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

10.1016/j.immuni.2020.10.023
Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity
Cited by: 173
Author(s): Hejun Liu, Nicholas C. Wu, Meng Yuan, Sandhya Bangaru, Jonathan L. Torres, Tom G. Caniels, Jelle van Schooten, Xueyong Zhu, Chang-Chun David Lee, Philip J.M. Brouwer, Marit J. van Gils, Rogier W. Sanders, Andrew B. Ward, Ian A. Wilson
Software Mentions: 1
Published: about 4 years ago
10.1107/S0021889809023528
Automatic multiple-zone rigid-body refinement with a large convergence radius
Cited by: 50
Author(s): Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Alexandre Urzhumtsev, Paul D. Adams
Software Mentions: 1
Published: over 15 years ago
10.1107/S0021889810010782
Autoindexing with outlier rejection and identification of superimposed lattices
Cited by: 23
Author(s): Nicholas K. Sauter, Billy K. Poon
Software Mentions: 1
Published: over 14 years ago
10.1107/S0021889810015608
<i>phenix.model_vs_data</i>: a high-level tool for the calculation of crystallographic model and data statistics
Cited by: 110
Author(s): Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Vincent B. Chen, Jeffrey J. Headd, Nigel W. Moriarty, Jane S. Richardson, David C. Richardson, Alexandre Urzhumtsev, Peter H. Zwart, Paul D. Adams
Software Mentions: 1
Published: over 14 years ago
10.1107/S1600576716004428
<i>DCC</i>: a Swiss army knife for structure factor analysis and validation
Cited by: 21
Author(s): Huanwang Yang, Ezra Peisach, John D. Westbrook, Jasmine Young, Helen M. Berman, S.K. Burley
Software Mentions: 1
Published: over 8 years ago
10.1107/S1600576719010318
A comparison of gas stream cooling and plunge cooling of macromolecular crystals
Cited by: 5
Author(s): Kaitlin Harrison, Zhenguo Wu, D.H. Juers
Software Mentions: 1
Published: over 5 years ago
10.1128/JB.00287-19
A DNA-Binding Protein Tunes Septum Placement during Bacillus subtilis Sporulation
Cited by: 6
Author(s): Emile N. Brown, Allyssa K. Miller, I.V. Krieger, Ryan M. Otto, James C. Sacchettini, Jennifer K. Herman
Software Mentions: 1
Published: over 5 years ago
10.1093/jb/mvaa054
Site-specific epitope insertion into recombinant proteins using the MAP tag system
Cited by: 13
Author(s): Ayami Wakasa, Mika K. Kaneko, Yukinari Kato, Junichi Takagi, Takao Arimori
Software Mentions: 1
Published: over 4 years ago
10.1074/jbc.M113.465963
Base-modified Donor Analogues Reveal Novel Dynamic Features of a Glycosyltransferase
Cited by: 15
Author(s): René Jørgensen, Thomas Pesnot, Ho Jun Lee, Monica M. Palcic, Gerd K. Wagner
Software Mentions: 1
Published: over 11 years ago
10.1074/jbc.M113.469841
Structural Analysis of Collagen Type I Interactions with Human Fibronectin Reveals a Cooperative Binding Mode
Cited by: 57
Author(s): Michà ̈le C. Erat, Barbara Sladek, Iain D. Campbell, Ioannis Vakonakis
Software Mentions: 1
Published: over 11 years ago
10.1074/jbc.M113.497149
Mechanism for Recognition of an Unusual Mycobacterial Glycolipid by the Macrophage Receptor Mincle
Cited by: 107
Author(s): H. Feinberg, Sabine A. F. Jégouzo, T.J.W. Rowntree, Yue Guan, M.A. Brash, Maureen E. Taylor, William I. Weis, Kurt Drickamer
