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187 entries « 1 of 4 »

2022

Westhof Eric

Data, data, burning deep, in the forests of the net Journal Article

In: Biochem Biophys Res Commun, vol. 633, pp. 42-44, 2022, ISSN: 1090-2104.

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

Tong Xiaoling, Han Min-Jin, Lu Kunpeng, Tai Shuaishuai, Liang Shubo, Liu Yucheng, Hu Hai, Shen Jianghong, Long Anxing, Zhan Chengyu, Ding Xin, Liu Shuo, Gao Qiang, Zhang Bili, Zhou Linli, Tan Duan, Yuan Yajie, Guo Nangkuo, Li Yan-Hong, Wu Zhangyan, Liu Lulu, Li Chunlin, Lu Yaru, Gai Tingting, Zhang Yahui, Yang Renkui, Qian Heying, Liu Yanqun, Luo Jiangwen, Zheng Lu, Lou Jinghou, Peng Yunwu, Zuo Weidong, Song Jiangbo, He Songzhen, Wu Songyuan, Zou Yunlong, Zhou Lei, Cheng Lan, Tang Yuxia, Cheng Guotao, Yuan Lianwei, He Weiming, Xu Jiabao, Fu Tao, Xiao Yang, Lei Ting, Xu Anying, Yin Ye, Wang Jian, Monteiro Antónia, Westhof Eric, Lu Cheng, Tian Zhixi, Wang Wen, Xiang Zhonghuai, Dai Fangyin

High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation Journal Article

In: Nat Commun, vol. 13, no. 1, pp. 5619, 2022, ISSN: 2041-1723.

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

Sosnowski P., Tidu A., Eriani G., Westhof E., Martin F.

Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses Journal Article

In: Rna, vol. 28, iss. 5, pp. 729-741, 2022, ISBN: 35236777, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).

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

Westhof E., Thornlow B., Chan P. P., Lowe T. M.

Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures Journal Article

In: Nucleic Acids Res, vol. 50, iss. 5, pp. 4100-4112, 2022, ISBN: 35380696, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article).

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

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, vol. 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 ., vol. 11, no. 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, vol. 26, no. 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, vol. 26, no. 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, vol. 11, no. 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, vol. 48, no. 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, vol. 48, no. 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, vol. 26, no. 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, vol. 10, no. 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, vol. 520, no. 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, vol. 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, vol. 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, vol. 46, no. 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, vol. 46, no. 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, vol. 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, vol. 9, no. 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, vol. 46, no. 14, pp. 7425-7435, 2018, ISBN: 29931292.

Abstract | Links | BibTeX | Tags: ARN-MS, 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, vol. 46, no. 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, vol. 19, no. 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, vol. 23, no. 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, vol. 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, vol. 23, no. 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, vol. 45, no. 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, vol. 23, no. 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, vol. 127, no. 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, vol. 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, vol. 44, no. 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, vol. 21, no. 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, vol. 44, no. 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, vol. 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, vol. 44, no. 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, vol. 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, vol. 44, no. 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, vol. 41, no. 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, vol. 354, no. 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, vol. 33, no. 9, pp. 928-929, 2015, ISBN: 26348961.

Links | BibTeX | Tags: Unité ARN, WESTHOF

Westhof E

Twenty years of RNA crystallography. Journal Article

In: RNA, vol. 21, no. 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, vol. 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, vol. 11, no. 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, vol. 43, no. 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, vol. 33, no. 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, vol. 21, no. 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, vol. 21, no. 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

187 entries « 1 of 4 »