cran: PHENIX | Projects | Ecosyste.ms: Papers

10.1002/pro.3299

Automating tasks in protein structure determination with the clipper python module
Cited by: 6
Author(s): Stuart McNicholas, Tristan I. Croll, Tom Burnley, Colin M. Palmer, Soon Wen Hoh, Huw T. Jenkins, E.J. Dodson, Kevin Cowtan, Jon Agirre
Software Mentions: 10
Published: over 7 years ago

10.1107/S2059798318004576

KAMO: towards automated data processing for microcrystals
Cited by: 174
Author(s): Keitaro Yamashita, Kunio Hirata, Masaki Yamamoto
Software Mentions: 8
Published: over 7 years ago

10.1016/j.molcel.2021.03.041

DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network
Cited by: 28
Author(s): Colin M. Hammond, Hongyu Bao, Ivo A. Hendriks, Massimo Carraro, Alberto García-Nieto, Yanhong Liu, Nazaret Reverón-Gómez, Christos Spanos, Liu Chen, Juri Rappsilber, Michael L. Nielsen, Dinshaw J. Patel, Hongda Huang, Anja Groth
Software Mentions: 8
Published: about 4 years ago

10.1107/S2059798317016035

CCP4i2: the new graphical user interface to theCCP4 program suite
Cited by: 353
Author(s): Liz Potterton, Jon Agirre, Charles Ballard, Kevin Cowtan, E.J. Dodson, Phil Evans, Huw T. Jenkins, Ronan Keegan, Eugene Krissinel, Kyle Stevenson, А. А. Лебедев, Stuart McNicholas, Robert A. Nicholls, M.E.M. Noble, Navraj S. Pannu, Christian Roth, George M. Sheldrick, Pavol Skubák, J.P. Turkenburg, Ville Uski, Frank von Delft, David Waterman, K.S. Wilson, Martyn Winn, Marcin Wojdyr
Software Mentions: 8
Published: over 7 years ago

10.1107/S2059798317007859

Recent developments in theCCP-EMsoftware suite
Cited by: 266
Author(s): Tom Burnley, Colin M. Palmer, Martyn Winn
Software Mentions: 7
Published: about 8 years ago

10.7554/eLife.45403

The dynamic conformational landscape of the protein methyltransferase SETD8
Cited by: 37
Author(s): Shi Chen, Rafal Wiewiora, Fanwang Meng, Nicolas Babault, Anqi Ma, Wenyu Yu, Kun Qian, Hao Hu, Hua Zou, Junyi Wang, Shijie Fan, Gil Blum, Fábio Pittella Silva, Kyle A. Beauchamp, W. Tempel, Hualiang Jiang, Kaixian Chen, R.J. Skene, Y. George Zheng, Peter J. Brown, Jian Jin, Cheng Luo, John D. Chodera, Minkui Luo
Software Mentions: 7
Published: about 6 years ago

10.1107/S2053273319011446

Bayesian machine learning improves single-wavelength anomalous diffraction phasing
Cited by: 10
Author(s): María-José García-Bonete, Gergely Katona
Software Mentions: 7
Published: almost 6 years ago

10.1107/S0907444909052925

PHENIX: a comprehensive Python-based system for macromolecular structure solution
Cited by: 19,578
Author(s): Paul D. Adams, Pavel V. Afonine, G. Bunkóczi, Vincent B. Chen, Ian Davis, Nathaniel Echols, Jeffrey J. Headd, Li Wei Hung, Gary J. Kapral, Ralf W. Grosse‐Kunstleve, Airlie J. McCoy, Nigel W. Moriarty, Robert D. Oeffner, Randy J. Read, David C. Richardson, Jane S. Richardson, Thomas C. Terwilliger, Peter H. Zwart
Software Mentions: 6
Published: over 15 years ago

10.1371/journal.pgen.1009492

A structural signature motif enlightens the origin and diversification of nuclear receptors
Cited by: 8
Author(s): Brice Beinsteiner, Gabriel V. Markov, Stéphane Erb, Yassmine Chebaro, A.G. McEwen, Sarah Cianférani, Vincent Laudet, Dino Moras, I. M. L. Billas
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.ppat.1005815

Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design
Cited by: 97
Author(s): Joseph G. Jardine, Devin Sok, Jean-Philippe Julien, Bryan Briney, Achyut Sarkar, Chi Liang, Erin A. Scherer, Carole J. Henry Dunand, Yumiko Adachi, Devan Diwanji, Jessica Hsueh, Meaghan Jones, Oleksandr Kalyuzhniy, Michael Kubitz, Skye Spencer, Matthias Pauthner, Karen L. Saye-Francisco, Fabian Sesterhenn, Patrick C. Wilson, Denise Galloway, Robyn L. Stanfield, Ian A. Wilson, Dennis R. Burton, William R. Schief
Software Mentions: 6
Published: almost 9 years ago