Software Mentions: 1
Published: about 11 years ago
10.1074/jbc.M113.496984
Inhibitory Mechanism of an Allosteric Antibody Targeting the Glucagon Receptor
Cited by: 30
Author(s): Susmith Mukund, Yonglei Shang, Holly J. Clarke, Azadeh Madjidi, Jacob E. Corn, Lance Kates, Ganesh Kolumam, Vicky Chiang, Elizabeth Luis, J.M. Murray, Yingnan Zhang, Isidro Hötzel, Christopher M. Koth, Bernard B. Allan
Software Mentions: 1
Published: about 11 years ago
10.1074/jbc.M113.528000
Common Polymorphisms in Human Langerin Change Specificity for Glycan Ligands
Cited by: 49
Author(s): H. Feinberg, T.J.W. Rowntree, S.L.W. Tan, Kurt Drickamer, William I. Weis, Maureen E. Taylor
Software Mentions: 1
Published: about 11 years ago
10.1074/jbc.M113.545384
Structures of Complexes of a Metal-independent Glycosyltransferase GT6 from Bacteroides ovatus with UDP-N-Acetylgalactosamine (UDP-GalNAc) and Its Hydrolysis Products
Cited by: 16
Author(s): Thuy Thi Thu Pham, Brittany Stinson, N. Thiyagarajan, Michelle Lizotte-Waniewski, Keith Brew, K. Ravi Acharya
Software Mentions: 1
Published: almost 11 years ago
10.1074/jbc.M113.527994
Crystal Structure and Molecular Imaging of the Nav Channel β3 Subunit Indicates a Trimeric Assembly
Cited by: 65
Author(s): Sivakumar Namadurai, Dilshan Balasuriya, Rajit Rajappa, Martin Wiemhöfer, Katherine Stott, Jürgen Klingauf, J. Michael Edwardson, Dimitri Y. Chirgadze, Antony P. Jackson
Software Mentions: 1
Published: over 10 years ago
10.1074/jbc.M114.547877
The Peptide-binding Cavity Is Essential for Als3-mediated Adhesion of Candida albicans to Human Cells
Cited by: 57
Author(s): Jing Lin, Soo Hee Oh, Rhian Jones, James A. Garnett, Paula S. Salgado, Sophia Rusnakova, Stephen Matthews, Lois L. Hoyer, Ernesto Cota
Software Mentions: 1
Published: over 10 years ago
10.1074/jbc.M114.590570
Structural and Mechanistic Insight into the Listeria monocytogenes Two-enzyme Lipoteichoic Acid Synthesis System
Cited by: 25
Author(s): Ivan Campeotto, Matthew G. Percy, James T. MacDonald, A. Förster, Paul S. Freemont, Angelika Gründling
Software Mentions: 1
Published: about 10 years ago
10.1074/jbc.M114.608448
Structure and Mechanism of the Bifunctional CinA Enzyme from Thermus thermophilus
Cited by: 12
Author(s): V. Karuppiah, Angela Thistlethwaite, Rana Dajani, Jim Warwicker, Jeremy P. Derrick
Software Mentions: 1
Published: about 10 years ago
10.1074/jbc.M114.619767
A Novel Cofactor-binding Mode in Bacterial IMP Dehydrogenases Explains Inhibitor Selectivity
Cited by: 30
Author(s): M. Makowska-Grzyska, Young Chang Kim, N. Maltseva, J. Osipiuk, M. Gu, Minjia Zhang, Kavitha Mandapati, Deviprasad R. Gollapalli, Suresh Kumar Gorla, Lizbeth Hedstrom, A. Joachimiak
Software Mentions: 1
Published: almost 10 years ago
10.1074/jbc.M115.653485
Olfactomedin-1 Has a V-shaped Disulfide-linked Tetrameric Structure
Cited by: 16
Author(s): Matti F. Pronker, Trusanne G. A. A. Bos, Thomas H. Sharp, Dominique M. E. Thies‐Weesie, B.J.C. Janssen
Software Mentions: 1
Published: over 9 years ago
10.1074/jbc.M115.660613
A Novel Mechanism for Binding of Galactose-terminated Glycans by the C-type Carbohydrate Recognition Domain in Blood Dendritic Cell Antigen 2
