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
10.1107/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
10.1016/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/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
10.1107/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
10.7554/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
10.7554/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
10.1107/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
10.1107/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.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
10.1371/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: over 8 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
10.1107/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
10.1107/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
10.1107/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: almost 14 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
10.7554/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: almost 10 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/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/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/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: almost 10 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
10.7554/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
10.1107/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: almost 7 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/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
10.7554/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: over 3 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
10.1002/2211-5463.12259
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/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.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
10.1111/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
10.3390/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
10.1016/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
10.3389/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
10.3389/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
10.1038/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
10.1007/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
10.7554/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: over 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
10.1371/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
10.1371/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: about 4 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/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.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/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
10.1107/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: over 6 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: about 5 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: almost 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
10.7554/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: almost 4 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/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
10.7554/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
10.1107/S139900471400087X
Anomalies in the refinement of isoleucine
Cited by: 3
Author(s): Karen R. M. Berntsen, Gert Vriend
Software Mentions: 4
Published: almost 11 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: over 6 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
10.1107/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
10.7554/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/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/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
10.1107/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: almost 7 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/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: almost 7 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
10.1107/S0907444911035943
High-resolution structure of a retroviral protease folded as a monomer
Cited by: 22
Author(s): Mirosław Gilski, Maciej Kazmierczyk, Szymon Krzywda, Helena Zábranská, Seth Cooper, Zoran Popović, Firas Khatib, Frank DiMaio, James Thompson, David Baker, Iva Pichová, Mariusz Jaskólski
Software Mentions: 3
Published: about 13 years ago
10.3390/cancers13133317
A Novel Nanobody Precisely Visualizes Phosphorylated Histone H2AX in Living Cancer Cells under Drug-Induced Replication Stress
Cited by: 12
Author(s): Eric Moeglin, Dominique Desplancq, Audrey Stoessel, Christian Massute, Jeremy Ranniger, A.G. McEwen, Gabrielle Zeder‐Lutz, Mustapha Oulad‐Abdelghani, Manuela Chiper, Pierre Lafaye, Barbara Di Ventura, Pascal Didier, Arnaud Poterszman, Étienne Weiss
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0036297
Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (PPAR) γ Activators and Pan-PPAR Partial Agonists
Cited by: 163
Author(s): M.V. Liberato, Alessandro S. Nascimento, Steven D. Ayers, Jean Z. Lin, Aleksandra Čvoro, Rodrigo L. Silveira, Leandro Martı́nez, Paulo C. T. Souza, Daniel Menezes Saidemberg, Tuo Deng, Angela Angelica Amato, Marie Togashi, Willa A. Hsueh, Kevin J. Phillips, Mário Sérgio Palma, Francisco de Assis Rocha Neves, Munir S. Skaf, Paul Webb, Igor Polikarpov
Software Mentions: 3
Published: over 12 years ago
10.1371/journal.pone.0156344
A Novel Phenanthridionone Based Scaffold As a Potential Inhibitor of the BRD2 Bromodomain: Crystal Structure of the Complex
Cited by: 11
Author(s): Shailesh Tripathi, Shruti Mathur, Prashant Deshmukh, R Manjula, Balasundaram Padmanabhan
Software Mentions: 3
Published: over 8 years ago
10.1107/S2059798320000418
Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction
Cited by: 13
Author(s): Nicholas K. Sauter, Jan Kern, Junko Yano, James M. Holton
Software Mentions: 3
Published: almost 5 years ago
10.1016/j.cell.2021.02.045
Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling
Cited by: 18