10.1107/S0907444913000863

New Python-based methods for data processing
Cited by: 92
Author(s): Nicholas K. Sauter, Johan Hattne, Ralf W. Grosse‐Kunstleve, Nathaniel Echols
Software Mentions: 6
Published: about 12 years ago

10.7554/eLife.10150

ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation
Cited by: 50
Author(s): Nataliya Nady, Ankit Gupta, Ziyang Ma, Tomek Swigut, Akiko Koide, Shohei Koide, Joanna Wysocka
Software Mentions: 6
Published: over 9 years ago

10.1140/epjc/s10052-014-2981-5

QCD and strongly coupled gauge theories: challenges and perspectives
Cited by: 407
Author(s): Nora Brambilla, S. Eidelman, P. Foka, Susan Gardner, A. S. Kronfeld, Mark Alford, Reinhard Alkofer, Mathias Butenschoen, Thomas D. Cohen, Johanna Erdmenger, L. Fabbietti, M. Faber, J. L. Goity, B. Ketzer, Huey‐Wen Lin, Felipe J. Llanes-Estrada, Harvey B. Meyer, P. Pakhlov, Elisabetta Pallante, M. I. Polikarpov, H. Sazdjian, Andreas Schmitt, W. M. Snow, Antonio Vairo, R. Vogt, Aleksi Vuorinen, Hartmut Wittig, Peter Arnold, P. Christakoglou, P. Di Nezza, Z. Fodor, Xavier Garcia i Tormo, Roman Höllwieser, M. A. Janik, A. Kalweit, D. Keane, Elias Kiritsis, A. Mischke, R. Mizuk, G. Odyniec, Kyriakos Papadodimas, Antonio Pich, R. Pittau, Jian Qiu, Giulia Ricciardi, Carlos A. Salgado, Kai Schwenzer, N. G. Stefanis, Georg von Hippel, В. И. Захаров
Software Mentions: 6
Published: almost 11 years ago

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: almost 5 years ago

10.1107/S2052252518000519

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering
Cited by: 23
Author(s): Michael E. Wall
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.02978

The pseudo GTPase CENP-M drives human kinetochore assembly
Cited by: 107
Author(s): Federica Basilico, Stefano Maffini, John R. Weir, Daniel Prumbaum, Ana M. Rojas, Tomasz Zimniak, De Antoni A, Sadasivam Jeganathan, Beate Voss, Suzan van Gerwen, Veronica Krenn, Lucia Massimiliano, Alfonso Valencia, Ingrid R. Vetter, Franz Herzog, Stefan Raunser, Sebastiano Pasqualato, Andrea Musacchio
Software Mentions: 5
Published: about 11 years ago

10.7554/eLife.05421

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals
Cited by: 106
Author(s): Monarin Uervirojnangkoorn, Oliver B. Zeldin, A.Y. Lyubimov, Johan Hattne, Aaron S. Brewster, Nicholas K. Sauter, Axel T. Brunger, William I. Weis
Software Mentions: 5
Published: over 10 years ago

10.1016/j.jbc.2021.101129

In silico and in vitro analysis of an Aspergillus niger chitin deacetylase to decipher its subsite sugar preferences
Cited by: 7
Author(s): Martin Bonin, Lisanne Hameleers, Lea Hembach, Thomas Roret, Stefan Cord‐Landwehr, Gurvan Michel, Bruno M. Moerschbacher
Software Mentions: 5
Published: almost 4 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 6 years ago

10.15252/embj.2020106807

Cryo‐EM structure of native human uromodulin, a zona pellucida module polymer
Cited by: 24
Author(s): A. Stsiapanava, Chenrui Xu, Martina Brunati, Sara Zamora-Caballero, Céline Schaeffer, Marcel Bokhove, Ling Han, Hans Hebert, Marta Carroni, Shigeki Yasumasu, Luca Rampoldi, Bin Wu, Luca Jovine
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.67518

The structure of photosystem I from a high-light-tolerant cyanobacteria
Cited by: 13
Author(s): Zachary Dobson, Safa Ahad, Jackson Vanlandingham, Hila Toporik, Natalie Vaughn, Michael Vaughn, Dewight Williams, Michael Reppert, Petra Fromme, Yuval Mazor
Software Mentions: 5
Published: almost 4 years ago

