gasser C, Fuchs E, Shi X, Siewert A, Lindner H, Kreutz C, Micura R, Joseph S, Höbartner C, Westhof E, Hüttenhofer A, Erlacher M D

Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions Journal Article

In: Nat Commun, 9 (1), pp. 4865, 2018, ISBN: 30451861.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Rozov A, Wolff P, Grosjean H, Yusupov M, Yusupova G, Westhof E

Tautomeric G*U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria Journal Article

In: Nucleic Acids Res, 46 (14), pp. 7425-7435, 2018, ISBN: 29931292.

Abstract | Links | BibTeX | Tags: ENNIFAR, Unité ARN, WESTHOF

Hosseini M, Roy P, Sissler M, Zirbel C L, Westhof E, Leontis N

How to fold and protect mitochondrial ribosomal RNA with fewer guanines Journal Article

In: Nucleic Acids Res, 46 (20), pp. 10946-10968, 2018, ISBN: 30215760.

Abstract | Links | BibTeX | Tags: SISSLER, Unité ARN, WESTHOF

Akbergenov R, Duscha S, Fritz A K, Juskeviciene R, Oishi N, Schmitt K, Shcherbakov D, Teo Y, Boukari H, Freihofer P, Isnard-Petit P, Oettinghaus B, Frank S, Thiam K, Rehrauer H, Westhof E, Schacht J, Eckert A, Wolfer D, Böttger E C

Mutant MRPS5 affects mitoribosomal accuracy and confers stress-related behavioral alterations Journal Article

In: EMBO Rep, 19 (11), pp. e46193, 2018, ISBN: 30237157.

Abstract | Links | BibTeX | Tags: aging disease misreading mitochondria protein synthesis, Unité ARN, WESTHOF

2017

Sissler M, González-Serrano L E, Westhof E

Recent Advances in Mitochondrial Aminoacyl-tRNA Synthetases and Disease Journal Article

In: Trends Mol Med, 23 (8), pp. 693-708, 2017, ISBN: 28716624.

Abstract | Links | BibTeX | Tags: aminoacyl-tRNA synthetase central nervous system mitochondrial disease mitochondrial translation moonlighting proteins unfolded protein response, SISSLER, Unité ARN, WESTHOF

Miao Z, Westhof E

RNA Structure: Advances and Assessment of 3D Structure Prediction. Journal Article

In: Annu Rev Biophys, 46 , pp. 483-503, 2017, ISBN: 28375730.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Miao Z, Adamiak R W, Antczak M, Batey R T, Becka A J, Biesiada M, Boniecki M J, Bujnicki J, Chen S J, Cheng C Y, Chou F C, Ferré-D'Amaré A R, Das R, Dawson W K, Feng D, Dokholyan N V, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Lach G E, Major F, Mann T H, Magnus M, Pachulska-Wieczorek K, Patel D J, Piccirilli J A, Popenda M, Purzycka K J, Ren A, Rice G M, Santalucia Jr. J, Sarzynska J, Szachniuk M, Tandon A, Trausch J J, Tian S, Wang J, Weeks K M, 2nd. B Williams, Xiao Y, Xu X, Zhang D, Zok T, Westhof E

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. Journal Article

In: RNA, 23 (5), pp. 655-672, 2017, ISBN: 28138060.

Abstract | Links | BibTeX | Tags: 3D prediction X-ray structures bioinformatics force fields models structure quality, Unité ARN, WESTHOF

Lai L B, Tanimoto A, Lai S M, Chen W Y, Marathe I A, Westhof E, Wysocki V H, Gopalan V

A novel double kink-turn module in euryarchaeal RNase P RNAs. Journal Article

In: Nucleic Acids Res, 45 (12), pp. 7432-7440, 2017, ISBN: 28525600.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Fernandez-Millan P, Autour A, Ennifar E, Westhof E, Ryckelynck M

Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI Journal Article

In: RNA, 23 (12), pp. 1788-1795, 2017, ISBN: 28939697.

Abstract | Links | BibTeX | Tags: DFHBI Spinach crystal structure fluorescence fluorogenic RNA aptamer, ENNIFAR, RYCKELYNCK, Unité ARN, WESTHOF

Carapito R, Konantz M, Paillart J C, Miao Z, Pichot A, Leduc M S, Yang Y, Bergstrom K L, Mahoney D H, Shardy D L, Alsaleh G, Naegely L, Kolmer A, Paul N, Hanauer A, Rolli V, Müller J S, Alghisi E, Sauteur L, Macquin C, Morlon A, Sancho C S, Amati-Bonneau P, Procaccio V, Mosca-Boidron A L, Marle N, Osmani N, Lefebvre O, Goetz J G, Unal S, Akarsu N A, Radosavljevic M, Chenard M P, Rialland F, Grain A, Béné M C, Eveillard M, Vincent M, Guy J, Faivre L, Thauvin-Robinet C, Thevenon J, Myers K, Fleming M D, Shimamura A, Bottollier-Lemallaz E, Westhof E, Lengerke C, Isidor B, Bahram S

Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond-like features Journal Article

In: J Clin Invest, 127 (11), pp. 4090-4103, 2017, ISBN: 28972538.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

2016

Westhof E

Perspectives and Pitfalls in Nucleic Acids Crystallography Book Chapter

In: Ennifar, E (Ed.): Nucleic Acid Crystallography: Methods and Protocols, 1320 , pp. 3-8, Humana Press, NY, 2016, ISBN: 26227033.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Rozov A, Westhof E, Yusupov M, Yusupova G

The ribosome prohibits the G•U wobble geometry at the first position of the codon-anticodon helix. Journal Article