Cited by: 31
Author(s): Sabine A. F. Jégouzo, H. Feinberg, Tabassum Dungarwalla, Kurt Drickamer, William I. Weis, Maureen E. Taylor
Software Mentions: 1
Published: over 9 years ago
10.1074/jbc.M115.640029
Two Putative Polysaccharide Deacetylases Are Required for Osmotic Stability and Cell Shape Maintenance in Bacillus anthracis
Cited by: 26
Author(s): Sofia Arnaouteli, Petros Giastas, Athena Andreou, Mary Tzanodaskalaki, Christine Aldridge, Socrates J. Tzartos, Waldemar Vollmer, Elias Eliopoulos, Vassilis Bouriotis
Software Mentions: 1
Published: over 9 years ago
10.1074/jbc.M115.658781
The Cell Shape-determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of l,d-Carboxypeptidase
Cited by: 29
Author(s): Hyoun Sook Kim, Ha Na Im, Doo Ri An, Ji Young Yoon, Jun Young Jang, Shahriar Mobashery, Dušan Hesek, Mijoon Lee, Jakyung Yoo, Minghua Cui, Sun Choi, Cheol-Hee Kim, Nam Ki Lee, Soon Jong Kim, Jin Young Kim, Geul Bang, Byung Woo Han, Byung Il Lee, Hye Jin Yoon, Se Won Suh
Software Mentions: 1
Published: about 9 years ago
10.1074/jbc.M115.683268
Structural Insights into the MMACHC-MMADHC Protein Complex Involved in Vitamin B12 Trafficking
Cited by: 29
Author(s): D. Sean Froese, J. Kopec, Fiona Fitzpatrick, M. Schuller, Thomas J. McCorvie, R. Chalk, Tanja Plessl, Victoria Fettelschoss, Brian Fowler, Matthias R. Baumgartner, Wyatt W. Yue
Software Mentions: 1
Published: about 9 years ago
10.1074/jbc.M116.718841
Molecular Insights into Toluene Sensing in the TodS/TodT Signal Transduction System
Cited by: 23
Author(s): Sung-Cheol Koh, Jun Hyun Hwang, Koushik Guchhait, Eun-Gyeong Lee, Sang Yoon Kim, Sujin Kim, Sang‐Min Lee, Jeong Min Chung, Hyun Suk Jung, Sang Jun Lee, Choong‐Min Ryu, Dae-Hee Lee, Tae-Kwang Oh, Ohsuk Kwon, Myung Hee Kim
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.ppat.1004756
Structure of the Low pH Conformation of Chandipura Virus G Reveals Important Features in the Evolution of the Vesiculovirus Glycoprotein
Cited by: 21
Author(s): Eduard Baquero, Aurélie A. Albertini, Hélène Raux, Linda Buonocore, John K. Rose, Stéphane Bressanelli, Yves Gaudin
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.ppat.1005035
Characterization of a Prefusion-Specific Antibody That Recognizes a Quaternary, Cleavage-Dependent Epitope on the RSV Fusion Glycoprotein
Cited by: 101
Author(s): M.S.A. Gilman, Syed M. Moin, Vicente Más, Man Chen, Nita Patel, Kramer Kari, Qing Zhu, Stephanie C. Kabeche, Abhinav Kumar, Concepción Palomo, Tim Beaumont, Ulrich Baxa, Nancy D. Ulbrandt, José A. Melero, Barney S. Graham, Jason S. McLellan
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.ppat.1005042
Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques
Cited by: 132
Author(s): Sampa Santra, Georgia D. Tomaras, Ranjit Warrier, Nathan I. Nicely, Hua‐Xin Liao, Justin Pollara, Pinghuang Liu, S. Munir Alam, Ruijun Zhang, Sarah L. Cocklin, Xiaoying Shen, Ryan Duffy, Shi-Mao Xia, Robert J. Schutte, Charles W. Pemble, S. Moses Dennison, Hui Li, Andrew Chao, Kora Vidnovic, Abbey Evans, Katja Klein, Amit Kumar, James E. Robinson, Gary Landucci, Donald N. Forthal, David C. Montefiori, Jaranit Kaewkungwal, Sorachai Nitayaphan, Punnee Pitisuttithum, Supachai Rerks-Ngarm, Merlin L. Robb, Nelson L. Michael, Jerome H. Kim, Kelly A. Soderberg, Elena E. Giorgi, Lily Blair, Bette T. Korber, Christiane Moog, Robin J. Shattock, Norman L. Letvin, Jörn E. Schmitz, M. Anthony Moody, Feng Gao, Guido Ferrari, George M. Shaw, Barton F. Haynes