10.1107/S0021889812017293

Graphical tools for macromolecular crystallography inPHENIX
Cited by: 136
Author(s): Nathaniel Echols, Ralf W. Grosse‐Kunstleve, Pavel V. Afonine, G. Bunkóczi, Vincent B. Chen, Jeffrey J. Headd, Airlie J. McCoy, Nigel W. Moriarty, Randy J. Read, David C. Richardson, Jane S. Richardson, Thomas C. Terwilliger, Paul D. Adams
Software Mentions: 5
Published: about 13 years ago

10.1107/S2059798318003455

Recent developments inMrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment
Cited by: 34
Author(s): Ronan Keegan, Stuart McNicholas, Jens M. H. Thomas, Adam J Simpkin, Felix Šimkovic, Ville Uski, Charles Ballard, Martyn Winn, K.S. Wilson, Daniel J. Rigden
Software Mentions: 5
Published: over 7 years ago

10.1107/S2059798318006551

Real-space refinement inPHENIXfor 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: about 7 years ago

10.1002/2211-5463.12259

Structural flexibility of human α-dystroglycan
Cited by: 12
Author(s): Sonia Covaceuszach, Manuela Bozzi, Maria Giulia Bigotti, Francesca Sciandra, Petr V. Konarev, Andrea Brancaccio, Alberto Cassetta
Software Mentions: 5
Published: about 8 years ago

10.1107/S1399004715009220

From bacterial to human dihydrouridine synthase: automated structure determination
Cited by: 12
Author(s): Fiona Whelan, Huw T. Jenkins, Samuel C. Griffiths, Robert T. Byrne, E.J. Dodson, A.A. Antson
Software Mentions: 5
Published: about 10 years ago

10.1107/S0907444910045749

Overview of theCCP4 suite and current developments
Cited by: 10,663
Author(s): Martyn Winn, Charles Ballard, Kevin Cowtan, E.J. Dodson, Paul Emsley, Phil Evans, Ronan Keegan, Eugene Krissinel, Andrew G. W. Leslie, Airlie J. McCoy, Stuart McNicholas, Garib N. Murshudov, Navraj S. Pannu, E. A. Potterton, Harold R. Powell, Randy J. Read, A.A. Vagin, K.S. Wilson
Software Mentions: 5
Published: over 14 years ago

10.1107/S1399004715007415

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles
Cited by: 14
Author(s): A.H. Van Benschoten, Pavel V. Afonine, Thomas C. Terwilliger, Michael E. Wall, Colin J. Jackson, Nicholas K. Sauter, Paul D. Adams, Alexandre Urzhumtsev, James S. Fraser
Software Mentions: 5
Published: almost 10 years ago

10.1107/S0907444913022750

Phaser.MRage: automated molecular replacement
Cited by: 204
Author(s): G. Bunkóczi, Nathaniel Echols, Airlie J. McCoy, Robert D. Oeffner, Paul D. Adams, Randy J. Read
Software Mentions: 5
Published: almost 12 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 10 years ago

10.1107/S2059798318002425

ISOLDE: 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 7 years ago

10.7554/eLife.51179

Structure of a mitochondrial ATP synthase with bound native cardiolipin
Cited by: 65
Author(s): A. Muhleip, Sarah McComas, Alexey Amunts
Software Mentions: 5
Published: over 5 years ago

10.3389/fmolb.2021.624264

Serial Electron Diffraction Data Processing With diffractem and CrystFEL
Cited by: 7
Author(s): Robert Bücker, Pascal Hogan-Lamarre, R. J. Dwayne Miller
Software Mentions: 5
Published: about 4 years ago

10.1107/S2059798317000031

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode
Cited by: 18
Author(s): Kimberly A. Stanek, Jennifer Patterson-West, Peter S. Randolph, Cameron Mura
Software Mentions: 5
Published: over 8 years ago

10.1038/s41421-018-0027-0

Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity
Cited by: 38
Author(s): Chih Chao Hsu, Dan Zhao, Jiejun Shi, Danni Peng, Haipeng Guan, Yuanyuan Li, Yaling Huang, Hong Wen, Wei Li, Haitao Li, Xiaobing Shi
Software Mentions: 4
Published: about 7 years ago

10.1111/febs.14688

The structure of PghL hydrolase bound to its substrate poly‐γ‐glutamate
Cited by: 2
Author(s): Sneha Ramaswamy, Masooma Rasheed, Carlo F. Morelli, Cinzia Calvio, Brian J. Sutton, Annalisa Pastore
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0080371

Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus
Cited by: 33
Author(s): C. Leyrat, Max Renner, K. Harlos, Jonathan M. Grimes
Software Mentions: 4
Published: over 11 years ago