In: Nucleic Acids Res, 44 (13), pp. 6434-6441, 2016, ISBN: 27174928.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Rozov A, Demeshkina N, Khusainov I, Westhof E, Yusupov M, Yusupova G

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code. Journal Article

In: Nat Commun, 21 (7), pp. 10457, 2016, ISBN: 26791911.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Miao Z, Westhof E

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database. Journal Article

In: Nucleic Acids Res, 44 (W1), pp. W562-W567, 2016, ISBN: 27084949.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Miao Z, Cao Y

Quantifying side-chain conformational variations in protein structure. Journal Article

In: Sci Rep, 6 , pp. 37024, 2016, ISBN: 27845406.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Grosjean H, Westhof E

An integrated, structure- and energy-based view of the genetic code. Journal Article

In: Nucleic Acids Res, 44 (17), pp. 8020-8040, 2016, ISBN: 27448410.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

D'Ascenzo L, Auffinger P

Anions in Nucleic Acid Crystallography Book Chapter

In: Ennifar, E (Ed.): Nucleic Acid Crystallography: Methods and Protocols, 1320 , pp. 337-351, Humana Press, NY, 2016, ISBN: 26227054.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Autour A, Westhof E, Ryckelynck M

iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications. Journal Article

In: Nucleic Acids Res, 44 (6), pp. 2491-2500, 2016, ISBN: 26932363.

Abstract | Links | BibTeX | Tags: RYCKELYNCK, Unité ARN, WESTHOF

Rozov A, Demeshkina N, Westhof E, Yusupov M, Yusupova G

New Structural Insights into Translational Miscoding. Journal Article

In: Trends Biochem Sci, 41 (9), pp. 798-814, 2016, ISBN: 27372401.

Abstract | Links | BibTeX | Tags: crystallography decoding ribosome structure translation, Unité ARN, WESTHOF

Costa M, Walbott H, Monachello D, Westhof E, Michel F

Crystal structures of a group II intron lariat primed for reverse splicing. Journal Article

In: Science, 354 (6316), pp. aaf9258, 2016, ISBN: 27934709.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

2015

Westhof E

RNA structure from deep sequencing. Journal Article

In: Nat Biotechnol, 33 (9), pp. 928-929, 2015, ISBN: 26348961.

Links | BibTeX | Tags: Unité ARN, WESTHOF

Westhof E

Twenty years of RNA crystallography. Journal Article

In: RNA, 21 (4), pp. 486-487, 2015, ISBN: 25780106.

Links | BibTeX | Tags: Unité ARN, WESTHOF

Rozov A, Demeshkina N, Westhof E, Yusupov M, Yusupova G

Structural insights into the translational infidelity mechanism. Journal Article

In: Nat Commun, 6 , pp. 7251, 2015, ISBN: 26037619.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Miao Z, Westhof E

A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs. Journal Article

In: PLoS Comput Biol, 11 (12), pp. e1004639, 2015, ISBN: 26681179.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Miao Z, Westhof E

Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score. Journal Article

In: Nucleic Acids Res, 43 (11), pp. 5340-5351, 2015, ISBN: 25940624.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

D'Ascenzo L, Auffinger P

106 Ion-π interactions in biomolecular systems. Journal Article

In: J Biomol Struct Dyn, 33 (Suppl 1), pp. 67, 2015, ISBN: 26103317.

Links | BibTeX | Tags: Unité ARN, WESTHOF

Ryckelynck M, Baudrey S, Rick C, Marin A, Coldren F, Westhof E, Griffiths A D

Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions. Journal Article

In: RNA, 21 (3), pp. 458-469, 2015, ISBN: 25605963.

Abstract | Links | BibTeX | Tags: RNA droplet-based microfluidics high-throughput screening in vitro evolution ribozymes, RYCKELYNCK, Unité ARN, WESTHOF

Miao Z, Adamiak R W, Blanchet M F, Boniecki M, Bujnicki J M, Chen S J, Cheng C, Chojnowski G, Chou F C, Cordero P, Cruz J A, Ferré-D'amaré A R, Das R, Ding F, Dokholyan N V, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann T H, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka K J, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. Journal Article

In: RNA, 21 (6), pp. 1066-1084, 2015, ISBN: 25883046.

Abstract | Links | BibTeX | Tags: 3D prediction X-ray structures bioinformatics force fields models structure quality, Unité ARN, WESTHOF

D'Ascenzo L, Auffinger P

A comprehensive classification and nomenclature of carboxyl-carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems. Journal Article

In: Acta Crystallogr B Struct Sci Cryst Eng Mater, 71 (Pt 2), pp. 164-175, 2015, ISBN: 25827369.

Abstract | Links | BibTeX | Tags: biomolecular systems crystal engineering pharmaceuticals supramolecular motifs, Unité ARN, WESTHOF

2014

Westhof E, Yusupov M, Yusupova G

Recognition of Watson-Crick base pairs: constraints and limits due to geometric selection and tautomerism Journal Article

In: F1000Prime Rep, 6 , pp. 19, 2014, ISBN: 24765524.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Westhof E

Isostericity and tautomerism of base pairs in nucleic acids. Journal Article

In: FEBS Lett, 588 (15), pp. 2464-2469, 2014, ISBN: 24950426.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

Ren A, Košutić M, Rajashankar K R, Frener M, Santner T, Westhof E, Micura R, Patel D J

In-line alignment and Mg(2+) coordination at the cleavage site of the env22 twister ribozyme. Journal Article

In: Nat Commun, 5 , pp. 5534, 2014, ISBN: 25410397.

Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF

183 entries « 1 of 4 »