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.ppat.1005203
Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection
Cited by: 102
Author(s): Nai Chi Chen, Masato Yoshimura, Hongbing Guan, Ting Yu Wang, Yuko Misumi, Chi‐Chang Lin, Phimonphan Chuankhayan, Atsushi Nakagawa, Sunney I. Chan, Tomitake Tsukihara, Tzong Yueh Chen, Chun‐Jung Chen
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.ppat.1005269
Structural Insight into Archaic and Alternative Chaperone-Usher Pathways Reveals a Novel Mechanism of Pilus Biogenesis
Cited by: 28
Author(s): Natalia Pakharukova, James A. Garnett, Minna Tuittila, Sari Paavilainen, Mamou Diallo, Yingqi Xu, Stephen Matthews, Anton V. Zavialov
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.ppat.1005411
An Open Receptor-Binding Cavity of Hemagglutinin-Esterase-Fusion Glycoprotein from Newly-Identified Influenza D Virus: Basis for Its Broad Cell Tropism
Cited by: 81
Author(s): Hao Song, Jianxun Qi, Zahra Khedri, Sandra Díaz, Hai Yu, Xi Chen, Ajit Varki, Yi Shi, George F. Gao
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.ppat.1005414
BS69/ZMYND11 C-Terminal Domains Bind and Inhibit EBNA2
Cited by: 21
Author(s): Matthew R. Harter, Cheng-Der Liu, Chih-Lung Shen, Elsie Gonzalez-Hurtado, Zhimin Zhang, Muyu Xu, Ernest Martinez, Chih‐Wen Peng, Jikui Song
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.ppat.1005523
Initiation of RNA Polymerization and Polymerase Encapsidation by a Small dsRNA Virus
Cited by: 39
Author(s): Aaron M. Collier, Outi Lyytinen, Yusong R. Guo, Yukimatsu Toh, Minna M. Poranen, Yizhi Jane Tao
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.ppat.1005635
Atomic Structure and Biochemical Characterization of an RNA Endonuclease in the N Terminus of Andes Virus L Protein
Cited by: 27
Author(s): Fernández-García Yaiza, Juan Reguera, Carola Busch, Gregor Witte, Sánchez-Ramos Oliberto, Christian Betzel, Stephen Cusack, Stephan Günther, Sophia Reindl
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.ppat.1005779
How Quorum Sensing Connects Sporulation to Necrotrophism in Bacillus thuringiensis
Cited by: 36
Author(s): Stéphane Perchat, Antoine Talagas, Sandrine Poncet, Noureddine Lazar, I. Li de la Sierra-Gallay, Michel Gohar, Didier Lereclus, Sylvie Nessler
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.ppat.1005859
Engineering, Structure and Immunogenicity of the Human Metapneumovirus F Protein in the Postfusion Conformation
Cited by: 42
Author(s): Vicente Más, Rodriguez Laura, Eduardo Olmedillas, Olga Cano, Concepción Palomo, María C. Terrón, Daniel Luque, José A. Melero, Jason S. McLellan
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.ppat.1005948
Crystal Structure of Glycoprotein C from a Hantavirus in the Post-fusion Conformation
Cited by: 48