10.1107/S1399004715011426

From deep TLS validation to ensembles of atomic models built from elemental motions
Cited by: 14
Author(s): Alexandre Urzhumtsev, Pavel V. Afonine, A.H. Van Benschoten, James S. Fraser, Paul D. Adams
Software Mentions: 4
Published: almost 10 years ago

10.1107/S2059798318001353

Gyreandgimble: a maximum-likelihood replacement for Patterson correlation refinement
Cited by: 13
Author(s): Airlie J. McCoy, Robert D. Oeffner, Claudia Millán, Massimo Sammito, Isabel Usón, Randy J. Read
Software Mentions: 4
Published: over 7 years ago

10.1016/j.jmb.2018.06.007

The FapF Amyloid Secretion Transporter Possesses an Atypical Asymmetric Coiled Coil
Cited by: 10
Author(s): Sarah L. Rouse, Fisentzos Stylianou, Howie Wu, Jamie-Lee Berry, Lee Sewell, Rhodri M. L. Morgan, Andrea C. Sauerwein, Steve Matthews
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-52537-3

Structural characterization of the RH1-LZI tandem of JIP3/4 highlights RH1 domains as a cytoskeletal motor-binding motif
Cited by: 19
Author(s): Fernando Vilela, Christophe Velours, Mélanie Chenon, Magali Aumont-Niçaise, Valérie Campanacci, Aurélien Thureau, Olena Pylypenko, Jessica Andréani, P. Llinas, J. Menetrey
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pbio.1002146

The Structure of an NDR/LATS Kinase–Mob Complex Reveals a Novel Kinase–Coactivator System and Substrate Docking Mechanism
Cited by: 45
Author(s): Gergő Gógl, Kyle D. Schneider, Brian J. Yeh, Alam Nashida, Alex N Nguyen Ba, Alan M. Moses, Csaba Hetényi, Attila Reményi, Eric L. Weiss
Software Mentions: 4
Published: about 10 years ago

10.1107/S2059798316001224

Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry
Cited by: 5
Author(s): Blaine H. M. Mooers
Software Mentions: 4
Published: over 9 years ago

10.1107/S1399004713032549

Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D
Cited by: 29
Author(s): Federico Forneris, B. Tom Burnley, Piet Gros
Software Mentions: 4
Published: over 11 years ago

10.1107/S2059798316020234

TheXChemExplorergraphical workflow tool for routine or large-scale protein–ligand structure determination
Cited by: 68
Author(s): T. Krojer, R. Talon, Nicholas M. Pearce, P. Collins, A. Douangamath, J. Brandão-Neto, A. Dias, Brian D. Marsden, Frank von Delft
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms18010228

Molecular Basis for the Neutralization of Tumor Necrosis Factor α by Certolizumab Pegol in the Treatment of Inflammatory Autoimmune Diseases
Cited by: 32
Author(s): Jee Un Lee, Woo‐Ri Shin, Ji Young Son, Kyung Yeon Yoo, Yong‐Seok Heo
Software Mentions: 4
Published: over 8 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: almost 7 years ago

10.7554/eLife.16761

Origin of a folded repeat protein from an intrinsically disordered ancestor
Cited by: 40
Author(s): Hongbo Zhu, Edgardo Sepúlveda, M.D. Hartmann, Manjunatha Kogenaru, Astrid Ursinus, Eva Sulz, R. Albrecht, Murray Coles, Jörg Martin, Andrei N. Lupas
Software Mentions: 4
Published: almost 9 years ago

10.3390/biom10040527

Aspirin: A Suicide Inhibitor of Carbonic Anhydrase II
Cited by: 10
Author(s): Jacob T. Andring, Jacob Combs, Robert McKenna
Software Mentions: 4
Published: over 5 years ago

10.1007/s10295-019-02189-z

Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases
Cited by: 6
Author(s): Jesus F. Barajas, R.P. McAndrew, Mitchell G. Thompson, Tyler W. H. Backman, Bo Pang, Tristan de Rond, J.H. Pereira, Veronica T. Benites, Héctor García Martín, Edward E. K. Baidoo, Nathan J. Hillson, Paul D. Adams, Jay D. Keasling
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pbio.3000123

Structural basis of DSF recognition by its receptor RpfR and its regulatory interaction with the DSF synthase RpfF
Cited by: 22
Author(s): E.J. Waldron, Donald R. Snyder, Nicolas L. Fernandez, Emily Sileo, Daigo Inoyama, Joel S. Freundlich, Christopher M. Waters, Vaughn S. Cooper, Matthew B. Neiditch
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.02581

