Ecosyste.ms: Papers

10.7554/eLife.60265

The cryo-EM structure of the human uromodulin filament core reveals a unique assembly mechanism
Cited by: 20
Author(s): Jessica J. Stanisich, Dawid Zyla, Pavel Afanasyev, Jianlin Xu, Anne Kipp, Eric Olinger, Olivier Devuyst, Martin Pilhofer, Daniel Boehringer, Rudi Glockshuber
Software Mentions: 6
Published: about 4 years ago

10.1107/S1399004714028132

FEM: feature-enhanced map
Cited by: 155
Author(s): Pavel V. Afonine, Nigel W. Moriarty, Marat Mustyakimov, Oleg Sobolev, Thomas C. Terwilliger, Dušan Turk, Alexandre Urzhumtsev, Paul D. Adams
Software Mentions: 5
Published: over 9 years ago

10.1107/S2059798318006551

Real-space refinement in<i>PHENIX</i>for cryo-EM and crystallography
Cited by: 1,815
Author(s): Pavel V. Afonine, Billy K. Poon, Randy J. Read, Oleg Sobolev, Thomas C. Terwilliger, Alexandre Urzhumtsev, Paul D. Adams
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0240932

Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1
Cited by: 27
Author(s): Guillaume Gaullier, Genevieve Roberts, Uma M. Muthurajan, Samuel Bowerman, Johannes Rudolph, Jyothi Mahadevan, Asmita Jha, Purushka S. Rae, Karolin Luger
Software Mentions: 5
Published: almost 4 years ago

10.1107/S2059798318002425

<i>ISOLDE</i>: a physically realistic environment for model building into low-resolution electron-density maps
Cited by: 933
Author(s): Tristan I. Croll
Software Mentions: 5
Published: over 6 years ago

10.18632/oncotarget.25218

Comprehensive identification of long noncoding RNAs in colorectal cancer
Cited by: 15
Author(s): Eric James de Bony, Martin Bizet, Olivier Van Grembergen, Bouchra Hassabi, Emilie Calonne, Pascale Putmans, Gianluca Bontempi, François Fuks
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.46070

Large protein organelles form a new iron sequestration system with high storage capacity
Cited by: 83
Author(s): Tobias W. Giessen, Benjamin J. Orlando, Andrew A Verdegaal, Melissa G. Chambers, Jules Gardener, David C. Bell, Gabriel Birrane, Maofu Liao, Pamela A. Silver
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-31850-3

Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA
Cited by: 31
Author(s): Satabdi Mishra, Tofayel Ahmed, Anu Tyagi, Jing Shi, Shashi Bhushan
Software Mentions: 4
Published: about 6 years ago

10.1126/sciadv.abg9923

Structure of the mycobacterial ESX-5 type VII secretion system pore complex
Cited by: 38
Author(s): Katherine S. H. Beckham, Christina Ritter, Grzegorz Chojnowski, Daniel S. Ziemianowicz, Edukondalu Mullapudi, Mandy Rettel, Mikhail M. Savitski, Simon A. Mortensen, Jan Kosiński, Matthias Wilmanns
Software Mentions: 4
Published: about 3 years ago

10.1107/S2059798320015879

<i>CERES</i>: a cryo-EM re-refinement system for continuous improvement of deposited models
Cited by: 11
Author(s): Dorothée Liebschner, Pavel V. Afonine, Nigel W. Moriarty, Billy K. Poon, Vincent B. Chen, Paul D. Adams
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.38888

Structural principles of SNARE complex recognition by the AAA+ protein NSF
Cited by: 68
Author(s): K. Ian White, Minglei Zhao, Ucheor B. Choi, Richard A. Pfuetzner, Axel T. Brunger
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.32481

Molecular structure of human KATP in complex with ATP and ADP
Cited by: 127
Author(s): Kenneth Pak Kin Lee, Jue Chen, Roderick MacKinnon
Software Mentions: 4
Published: over 6 years ago

10.1126/sciadv.aax8286

Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunity
Cited by: 53
Author(s): Ni Tien, Fang Jiao, Xiulian Yu, Saša Aden, Lucy Ginger, Sophie I. Williams, Fangfang Bai, Vojtěch Pražák, Dimple Karia, Phillip J. Stansfeld, Peijun Zhang, George P. Munson, Gregor Anderluh, Simon Scheuring, R.J.C. Gilbert
Software Mentions: 4
Published: over 4 years ago