Author(s): Willensky Shmuel, Bar-Rogovsky Hagit, Eduardo A Bignon, Nicole D. Tischler, Yorgo Modis, Moshe Dessau
Software Mentions: 1
Published: about 8 years ago
10.1371/journal.ppat.1005813
Mechanistic Insight into Bunyavirus-Induced Membrane Fusion from Structure-Function Analyses of the Hantavirus Envelope Glycoprotein Gc
Cited by: 63
Author(s): Pablo Guardado-Calvo, Eduardo A Bignon, Eva Styková, Scott A. Jeffers, Jimena Pérez‐Vargas, Gérard Péhau‐Arnaudet, M. Alejandra Tortorici, Jean Luc Jestin, Patrick England, Nicole D. Tischler, F.A. Rey
Software Mentions: 1
Published: about 8 years ago
10.1371/journal.ppat.1005980
Structural Insights into Streptococcal Competence Regulation by the Cell-to-Cell Communication System ComRS
Cited by: 43
Author(s): Antoine Talagas, Laetitia Fontaine, Ledesma-Garca Laura, Johann Mignolet, I. Li de la Sierra-Gallay, Noureddine Lazar, Magali Aumont-Niçaise, Michael J. Federle, Gerd Prehna, Pascal Hols, Sylvie Nessler
Software Mentions: 1
Published: about 8 years ago
10.1371/journal.ppat.1006074
Structure and Recognition of a Novel HIV-1 gp120-gp41 Interface Antibody that Caused MPER Exposure through Viral Escape
Cited by: 32
Author(s): Constantinos Kurt Wibmer, Jason Gorman, Gabriel Ozorowski, Jinal N. Bhiman, Daniel J. Sheward, Debra Elliott, Julie A. Rouelle, Ashley Smira, Michael Joyce, Nonkululeko Ndabambi, Aliaksandr Druz, Mangaiarkarasi Asokan, Dennis R. Burton, Mark Connors, Salim Safurdeen. Abdool Karim, John R. Mascola, James E. Robinson, Andrew B. Ward, Carolyn Williamson, Peter D. Kwong, Lynn Morris, Penny L. Moore
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.ppat.1006182
Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial
Cited by: 38
Author(s): David Easterhoff, M. Anthony Moody, Daniela Fera, Hao Cheng, Margaret E. Ackerman, Kevin Wiehe, Kevin O. Saunders, Justin Pollara, Nathan Vandergrift, Rob Parks, Jerome Kim, Nelson L. Michael, Robert J. O’Connell, Jean–Louis Excler, Merlin L. Robb, Sandhya Vasan, Supachai Rerks-Ngarm, Jaranit Kaewkungwal, Punnee Pitisuttithum, Sorachai Nitayaphan, Faruk Sinangil, James Tartaglia, Sanjay Phogat, Thomas B. Kepler, S. Munir Alam, Hua‐Xin Liao, Guido Ferrari, Michael S. Seaman, David C. Montefiori, Georgia D. Tomaras, Stephen C. Harrison, Barton F. Haynes
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.ppat.1006394
Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein
Cited by: 49
Author(s): Jianhua Zhao, Ksenia Beyrakhova, Yao Liu, Claudia P. Alvarez, Stephanie A. Bueler, Li Xu, Caishuang Xu, Michal T. Boniecki, Voula Kanelis, Zhao‐Qing Luo, Mirosław Cygler, J.L. Rubinstein
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.ppat.1006474
Crystal structure of Middle East respiratory syndrome coronavirus helicase
Cited by: 105
Author(s): Hao Wu, Justyna Aleksandra Wojdyla, Rong Zhao, Ruiyun Han, Rajat S. Das, Ivan Zlatev, Muthiah Manoharan, Meitian Wang, Sheng Cui
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.ppat.1006636
Nanobodies targeting norovirus capsid reveal functional epitopes and potential mechanisms of neutralization
Cited by: 45
Author(s): A.D. Koromyslova, Grant S. Hansman
Software Mentions: 1