Structural and Functional Characterization of PA14/Flo5-Like Adhesins From Komagataella pastoris
Cited by: 6
Author(s): Michael D. Kock, Stefan Brückner, Nina Wozniak, M. Maestre-Reyna, M. Veelders, Julia Schlereth, Hans‐Ulrich Mösch, Lars‐Oliver Essen
Software Mentions: 4
Published: over 6 years ago

10.1107/S2059798316020143

Ligand fitting withCCP4
Cited by: 17
Author(s): Robert A. Nicholls
Software Mentions: 4
Published: over 8 years ago

10.1107/S205979831801570X

Choosing your (Friedel) mates wisely: grouping data sets to improve anomalous signal
Cited by: 6
Author(s): Nicolas Foos, Michele Cianci, Max H. Nanao
Software Mentions: 4
Published: over 6 years ago

10.1107/S2059798318002310

Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases inAMPLE
Cited by: 14
Author(s): Daniel J. Rigden, Jens M. H. Thomas, Felix Šimkovic, Adam J Simpkin, Martyn Winn, Olga Mayans, Ronan Keegan
Software Mentions: 4
Published: over 7 years ago

10.1107/S2059798317017582

ARCIMBOLDOon coiled coils
Cited by: 39
Author(s): Iracema Caballero, Massimo Sammito, Claudia Millán, А. А. Лебедев, Nicolas Soler, Isabel Usón
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2018.00231

Structural and Biochemical Characterization of BdsA from Bacillus subtilis WU-S2B, a Key Enzyme in the “4S” Desulfurization Pathway
Cited by: 14
Author(s): Tianning Su, Jing Su, Shiheng Liu, Conggang Zhang, Jing He, Yan Huang, Sujuan Xu, Lichuan Gu
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pntd.0007919

Polymorphism analyses and protein modelling inform on functional specialization of Piwi clade genes in the arboviral vector Aedes albopictus
Cited by: 16
Author(s): Michele Marconcini, Luis Miguel Hernández, Giuseppe Iovino, Vincent Houé, Federica Valerio, Umberto Palatini, Elisa Pischedda, Jacob E. Crawford, Bradley J. White, Teresa Lin, Rebeca Carballar-Lejarazú, Lino Ometto, Federico Forneris, Anna‐Bella Failloux, Mariangela Bonizzoni
Software Mentions: 4
Published: over 5 years ago

10.1107/S139900471400087X

Anomalies in the refinement of isoleucine
Cited by: 3
Author(s): Karen R. M. Berntsen, Gert Vriend
Software Mentions: 4
Published: over 11 years ago

10.1107/S2052252517008557

Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography
Cited by: 22
Author(s): Keitaro Yamashita, N. Kuwabara, Takanori Nakane, Taichi Murai, Eiichi Mizohata, Michihiro Sugahara, Dongqing Pan, Tetsuya Masuda, Mamoru Suzuki, Tomomi Satō, Atsushi Kodan, Tomohiro Yamaguchi, Eriko Nango, Tomoyuki Tanaka, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Hiroshi Manya, Tamao Endo, Ryuichi Kato, Toshiya Senda, Hiroaki Katô, So Iwata, Hideo Ago, Masaki Yamamoto, Fumiaki Yumoto, Toru Nakatsu
Software Mentions: 4
Published: almost 8 years ago

10.1038/s42003-021-02419-0

14-3-3-protein regulates Nedd4-2 by modulating interactions between HECT and WW domains
Cited by: 23
Author(s): Pavel Pohl, Rohit Joshi, Olívia Petrvalská, Tomáš Obšil, Veronika Obšilová
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.63429

Structural basis for human TRPC5 channel inhibition by two distinct inhibitors
Cited by: 33
Author(s): Kangcheng Song, Mengping Wei, Wenjun Guo, Quan Li, Yimin Kang, Jing-Xiang Wu
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.02304

An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases
Cited by: 71
Author(s): Jeffrey I. Boucher, Joseph Jacobowitz, Brian C Beckett, Scott Classen, Douglas L. Theobald
Software Mentions: 4
Published: about 11 years ago

10.15252/embj.2019102926

Structural basis of semaphorin‐plexin cis interaction
Cited by: 15
Author(s): Daniel Rozbeský, Marieke G. Verhagen, Dimple Karia, Gergely Nagy, Luis Álvarez, R.A. Robinson, K. Harlos, Sergi Padilla‐Parra, R. Jeroen Pasterkamp, Emma Jones
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0242677

Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats
Cited by: 16
Author(s): Sara Sajko, Irina Grishkovskaya, Július Košťan, Melissa A. Graewert, Kim Setiawan, Linda Trübestein, Korbinian Niedermüller, Charlotte Gehin, Antonio Sponga, Martin Puchinger, Anne‐Claude Gavin, Thomas A. Leonard, D. I. Svergun, Terry Smith, Brooke Morriswood, Kristina Djinović-Carugo
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0092257

Esterase LpEst1 from Lactobacillus plantarum: A Novel and Atypical Member of the αβ Hydrolase Superfamily of Enzymes
Cited by: 23
Author(s): Y. Álvarez, María Esteban-Torres, Álvaro Cortés-Cabrera, Federico Gago, I. Acebrón, R. Benavente, Karin Mardo, Blanca de las Rivas, Rosario Múñoz, José M. Mancheño
Software Mentions: 4
Published: over 11 years ago

10.1038/s41598-017-14959-9

Crystal Structure of Borrelia turicatae protein, BTA121, a differentially regulated gene in the tick-mammalian transmission cycle of relapsing fever spirochetes
Cited by: 2
Author(s): Zhipu Luo, Alan Kelleher, Rabih Darwiche, Elissa M. Hudspeth, Oluwatosin Kudirat Shittu, Aparna Krishnavajhala, Roger Schneiter, Job E. López, Oluwatoyin A. Asojo
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0219823

Structures of TOG1 and TOG2 from the human microtubule dynamics regulator CLASP1
Cited by: 11
Author(s): Jonathan B. Leano, Kevin C. Slep
Software Mentions: 4
Published: about 6 years ago

10.1038/srep24019

Multiple oligomeric structures of a bacterial small heat shock protein
Cited by: 25
Author(s): Nandini Mani, Spraha Bhandari, Rodolfo Moreno, Liya Hu, B. V. Venkataram Prasad, K. Suguna
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.65282

Malaria parasites use a soluble RhopH complex for erythrocyte invasion and an integral form for nutrient uptake
Cited by: 31
Author(s): Marc A. Schureck, Joseph E. Darling, Alan Merk, Jinfeng Shao, Geervani Daggupati, Prakash Srinivasan, Paul Dominic B. Olinares, Michael P. Rout, Brian T. Chait, Kurt Wollenberg, Sriram Subramaniam, Sanjay A. Desai
Software Mentions: 4
Published: over 4 years ago

10.1021/acs.jcim.1c00362

Data-Driven Ensemble Docking to Map Molecular Interactions of Steroid Analogs with Hepatic Organic Anion Transporting Polypeptides
Cited by: 5
Author(s): Alzbeta Tuerkova, Orsolya Ungvári, Réka Laczkó-Rigó, Erzsébet Mernyák, Gergely Szakács, Csilla Özvegy‐Laczka, Barbara Zdrazil
Software Mentions: 4
Published: about 4 years ago

10.1128/mBio.01408-18

Heterosubtypic Protections against Human-Infecting Avian Influenza Viruses Correlate to Biased Cross-T-Cell Responses
Cited by: 23
Author(s): Min Zhao, Kefang Liu, Jiejian Luo, Shuguang Tan, Chuansong Quan, Shuijun Zhang, Yan Chai, Jianxun Qi, Yan Li, Yang Bi, Haixia Xiao, Gary Wong, Jianfang Zhou, Taijiao Jiang, Wenjun Liu, Hongjie Yu, Jinghua Yan, Yingxia Liu, Yuelong Shu, Guizhen Wu, Aiping Wu, George F. Gao, William J. Liu
Software Mentions: 4
Published: almost 7 years ago

10.1016/j.str.2017.12.005

Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa
Cited by: 27
Author(s): Osman Salih, Shaoda He, Sara Planamente, Lasse Stach, James T. MacDonald, Eleni Manoli, S.H.W. Scheres, Alain Filloux, Paul S. Freemont
Software Mentions: 3
Published: over 7 years ago

10.15252/embj.2021107985

Neutralization of SARS‐CoV‐2 by highly potent, hyperthermostable, and mutation‐tolerant nanobodies
Cited by: 56
Author(s): Thomas Güttler, Metin Aksu, Antje Dickmanns, Kim M. Stegmann, Kathrin Gregor, Renate Rees, Waltraud Taxer, Oleh Rymarenko, Jürgen Schünemann, Christian Dienemann, Philip Gunkel, Bianka Mußil, Jens Krull, Ulrike Teichmann, Uwe Groß, Volker C. Cordes, Matthias Dobbelstein, Dirk Görlich
Software Mentions: 3
Published: almost 4 years ago

