Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: PHENIX

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/PHENIX

Phenotypic Integration Index
7 versions
Latest release: over 7 years ago
1 dependent package
161 downloads last month

Papers Mentioning PHENIX 2,287

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: about 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: over 3 years ago
10.1107/S2059798318004576
<i>KAMO</i>: towards automated data processing for microcrystals
Cited by: 174
Author(s): Keitaro Yamashita, Kunio Hirata, Masaki Yamamoto
Software Mentions: 8
Published: over 6 years ago
10.1107/S2059798317016035
<i>CCP</i>4<i>i</i>2: the new graphical user interface to the<i>CCP</i>4 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: almost 7 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: about 5 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: over 5 years ago
10.1107/S2059798317007859
Recent developments in the<i>CCP-EM</i>software suite
Cited by: 266
Author(s): Tom Burnley, Colin M. Palmer, Martyn Winn
Software Mentions: 7
Published: over 7 years ago
10.1107/S0907444909052925
<i>PHENIX</i>: 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: almost 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 3 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: about 9 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: about 8 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: over 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: over 4 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: about 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: about 3 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: about 4 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: almost 7 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: over 3 years ago
10.1107/S2059798318003455
Recent developments in<i>MrBUMP</i>: 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 6 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: about 5 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: over 10 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
10.1107/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: over 9 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: over 9 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
10.7554/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: about 3 years ago
10.1107/S0907444913022750
<i>Phaser.MRage</i>: 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: about 11 years ago
10.1107/S0021889812017293
Graphical tools for macromolecular crystallography in<i>PHENIX</i>
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: over 12 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 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
10.7554/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: over 5 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: over 7 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 7 years ago
10.1107/S0907444910045749
Overview of the<i>CCP</i>4 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 13 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: about 11 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: almost 6 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 10 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: almost 4 years ago
10.1107/S2059798318001353
<i>Gyre</i>and<i>gimble</i>: 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 6 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: over 5 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: about 5 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: 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: almost 11 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: over 9 years ago
10.1107/S2059798316020234
The<i>XChemExplorer</i>graphical 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 7 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 3 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: almost 5 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
10.7554/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: over 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 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: over 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: almost 6 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 10 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: about 8 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: over 5 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 4 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: about 6 years ago
10.1107/S2059798316020143
Ligand fitting with<i>CCP</i>4
Cited by: 17
Author(s): Robert A. Nicholls
Software Mentions: 4
Published: almost 8 years ago
10.1107/S2059798318002310
Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in<i>AMPLE</i>
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 6 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: almost 7 years ago
10.1107/S2059798317017582
<i>ARCIMBOLDO</i>on 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 6 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: about 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: about 6 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: almost 4 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: almost 8 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: about 7 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: 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 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: over 3 years ago
10.15252/embj.2019102926
Structural basis of semaphorin‐plexin <i>cis</i> 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: 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: over 3 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: over 7 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: over 5 years ago
10.1038/s41422-018-0104-9