Published: about 7 years ago
10.1371/journal.ppat.1006667
In vitro characterization of the antivirulence target of Gram-positive pathogens, peptidoglycan O-acetyltransferase A (OatA)
Cited by: 32
Author(s): David Sychantha, Carys S Jones, Dustin J. Little, Patrick J. Moynihan, Howard Robinson, Nicola F. Galley, David I. Roper, Christopher G. Dowson, P. Lynne Howell, Anthony J. Clarke
Software Mentions: 1
Published: about 7 years ago
10.1371/journal.ppat.1006777
Two classes of protective antibodies against Pseudorabies virus variant glycoprotein B: Implications for vaccine design
Cited by: 29
Author(s): Xiangdong Li, Fulun Yang, Xule Hu, Feifei Tan, Jianxun Qi, Ruchao Peng, Min Wang, Yan Chai, Liqing Hao, Junhua Deng, Chenyu Bai, Juan Wang, Hao Song, Shuguang Tan, Guangwen Lu, George F. Gao, Yi Shi, Kegong Tian
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.ppat.1006811
Indole-3-acetaldehyde dehydrogenase-dependent auxin synthesis contributes to virulence of Pseudomonas syringae strain DC3000
Cited by: 99
Author(s): Sheri A. McClerklin, Soon Goo Lee, Christopher P. Harper, Ron Nwumeh, Joseph M. Jez, Barbara N. Kunkel
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.ppat.1006998
PgaB orthologues contain a glycoside hydrolase domain that cleaves deacetylated poly-β(1,6)-N-acetylglucosamine and can disrupt bacterial biofilms
Cited by: 52
Author(s): Dustin J. Little, Roland Pfoh, François Le Mauff, Natalie C. Bamford, Christina Notte, Perrin Baker, Manita Guragain, Howard Robinson, Gerald B. Pier, Mark Nitz, Rajendar Deora, Donald C. Sheppard, P. Lynne Howell
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.ppat.1007052
RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization
Cited by: 15
Author(s): David G. Glanville, Lu Han, Andrew J. Maule, Alexandra Woodacre, Devsaagar Thanki, Iman Tajer Abdullah, Julie A. Morrissey, Tom Clarke, Hasan Yeşilkaya, N.R. Silvaggi, Andrew T. Ulijasz
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.ppat.1007236
Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2
Cited by: 684
Author(s): Wenchao Song, Miao Gui, Xinquan Wang, Ye Xiang
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.ppat.1007224
Molecular basis for CesT recognition of type III secretion effectors in enteropathogenic Escherichia coli
Cited by: 13
Author(s): Dustin J. Little, Brian K. Coombes
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.ppat.1007304
Crystal structure of a soluble fragment of poliovirus 2CATPase
Cited by: 24
Author(s): Hongxin Guan, Juan Tian, Chu Zhang, Bo Qin, Sheng Cui
Software Mentions: 1
Published: about 6 years ago
10.1371/journal.ppat.1007343
Structure-guided disruption of the pseudopilus tip complex inhibits the Type II secretion in Pseudomonas aeruginosa
Cited by: 15
Author(s): Yichen Zhang, Frédérick Faucher, Wenwen Zhang, Shu Wang, Nolan Neville, Keith Poole, Jun Zheng, Zongchao Jia
Software Mentions: 1
Published: about 6 years ago
10.1371/journal.ppat.1007562
Structural roles of PCV2 capsid protein N-terminus in PCV2 particle assembly and identification of PCV2 type-specific neutralizing epitope
Cited by: 35