10.1107/S2059798318009324

New tools for the analysis and validation of cryo-EM maps and atomic models
Cited by: 536
Author(s): Pavel V. Afonine, Bruno P. Klaholz, Nigel W. Moriarty, Billy K. Poon, Oleg V. Sobolev, Thomas C. Terwilliger, Paul D. Adams, Alexandre Urzhumtsev
Software Mentions: 4
Published: about 6 years ago

10.1107/S2052252519007619

<i>Namdinator</i> – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps
Cited by: 242
Author(s): Rune T. Kidmose, Jonathan Juhl, Poul Nissen, Thomas Boesen, Jesper Lykkegaard Karlsen, Bjørn Panyella Pedersen
Software Mentions: 3
Published: about 5 years ago

10.3390/s16071132

On Inertial Body Tracking in the Presence of Model Calibration Errors
Cited by: 75
Author(s): Markus Miezal, Bertram Taetz, Gabriele Bleser
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.52983

The structure of the endogenous ESX-3 secretion system
Cited by: 53
Author(s): Nicole Poweleit, Nadine Czudnochowski, Rachel Nakagawa, Donovan Trinidad, Kenan C. Murphy, Christopher M. Sassetti, Oren S. Rosenberg
Software Mentions: 3
Published: over 4 years ago

10.1016/j.molcel.2020.04.012

Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork
Cited by: 100
Author(s): Domagoj Baretić, Michael Jenkyn-Bedford, Valentina Aria, Giuseppe Cannone, Mark Skehel, Joseph T.P. Yeeles
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.50175

Ligand recognition and gating mechanism through three ligand-binding sites of human TRPM2 channel
Cited by: 64
Author(s): Yongyang Huang, Becca Roth, Wei Lü, Juan Du
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.46417

Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
Cited by: 58
Author(s): Gregory M. Martin, Min Woo Sung, Zhongying Yang, Laura Innes, Krishnaswamy Balamurugan, Larry L. David, Craig Yoshioka, Show Ling Shyng
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pbio.3000958

Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome
Cited by: 14
Author(s): Kai Ehrenbolger, Nathan Jespersen, Himanshu Sharma, Yuliya Y. Sokolova, Yuri S. Tokarev, Charles R. Vossbrinck, Jonas Barandun
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.53243

Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation
Cited by: 42
Author(s): Matthew C. Johnson, Justin M. Kollman
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.22086

Molecular architecture of the 90S small subunit pre-ribosome
Cited by: 116
Author(s): Qiaoyan Sun, Xing Zhu, Qiong Jia, Wenling An, Pengfei Lan, Dan Tan, Rongchang Chen, Bing Wang, Sanduo Zheng, Cheng Zhang, Xining Chen, Wei Zhang, Jing Chen, Meng‐Qiu Dong, Keqiong Ye
Software Mentions: 3
Published: over 7 years ago

10.1038/cr.2017.124

A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value
Cited by: 152
Author(s): Changsong Zou, A Chen, Li Xiao, H.-A. Müller, Peter Ache, Georg Haberer, M Zhang, Jia Wei, Ping Deng, Ru Huang, Daniel Lang, Li Feng, Dong Zhan, Xiaoyong Wu, H Zhang, Jennifer Böhm, Ruirui Liu, Lana Shabala, Rainer Hedrich, J-K Zhu
Software Mentions: 3
Published: almost 7 years ago

10.1038/s42003-021-01919-3

High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams
Cited by: 39
Author(s): Koji Kato, Naoyuki Miyazaki, Tasuku Hamaguchi, Yoshiki Nakajima, Fusamichi Akita, Koji Yonekura, Jian‐Ren Shen
Software Mentions: 3
Published: over 3 years ago

10.15252/embj.2018100825

Diverse roles of TssA‐like proteins in the assembly of bacterial type VI secretion systems
Cited by: 34
Author(s): Johannes Schneider, Sergey Nazarov, Ricardo Adaixo, Martina Liuzzo, Peter David Ringel, Henning Stahlberg, Marek Basler
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.59018

Structural ordering of the Plasmodium berghei circumsporozoite protein repeats by inhibitory antibody 3D11
Cited by: 10
Author(s): Iga Kucharska, Elaine Thai, Ananya Srivastava, John L. Rubinstein, Régis Pomès, Jean-Philippe Julien
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41421-021-00259-0

Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis
Cited by: 11
Author(s): Sensen Zhang, Baolei Yuan, Jordy Homing Lam, Jun Zhou, Xuan Zhou, Gerardo Ramos‐Mandujano, Xin‐Xia Tian, Yang Liu, Han Ren, Li Yu, Xin Gao, Maojun Yang
Software Mentions: 2
Published: over 3 years ago

10.3390/molecules26020399

Identification of Phytochemical-Based β-Catenin Nuclear Localization Inhibitor in NSCLC: Differential Targeting Population from Member of Isothiocyanates
Cited by: 9
Author(s): Win Sen Heng, Shiau‐Chuen Cheah
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0136820

Reference Gene Selection for qPCR Analysis in Tomato-Bipartite Begomovirus Interaction and Validation in Additional Tomato-Virus Pathosystems
Cited by: 40
Author(s): A. L. M. Lacerda, Leonardo N. Fonseca, Rosana Blawid, L. S. Boiteux, S. G. Ribeiro, Ana Cristina Miranda Brasileiro
Software Mentions: 2
Published: about 9 years ago

10.15252/embr.201948451

Elucidation of the viral disassembly switch of tobacco mosaic virus
Cited by: 18
Author(s): Félix Weis, Maximilian Beckers, Iris von der Hocht, Carsten Sachse
Software Mentions: 2
Published: about 5 years ago

10.1126/sciadv.aba8381

Architecture of the AP2/clathrin coat on the membranes of clathrin-coated vesicles
Cited by: 68
Author(s): Oleksiy Kovtun, Veronica Kane Dickson, Bernard T. Kelly, David J. Owen, John Briggs
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.46041

Cryo-EM structure of the rhodopsin-Gαi-βγ complex reveals binding of the rhodopsin C-terminal tail to the gβ subunit
Cited by: 50
Author(s): Ching‐Ju Tsai, Jacopo Marino, Ricardo Adaixo, Filip Pamula, J. Muehle, Shoji Maeda, Tilman Flock, Nicholas M. I. Taylor, I. Mohammed, Hugues Matile, Roger Dawson, Xavier Deupí, Henning Stahlberg, Gebhard F. X. Schertler
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.45185

Conformational switches control early maturation of the eukaryotic small ribosomal subunit
Cited by: 32
Author(s): Mirjam Hunziker, Jonas Barandun, Olga Buzovetsky, Caitlin Steckler, Henrik Molina, Sebastian Klinge
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.28384

Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 at 3.7 angstrom resolution
Cited by: 35
Author(s): Luis Miguel Díaz-Santín, Natalya Lukoyanova, Emir Aciyan, Alan C. M. Cheung
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.56862

Mechanical inhibition of isolated Vo from V/A-ATPase for proton conductance
Cited by: 11
Author(s): Jun-ichi Kishikawa, Atsuko Nakanishi, Aya Furuta, Takayuki Kato, Keiichi Namba, Masatada Tamakoshi, Kaoru Mitsuoka, Ken Yokoyama
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.39775

Ligand discrimination and gating in cyclic nucleotide-gated ion channels from apo and partial agonist-bound cryo-EM structures
Cited by: 36
Author(s): Jan Rheinberger, Xiaolong Gao, Philipp A. M. Schmidpeter, Crina M. Nimigean
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.55954

Near-atomic structures of the BBSome reveal the basis for BBSome activation and binding to GPCR cargoes
Cited by: 32
Author(s): Shuang Yang, Kriti Bahl, Hui‐Ting Chou, Jonathan Woodsmith, Ulrich Stelzl, Thomas Walz, Maxence V. Nachury
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.68806

Visualizing formation of the active site in the mitochondrial ribosome
Cited by: 19
Author(s): Viswanathan Chandrasekaran, Nirupa Desai, Nick Burton, Hongxin Yang, Jonathan Price, Eric A. Miska, V. Ramakrishnan
Software Mentions: 2
Published: almost 3 years ago

10.7554/eLife.71188

Analysis of the mechanosensor channel functionality of TACAN
Cited by: 19
Author(s): Yiming Niu, Xiao Tao, George Vaisey, Paul Dominic B. Olinares, Hanan Alwaseem, Brian T. Chait, Roderick MacKinnon
Software Mentions: 2
Published: about 3 years ago