10.1107/S205225251900246X

Subatomic resolution X-ray structures of green fluorescent protein
Cited by: 24
Author(s): Kiyotsugu Takaba, Yang Tai, Haruhiko Eki, Hoang Anh Dao, Yuya Hanazono, Kazuya Hasegawa, Kunio Miki, Kazuki Takeda
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0039550

On the Structure and Function of the Phytoene Desaturase CRTI from Pantoea ananatis, a Membrane-Peripheral and FAD-Dependent Oxidase/Isomerase
Cited by: 74
Author(s): Patrick Schaub, Qiuju Yu, Sandra Gemmecker, Pierre Poussin-Courmontagne, J. Mailliot, A.G. McEwen, Sandro Ghisla, Salim Al‐Babili, Jean Cavarelli, Peter Beyer
Software Mentions: 3
Published: about 13 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: almost 6 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: almost 6 years ago

10.1016/j.str.2020.04.010

CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions
Cited by: 16
Author(s): Takashi Ochi, Valentina Quarantotti, Huawen Lin, Jérôme Jullien, Ivan Rosa e Silva, Francesco Boselli, Deepak D. Barnabas, Christopher M. Johnson, Stephen H. McLaughlin, Stefan Freund, Andrew N. Blackford, Yuu Kimata, Raymond E. Goldstein, Stephen Jackson, Tom L. Blundell, Susan K. Dutcher, Fanni Gergely, M. van Breugel
Software Mentions: 3
Published: about 5 years ago

10.1111/cea.12230

Human <scp>I</scp> g <scp>E</scp> against the major allergen <scp>B</scp> et v 1 – defining an epitope with limited cross‐reactivity between different <scp>PR</scp> ‐10 family proteins
Cited by: 20
Author(s): Mattias Levin, Anna M. Davies, Maria Liljekvist, Fredrika Carlsson, Hannah J. Gould, Brian J. Sutton, Mats Ohlin
Software Mentions: 3
Published: over 11 years ago

10.7554/eLife.03583

Structure and transport mechanism of the sodium/proton antiporter MjNhaP1
Cited by: 65
Author(s): Cristina Paulino, David Wöhlert, Ekaterina Kapotova, Özkan Yıldız, Werner Kühlbrandt
Software Mentions: 3
Published: over 10 years ago

10.1038/s42003-021-02518-y

14-3-3 proteins inactivate DAPK2 by promoting its dimerization and protecting key regulatory phosphosites
Cited by: 18
Author(s): Matej Horvath, Olívia Petrvalská, Petr Heřman, Veronika Obšilová, Tomáš Obšil
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.65339

Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein
Cited by: 12
Author(s): Xiangrong Chen, Yusuf Ali, Charlotte E L Fisher, Raquel Arribas-Bosacoma, Mohan B. Rajasekaran, Gareth Williams, Sarah Walker, Jessica R Booth, Jessica J. R. Hudson, S. Mark Roe, Laurence H. Pearl, Simon E. Ward, Frances M. G. Pearl, Antony W. Oliver
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0232959

Crystal structure of Thermus thermophilus methylenetetrahydrofolate dehydrogenase and determinants of thermostability
Cited by: 7
Author(s): Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0232846

Diversity in kinetics correlated with structure in nano body-stabilized LacY
Cited by: 3
Author(s): Atul Kumar Johri, J. Finer-Moore, И. Н. Смирнова, Vladimir N. Kasho, Els Pardon, Jan Steyaert, H. Ronald Kaback, Robert M. Stroud
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.27829

Structure-based analysis of CysZ-mediated cellular uptake of sulfate
Cited by: 9
Author(s): Zahra Assur Sanghai, Qun Liu, Oliver B Clarke, Meagan Belcher Dufrisne, Pattama Wiriyasermkul, Maria Giese, Edgar Leal-Pinto, Brian Kloss, Shantelle Tabuso, J. Love, Marco Punta, Surajit Banerjee, Kanagalaghatta R. Rajashankar, Burkhard Rost, Diomedes E. Logothetis, Matthias Quick, Wayne A. Hendrickson, Filippo Mancia
Software Mentions: 3
Published: about 7 years ago

10.1107/S2052252519007668

Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder
Cited by: 10
Author(s): Jeong Kuk Park, Keon Young Kim, Yeo Won Sim, Young Dong Kim, Jin Kyun Kim, Cheol Lee, Jeongran Han, Chae Un Kim, J. Eugene Lee, SangYoun Park
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.41741

Crystal structure of a natural light-gated anion channelrhodopsin
Cited by: 30
Author(s): Hai Li, Chia‐Ying Huang, Elena G. Govorunova, Christopher T. Schafer, Oleg A. Sineshchekov, Meitian Wang, Lei Zheng, John L. Spudich
Software Mentions: 3
Published: over 6 years ago