Author(s): Xiaobing Mo, Xiangdong Li, Biaolin Yin, Junhua Deng, Kegong Tian, Adam Yuan
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.ppat.1007659
Structural determination of the complement inhibitory domain of Borrelia burgdorferi BBK32 provides insight into classical pathway complement evasion by Lyme disease spirochetes
Cited by: 32
Author(s): Jialei Xie, Hui Zhi, Ryan J. Garrigues, Andrew Keightley, Brandon L. Garcia, Jon T. Skare
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.ppat.1007829
Structure of a functional cap-binding domain in Rift Valley fever virus L protein
Cited by: 37
Author(s): Nadja Gogrefe, Sophia Reindl, Stephan Günther, Maria Rosenthal
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.ppat.1008165
Cooperation between somatic mutation and germline-encoded residues enables antibody recognition of HIV-1 envelope glycans
Cited by: 5
Author(s): Nelson R. Wu, Nathan I. Nicely, Esther M. Lee, Rachel K. Reed, Brian Watts, Fangping Cai, William E. Walkowicz, Baptiste Aussedat, Julia A. Jones, Amanda Eaton, Ashley M. Trama, S. Munir Alam, David C. Montefiori, Barton F. Haynes, Kevin O. Saunders
Software Mentions: 1
Published: about 5 years ago
10.1371/journal.ppat.1008314
Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage
Cited by: 49
Author(s): James L. Kizziah, Keith A. Manning, Altaira D. Dearborn, Terje Dokland
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.ppat.1008336
The role of 9-O-acetylated glycan receptor moieties in the typhoid toxin binding and intoxication
Cited by: 27
Author(s): Tri Nguyen, Sohyoung Lee, Yi Yang, Changhwan Ahn, Ji Hyun Sim, Tiffany G. Kei, Karen N. Barnard, Hai Yu, Shawn K. Millano, Xi Chen, Colin R. Parrish, Jeongmin Song
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.ppat.1007806
Potent, specific MEPicides for treatment of zoonotic staphylococci
Cited by: 12
Author(s): Rachel L. Edwards, Isabel Heueck, Soon Goo Lee, Ishaan Shah, Jenna Miller, Andrew J. Jezewski, Marwa O. Mikati, Xu Wang, Kenneth M. Heidel, Damon M. Osbourn, Carey-Ann D. Burnham, Sophie Alvarez, Stephanie A. Fritz, Cynthia S. Dowd, Joseph M. Jez, Audrey Odom John
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.ppat.1008734
Structural insight into the membrane targeting domain of the Legionella deAMPylase SidD
Cited by: 4
Author(s): Igor Tascón, Xiao Li, María Lucas, D’anna M. Nelson, A. Vidaurrazaga, Yi‐Han Lin, Adriana L. Rojas, Aitor Hierro, Matthias P. Machner
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.ppat.1009062
Structural intermediates in the low pH-induced transition of influenza hemagglutinin
Cited by: 12
Author(s): Jingjing Gao, Miao Gui, Ye Xiang
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.ppat.1009089
A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody
Cited by: 49
Author(s): Nicholas C. Wu, Meng Yuan, Sandhya Bangaru, Deli Huang, Xueyong Zhu, Chang-Chun David Lee, Hannah L. Turner, Linghang Peng, Linlin Yang, Dennis R. Burton, David Nemazee, Andrew B. Ward, Ian A. Wilson
Software Mentions: 1
Published: about 4 years ago
10.1073/pnas.1906717116
A structure-based rationale for sialic acid independent host-cell entry of Sosuga virus
Cited by: 10