10.7554/eLife.70871

Regulation of human mTOR complexes by DEPTOR
Cited by: 11
Author(s): Matthias Wälchli, Karolin Berneiser, Francesca Mangia, Stefan Imseng, Louise-Marie Craigie, Edward Stuttfeld, Michael N. Hall, Timm Maier
Software Mentions: 2
Published: about 3 years ago

10.7554/eLife.60482

Structure of the bacterial ribosome at 2 Å resolution
Cited by: 125
Author(s): Zoe L Watson, Fred R. Ward, Raphaël Méheust, Omer Ad, Alanna Schepartz, Jillian F. Banfield, Jamie H. D. Cate
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.62611

Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients
Cited by: 57
Author(s): Lakshmi E. Miller-Vedam, Bastian Bräuning, Katerina D. Popova, Nicole T. Schirle Oakdale, Jessica L. Bonnar, J.R. Prabu, Elizabeth A. Boydston, Natalia Sevillano, Matthew J. Shurtleff, Robert M. Stroud, Charles S. Craik, Brenda A. Schulman, Adam Frost, Jonathan S. Weissman
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.ppat.1006607

Structures of foot and mouth disease virus pentamers: Insight into capsid dissociation and unexpected pentamer reassociation
Cited by: 21
Author(s): Nayab Malik, Abhay Kotecha, Sarah Gold, Amin S. Asfor, Jingshan Ren, Juha T. Huiskonen, Tobias J. Tuthill, Elizabeth E. Fry, David I. Stuart
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.25642

The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling
Cited by: 74
Author(s): Ting Su, Jingdong Cheng, Daniel Sohmen, Rickard Hedman, Otto Berninghausen, Gunnar von Heijne, Daniel N. Wilson, Roland Beckmann
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.65703

eIF2B conformation and assembly state regulate the integrated stress response
Cited by: 39
Author(s): Michael Schoof, Morgane Boone, Lan Wang, Rosalie Lawrence, Adam Frost, Peter Walter
Software Mentions: 1
Published: over 3 years ago

10.3390/ani9121076

Transcriptome of Chicken Liver Tissues Reveals the Candidate Genes and Pathways Responsible for Adaptation into Two Different Climatic Conditions
Cited by: 9
Author(s): Himansu Kumar, Asankadyr U. Iskender, Krishnamoorthy Srikanth, Hana Kim, Asankadyr Zhunushov, Hyojun Chooq, Gul Won Jang, Youngjo Lim, Ki Duk Song
Software Mentions: 1
Published: almost 5 years ago

10.1038/s42003-020-01217-4

Apple latent spherical virus structure with stable capsid frame supports quasi-stable protrusions expediting genome release
Cited by: 7
Author(s): Hisashi Naitow, Tasuku Hamaguchi, Saori Maki-Yonekura, Masamichi Isogai, Nobuyuki Yoshikawa, Koji Yonekura
Software Mentions: 1
Published: about 4 years ago

10.1038/s42003-021-02222-x

3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme
Cited by: 3
Author(s): Melisa Lázaro, Roberto Melero, Charlotte Huet, Jorge P. López‐Alonso, Sandra Delgado, Alexandra Dodu, Eduardo M. Bruch, Luciano A. Abriata, P.M. Alzari, Mikel Valle, María‐Natalia Lisa
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0210749

Structure basis of neutralization by a novel site II/IV antibody against respiratory syncytial virus fusion protein
Cited by: 5
Author(s): Qingqing Xie, Zhao Wang, Fengyun Ni, Hong Chen, Jianpeng Ma, Nita Patel, Huanzhang Lü, Ye Liu, Jing-Hui Tian, David C. Flyer, Michael J. Massare, Larry Ellingsworth, Gregory M. Glenn, Gale Smith, Qinghua Wang
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.28560

Structure of RNA polymerase bound to ribosomal 30S subunit
Cited by: 79
Author(s): Gabriel Demo, Aviram Rasouly, Nikita Vasilyev, Vladimir Svetlov, A.B. Loveland, Rubén Díaz-Avalos, Nikolaus Grigorieff, А.A. Коростелев
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-12-313

Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences
Cited by: 65
Author(s): Srinivasan Yegnasubramanian, Zhijin Wu, Michael C. Haffner, David Esopi, Martin J. Aryee, Raghav Badrinath, Tony L. He, James D. Morgan, Benilton Carvalho, Qizhi Zheng, Angelo M. De Marzo, Rafael A. Irizarry, William G. Nelson
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0181240

Emergent multisystemic Enterococcus infection threatens endangered Christmas Island reptile populations
Cited by: 15
Author(s): Karrie Rose, Jessica E Agius, Jane Hall, Peggy Thompson, John‐Sebastian Eden, Mukesh Srivastava, Brendan Tiernan, Cheryl Jenkins, David N. Phalen
Software Mentions: 1
Published: about 7 years ago

10.7554/eLife.54575

A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate
Cited by: 13
Author(s): Ritam Neupane, Vera P. Pisareva, Carlos Fernández Rodríguez, Andrey V. Pisarev, I.S. Fernandez
Software Mentions: 1
Published: over 4 years ago

10.1128/mBio.00818-19

The Structure of an Injectisome Export Gate Demonstrates Conservation of Architecture in the Core Export Gate between Flagellar and Virulence Type III Secretion Systems
Cited by: 48
Author(s): Steven Johnson, Lucas Kuhlen, Justin C. Deme, Patrizia Abrusci, Susan M. Lea
Software Mentions: 1
Published: about 5 years ago

10.1107/S2052252520013482

High-resolution cryo-EM using beam-image shift at 200 keV
Cited by: 13
Author(s): Jennifer N. Cash, Sarah Kearns, Yilai Li, Michael A. Cianfrocco
Software Mentions: 1
Published: almost 4 years ago

10.1017/qrd.2020.16

A 3.4-Å cryo-electron microscopy structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles
Cited by: 9
Author(s): Kaiming Zhang, Shanshan Li, Grigore Pintilie, David Chmielewski, Michael F. Schmid, Graham Simmons, Jing Jin, Wah Chiu
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.7769

Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype
Cited by: 19
Author(s): Kenji Takata, Hiroki Taninaka, Manabu Nonaka, Fumihito Iwase, Taisei Kikuchi, Yoshihisa Suyama, Satoshi Nagai, Nina Yasuda
Software Mentions: 1
Published: almost 5 years ago

10.7554/eLife.38686

Distinct and evolutionary conserved structural features of the human nuclear exosome complex
Cited by: 40
Author(s): Piotr Gerlach, Jan M. Schuller, Fabien Bonneau, J. Basquin, Peter Reichelt, Sebastian Falk, Elena Conti
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.50003

A structural mechanism for phosphorylation-dependent inactivation of the AP2 complex
Cited by: 14
Author(s): Edward A Partlow, Richard W. Baker, Gwendolyn M Beacham, Joshua S. Chappie, Andres E. Leschziner, Gunther Hollopeter
Software Mentions: 1
Published: about 5 years ago

10.3390/v12090953

Structure of the Capsid Size-Determining Scaffold of “Satellite” Bacteriophage P4
Cited by: 12
Author(s): James L. Kizziah, Cynthia M. Rodenburg, Terje Dokland
Software Mentions: 1
Published: about 4 years ago

10.1007/s13238-017-0476-5

Cryo-EM structures of the mammalian endo-lysosomal TRPML1 channel elucidate the combined regulation mechanism
Cited by: 35
Author(s): Sensen Zhang, Ningning Li, Wenwen Zeng, Ning Gao, Maojun Yang
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.ppat.1008263

Cryo-EM structure of the Shigella type III needle complex
Cited by: 32
Author(s): Michele Lunelli, Antje Kamprad, Jörg Bürger, Thorsten Mielke, C.M.T. Spahn, Michael Kolbe
Software Mentions: 1
Published: over 4 years ago

10.7554/eLife.33660

Structure-based membrane dome mechanism for Piezo mechanosensitivity
Cited by: 275
Author(s): Yusong R. Guo, Roderick MacKinnon
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.23687

Mechanism of ribosome rescue by ArfA and RF2
Cited by: 47
Author(s): Gabriel Demo, Egor Svidritskiy, Rohini Madireddy, Rubén Díaz-Avalos, Tim Grant, Nikolaus Grigorieff, Duncan Sousa, А.A. Коростелев
Software Mentions: 1
Published: over 7 years ago