10.1016/j.str.2020.08.004

Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics
Cited by: 14
Author(s): D E. Nicholson, Thomas A. Edwards, Alex J. O’Neill, Neil A. Ranson
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.str.2017.01.002

Crystal Structure of the Heterotrimeric Integrin-Binding Region of Laminin-111
Cited by: 28
Author(s): David Pulido, Sadaf-Ahmahni Hussain, Erhard Hohenester
Software Mentions: 3
Published: over 8 years ago

10.1016/j.str.2021.04.004

Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein
Cited by: 8
Author(s): Patryk Ludzia, E.D. Lowe, Gabriele Marcianò, Shabaz Mohammed, Christina Redfield, Bungo Akiyoshi
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-10085-8

Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq
Cited by: 14
Author(s): Eike C. Schulz, Markus Seiler, Cecilia Zuliani, Franka Voigt, Vladimir Rybin, Vivian Pogenberg, Norbert Mücke, Matthias Wilmanns, Toby J. Gibson, O. Barábas
Software Mentions: 3
Published: almost 8 years ago

10.1128/mBio.02858-18

Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket
Cited by: 13
Author(s): Pierrick Craveur, A.T. Gres, Karen A. Kirby, Dandan Liu, John A. Hammond, Yisong Deng, Stefano Forli, David S. Goodsell, James R. Williamson, Stefan G. Sarafianos, Arthur J. Olson
Software Mentions: 3
Published: about 6 years ago

10.1107/S205225251700570X

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation
Cited by: 123
Author(s): José M. Martín-García, Chelsie E. Conrad, Garrett Nelson, Natasha Stander, Nadia A. Zatsepin, James Zook, Liya Zhu, James H. Geiger, Eugene Chun, David J. Kissick, Mark Hilgart, Craig M. Ogata, Andrii Ishchenko, Nirupa Nagaratnam, Shatabdi Roy-Chowdhury, Jesse Coe, Ganesh Subramanian, Alexander F. Schäffer, Daniel James, Gihan Ketwala, Nagarajan Venugopalan, Shenglan Xu, Stephen Corcoran, D.R. Ferguson, Uwe Weierstall, John C. H. Spence, Vadim Cherezov, Petra Fromme, Robert F. Fischetti, Wei Liu
Software Mentions: 3
Published: about 8 years ago

10.1038/s42003-021-02532-0

Modulation of Toll-like receptor 1 intracellular domain structure and activity by Zn2+ ions
Cited by: 7
Author(s): Владислав А. Лушпа, Marina V. Goncharuk, Cong Lin, Arthur O. Zalevsky, Irina A. Talyzina, Aleksandra Luginina, Daniil Vakhrameev, M.B. Shevtsov, Sergey A. Goncharuk, Alexander S. Arseniev, Valentin Borshchevskiy, Xiaohui Wang, K.S. Mineev
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.56889

An ER translocon for multi-pass membrane protein biogenesis
Cited by: 68
Author(s): Philip T. McGilvray, S. Anghel, Arunkumar Sundaram, Frank Zhong, Michael J. Trnka, James R. Fuller, Hong Yu Hu, Alma L. Burlingame, Robert J. Keenan
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-018-19991-x

Thermal stabilization of the deglycating enzyme Amadoriase I by rational design
Cited by: 18
Author(s): Federica Rigoldi, Stefano Donini, Francesca Giacomina, Federico Sorana, Alberto Redaelli, Tiziano Bandiera, Emilio Parisini, Alfonso Gautieri
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.48907

Two new polymorphic structures of human full-length alpha-synuclein fibrils solved by cryo-electron microscopy
Cited by: 191
Author(s): Ricardo C. Guerrero-Ferreira, Nicholas M. I. Taylor, Ana-Andreea Arteni, Pratibha Kumari, Daniel Mona, Philippe Ringler, Markus Britschgi, Matthias E. Lauer, Ali Makky, Joeri Verasdonck, Roland Riek, Ronald Melki, Beat H. Meier, Anja Böckmann, Luc Bousset, Henning Stahlberg
Software Mentions: 3
Published: over 5 years ago

10.1128/mBio.01569-16

The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment
Cited by: 24
Author(s): Leo Hanke, Kevin E. Knockenhauer, R. Camille Brewer, Eline van Diest, Florian I. Schmidt, Thomas Schwartz, Hidde L. Ploegh
Software Mentions: 3
Published: over 8 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 6 years ago

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Papers Mentioning PHENIX 2,287