Plant HP1 protein ADCP1 links multivalent H3K9 methylation readout to heterochromatin formation
Cited by: 71
Author(s): Shuai Zhao, Lan Cheng, Yifei Gao, Baichao Zhang, Xiangdong Zheng, Liang Wang, Pilong Li, Qianwen Sun, Haitao Li
Software Mentions: 3
Published: about 6 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: almost 7 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: about 3 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: over 3 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: over 4 years ago
10.1016/j.jbc.2021.100700
ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis
Cited by: 8
Author(s): Jitender Mehla, George W. Liechti, Randy M. Morgenstein, J. Harry Caufield, Ali Hosseinnia, Alla Gagarinova, Sadhna Phanse, Norman Goodacre, Mary R. Brockett, Neha Sakhawalkar, Mohan Babu, Rong Xiao, Gaetano T. Montelione, S.M. Vorobiev, T. den Blaauwen, J.F. Hunt, Peter Uetz
Software Mentions: 3
Published: almost 4 years ago
10.1074/jbc.RA120.012788
Small molecule AX-024 reduces T cell proliferation independently of CD3ϵ/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain
Cited by: 10
Author(s): Kirsten Richter, Arne C. Rufer, Magali Muller, Dominique Burger, Fabio Casagrande, Tabea Grossenbacher, Sylwia Huber, Melanie N. Hug, Philipp Koldewey, Andrea D’Osualdo, Daniel Schlatter, Theodor Stoll, M.G. Rudolph
Software Mentions: 3
Published: over 4 years ago
10.1074/jbc.RA118.004469
Discovery of peptide ligands targeting a specific ubiquitin-like domain–binding site in the deubiquitinase USP11
Cited by: 24
Author(s): Anastasios Spiliotopoulos, Lia Blokpoel Ferreras, Ruth M Densham, Simon G. Caulton, Ben C. Maddison, Joanna R. Morris, James E. Dixon, Kevin C. Gough, Ingrid Dreveny
Software Mentions: 3
Published: almost 6 years ago
10.1128/JVI.01664-19
Structure of Merkel Cell Polyomavirus Capsid and Interaction with Its Glycosaminoglycan Attachment Receptor
Cited by: 12
Author(s): Niklas Johannes Bayer, Dovile Januliene, Georg Zocher, Thilo Stehle, Arne Moeller, Bärbel S. Blaum
Software Mentions: 3
Published: about 4 years ago
10.1074/jbc.M116.730382
Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases
Cited by: 14
Author(s): Marco Igor Valencia-Sánchez, Annia Rodríguez‐Hernández, Ruben Ferreira, Hugo A. Santamaría-Suárez, Marcelino Arciniega, Anne-Catherine Dock-Brégeon, Dino Moras, Brice Beinsteiner, Haydyn D. T. Mertens, Dmitri I. Svergun, Luis G. Brieba, Morten Grøtli, Alfredo Torres‐Larios
Software Mentions: 3
Published: over 8 years ago
10.1074/jbc.M115.705863
Inhibition of PRL-2·CNNM3 Protein Complex Formation Decreases Breast Cancer Proliferation and Tumor Growth
Cited by: 38
Author(s): Elie Kostantin, Serge Hardy, William C. Valinsky, Andreas Kompatscher, Jeroen H. F. de Baaij, Yevgen Zolotarov, Mélissa Landry, Noriko Uetani, Luis Alfonso Martínez-Cruz, Joost G. J. Hoenderop, Alvin Shrier, Michel L. Tremblay
Software Mentions: 3
Published: over 8 years ago
10.1186/s13072-016-0051-y
Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis
Cited by: 51
Author(s): Takashi Urahama, Akihito Harada, Kazuhira Maehara, Naoki Horikoshi, Koichi Sato, Yuko Sato, Koji Shiraishi, Norihiro Sugino, Akihisa Osakabe, Hiroaki Tachiwana, Wataru Kagawa, Hiroshi Kimurâ, Yasuyuki Ohkawa, Hitoshi Kurumizaka
Software Mentions: 3
Published: almost 9 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: almost 8 years ago
10.1038/s41598-018-21667-5
Structure based function-annotation of hypothetical protein MGG_01005 from Magnaporthe oryzae reveals it is the dynein light chain orthologue of dynlt1/3
Cited by: 2
Author(s): Guorui Li, Jinguang Huang, Jun Yang, Dan He, Chao Wang, Xiaoxuan Qi, Ian A. Taylor, Junfeng Liu, You-Liang Peng
Software Mentions: 3
Published: over 6 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: about 7 years ago
10.1371/journal.ppat.1002957
De novo GTP Biosynthesis Is Critical for Virulence of the Fungal Pathogen Cryptococcus neoformans
Cited by: 53
Author(s): Carl A. Morrow, Eugene Valkov, Anna Stamp, Eve W. L. Chow, I. Russel Lee, Ania Wronski, Simon J. Williams, Jennifer Hill, Julianne T. Djordjevic, Ulrike Kappler, Boštjan Kobe, James S. Fraser
Software Mentions: 3
Published: about 12 years ago
10.1016/j.jbc.2021.100743
From integrative structural biology to cell biology
Cited by: 38
Author(s): Andrej Šali
Software Mentions: 3
Published: almost 4 years ago
10.3390/ijms22168631
The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales
Cited by: 5
Author(s): Marie-Caroline Müller, T. Wagner
Software Mentions: 3
Published: over 3 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: over 7 years ago
10.1098/rsob.160292
Structural, mechanistic and functional insight into gliotoxin <i>bis</i> -thiomethylation in <i>Aspergillus fumigatus</i>
Cited by: 32
Author(s): Stephen K. Dolan, Thomas Böck, Vanessa Hering, Rebecca A. Owens, Gary W. Jones, Wulf Blankenfeldt, Seán Doyle
Software Mentions: 3
Published: almost 8 years ago
10.1074/jbc.M117.776476
Allosteric mechanism of action of the therapeutic anti-IgE antibody omalizumab
Cited by: 57
Author(s): Anna M. Davies, Elizabeth G. Allan, Anthony H. Keeble, Jean Delgado, Benjamin P. Cossins, A.N. Mitropoulou, M.O.Y. Pang, Tom Ceska, Andrew J. Beavil, Graham Craggs, Marta Westwood, Alistair J. Henry, James M. McDonnell, Brian J. Sutton
Software Mentions: 3
Published: over 7 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: about 3 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: about 4 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: over 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 7 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 5 years ago
10.7554/eLife.21646
Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis
Cited by: 57
Author(s): Ashutosh Pudasaini, Jae Sung Shim, Young Hun Song, Hua Shi, Takatoshi Kiba, David E. Somers, Takato Imaizumi, Brian D. Zoltowski
Software Mentions: 3
Published: over 7 years ago