Author(s): R.A. Robinson, Samuel C. Griffiths, Lieke L van de Haar, Tomas Malinauskas, Eljo Y. van Battum, Pavol Zelina, Rebekka A. Schwab, Dimple Karia, L. Malinauskaite, Sara Brignani, Marleen H. van den Munkhof, O. Dudukcu, A.A. De Ruiter, Dianne M.A. van den Heuvel, B. Bishop, J. Elegheert, A. Radu Aricescu, R. Jeroen Pasterkamp, Christian Siebold
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0058333
Structural Insights into Putative Molybdenum Cofactor Biosynthesis Protein C (MoaC2) from Mycobacterium tuberculosis H37Rv
Cited by: 2
Author(s): Vijay Kumar Srivastava, Shubra Srivastava, Ashish Arora, J. Venkatesh Pratap
Software Mentions: 3
Published: almost 12 years ago
10.1371/journal.pone.0080947
Crystal Structures of the Human G3BP1 NTF2-Like Domain Visualize FxFG Nup Repeat Specificity
Cited by: 43
Author(s): T. Vognsen, Ingvar R. Möller, Ole Kristensen
Software Mentions: 3
Published: about 11 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: over 4 years ago
10.1038/cddis.2017.487
Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2
Cited by: 20
Author(s): M. Merski, Cátia Moreira, Rui M.V. Abreu, María J. Ramos, Pedro A. Fernandes, L. Miguel Martins, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro
Software Mentions: 3
Published: about 7 years ago
10.1371/journal.pone.0218300
The Dps4 from Nostoc punctiforme ATCC 29133 is a member of His-type FOC containing Dps protein class that can be broadly found among cyanobacteria
Cited by: 8
Author(s): Christoph Howe, Vamsi K. Moparthi, Felix M. Ho, Karina Persson, Karin Stensjö
Software Mentions: 3
Published: over 5 years ago
10.1107/S0907444910000272
Rapid chain tracing of polypeptide backbones in electron-density maps
Cited by: 5
Author(s): Thomas C. Terwilliger
Software Mentions: 3
Published: almost 15 years ago
10.1107/S0907444912001308
Towards automated crystallographic structure refinement with <i>phenix.refine</i>
Cited by: 4,334
Author(s): Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Nathaniel Echols, Jeffrey J. Headd, Nigel W. Moriarty, Marat Mustyakimov, Thomas C. Terwilliger, Alexandre Urzhumtsev, Peter H. Zwart, Paul D. Adams
Software Mentions: 3
Published: almost 13 years ago
10.1371/journal.pone.0022767
X-Ray Structure Reveals a New Class and Provides Insight into Evolution of Alkaline Phosphatases
Cited by: 18
Author(s): Subhash C. Bihani, Amit Kumar Das, Kayzad Nilgiriwala, Vishal Prashar, Michel Pirocchi, Shree Kumar Apte, Jean‐Luc Ferrer, M.V. Hosur
Software Mentions: 3
Published: over 13 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: over 4 years ago
10.1107/S1399004715005210
<i>In meso in situ</i> serial X-ray crystallography of soluble and membrane proteins
Cited by: 98
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Ezequiel Panepucci, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0077995
Structural and Enzymatic Characterization of the Phosphotriesterase OPHC2 from Pseudomonas pseudoalcaligenes
Cited by: 52
Author(s): Guillaume Gotthard, Julien Hiblot, Daniel H. González, Mikael Elias, Éric Chabrière
Software Mentions: 3
Published: about 11 years ago
10.1371/journal.pone.0214440
A DNA aptamer reveals an allosteric site for inhibition in metallo-β-lactamases
Cited by: 17
Author(s): Nazmul H Khan, Anthony A. Bui, Yang Xiao, R. Bryan Sutton, Robert W. Shaw, Benjamin J. Wylie, Michael P. Latham
Software Mentions: 3
Published: over 5 years ago
10.1107/S1399004715004514
Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams
Cited by: 112
Author(s): Nicolas Coquelle, Aaron S. Brewster, U. Kapp, Anastasya Shilova, Britta Weinhausen, Manfred Burghammer, J.P. Colletier
Software Mentions: 3
Published: over 9 years ago
10.1107/S2053273316010731
Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm
Cited by: 9
Author(s): Hongxing He, Hengrui Fang, Mitchell D. Miller, George N. Phillips, W. P. Su
Software Mentions: 3
Published: over 8 years ago
10.1107/S2059798317007707
DNA conformational transitions inferred from re-evaluation ofm|Fo| −D|Fc| electron-density maps
Cited by: 3
Author(s): Tomoko Sunami, Toshiyuki Chatake, Hidetoshi Kono
Software Mentions: 3
Published: over 7 years ago
10.1107/S2059798319003991
Structural analysis of a replication protein encoded by a plasmid isolated from a multiple sclerosis patient
Cited by: 5
Author(s): Turgay Kilic, A. Popov, Amelie Burk-Körner, A.D. Koromyslova, Harald zur Hausen, Timo Bund, Grant S. Hansman
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0156067
Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana
Cited by: 0
Author(s): Yuan Xie, Li Mei, Wenrui Chang
Software Mentions: 3
Published: over 8 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: over 12 years ago
10.1371/journal.pntd.0008091
Trypanosomatid selenophosphate synthetase structure, function and interaction with selenocysteine lyase
Cited by: 4
Author(s): Marco Túlio Alves da Silva, Ivan Rosa e Silva, Lívia Maria Faim, Natália Karla Bellini, Murilo Leão Pereira, Ana Laura Lima, Teresa Cristina Leandro de Jesus, Fernanda Cristina Costa, Tatiana F. Watanabe, H.M. Pereira, Sandro Roberto Valentini, Cleslei Fernando Zanelli, Júlio César Borges, Márcio Vinícius Bertacini Dias, Júlia Pinheiro Chagas da Cunha, Bidyottam Mittra, Norma W. Andrews, Otávio Henrique Thiemann
Software Mentions: 3
Published: about 4 years ago
10.1107/S1399004714027011
Three-dimensional structures of<i>Plasmodium falciparum</i>spermidine synthase with bound inhibitors suggest new strategies for drug design
Cited by: 12
Author(s): J. Sprenger, Bo Svensson, J.C. Halander, Jannette Carey, Lo Persson, Salam Al-Karadaghi
Software Mentions: 3
Published: almost 10 years ago
10.1371/journal.pone.0115082
Ethenoguanines Undergo Glycosylation by Nucleoside 2′-Deoxyribosyltransferases at Non-Natural Sites
Cited by: 10
Author(s): Wenjie Ye, Debajyoti Paul, Lina Gao, Jolita Šečkutė, R. Sangaiah, K. Jayaraj, Zhenfa Zhang, P.A. Kaminski, S.E. Ealick, Avram Gold, Louise M. Ball
Software Mentions: 3
Published: about 10 years ago
10.1107/S0907444910052224
Recent advances in the<i>CRANK</i>software suite for experimental phasing
Cited by: 79
Author(s): Navraj S. Pannu, Willem Jan Waterreus, Pavol Skubák, Irakli Sikharulidze, Jan Pieter Abrahams, R. A. G. de Graaff
Software Mentions: 3
Published: almost 14 years ago