Author(s): Alice J. Stelfox, Thomas A. Bowden
Software Mentions: 1
Published: about 5 years ago
10.1073/pnas.1917726117
Phage liquid crystalline droplets form occlusive sheaths that encapsulate and protect infectious rod-shaped bacteria
Cited by: 67
Author(s): Abul K. Tarafder, Andriko von Kügelgen, Adam J. Mellul, Ulrike Schulze, Dirk G. A. L. Aarts, Tanmay A. M. Bharat
Software Mentions: 1
Published: almost 5 years ago
10.1073/pnas.2008671117
Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome
Cited by: 28
Author(s): Zahira Batool, Ivan B. Lomakin, Yury S. Polikanov, Christopher G. Bunick
Software Mentions: 1
Published: over 4 years ago
10.1073/pnas.2013998117
Structure of the dimeric ATP synthase from bovine mitochondria
Cited by: 124
Author(s): T.E. Spikes, M.G. Montgomery, John E. Walker
Software Mentions: 1
Published: over 4 years ago
10.1073/pnas.2017637117
Structure of eukaryotic DNA polymerase δ bound to the PCNA clamp while encircling DNA
Cited by: 36
Author(s): Fengwei Zheng, Roxana E. Georgescu, Li H, Mike O'Donnell
Software Mentions: 1
Published: about 4 years ago
10.1073/pnas.2020216118
Cross-species recognition of SARS-CoV-2 to bat ACE2
Cited by: 69
Author(s): Kefang Liu, Shuguang Tan, Sheng Niu, Jia Wang, Lili Wu, Huan Sun, Yanfang Zhang, Xiaoqian Pan, Xiao Qu, Pei Du, Yumin Meng, Yunfei Jia, Qian Chen, Chu‐Xia Deng, Jinghua Yan, Hongwei Wang, Qihui Wang, Jianxun Qi, George F. Gao
Software Mentions: 1
Published: almost 4 years ago
10.1073/pnas.2024512118
Molecular mechanisms of assembly and TRIP13-mediated remodeling of the human Shieldin complex
Cited by: 16
Author(s): Wei Xie, Shengliu Wang, Juncheng Wang, M. Jason de la Cruz, Guotai Xu, Maurizio Scaltriti, Dinshaw J. Patel
Software Mentions: 1
Published: almost 4 years ago
10.1073/pnas.2022586118
The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2
Cited by: 124
Author(s): D.J. Benton, Antoni G. Wrobel, Chloë Roustan, Annabel Borg, Pengqi Xu, Stephen R. Martin, Peter B. Rosenthal, J.J. Skehel, S.J. Gamblin
Software Mentions: 1
Published: almost 4 years ago
10.1073/pnas.2022756118
Structure of Gcn1 bound to stalled and colliding 80S ribosomes
Cited by: 66
Author(s): Agnieszka A. Pochopien, Bertrand Beckert, Sergo Kasvandik, Otto Berninghausen, Roland Beckmann, Tanel Tenson, Daniel N. Wilson
Software Mentions: 1
Published: over 3 years ago
10.1073/pnas.2101918118
Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice
Cited by: 97
Author(s): Phillip Pymm, Amy Adair, Li‐Jin Chan, James P. Cooney, Francesca L Mordant, Cody Allison, Ester López, Ebene R Haycroft, Matthew T O'Neill, Li Lynn Tan, M.H. Dietrich, Damien R. Drew, Marcel Doerflinger, Michael A. Dengler, Nichollas E. Scott, Adam K. Wheatley, Nicholas A. Gherardin, Hariprasad Venugopal, Deborah Cromer, Miles P. Davenport, Raelene Pickering, Dale I. Godfrey, Damian F. J. Purcell, Stephen J. Kent, Amy W. Chung, Kanta Subbarao, Marc Pellegrini, Alisa Glukhova, Wai‐Hong Tham
Software Mentions: 1
Published: over 3 years ago
10.1007/s13238-014-0035-2
Revisiting the TALE repeat
Cited by: 35
Author(s): Dong Deng, Chuangye Yan, Jianping Wu, Xiaojing Pan, Nieng Yan
Software Mentions: 1
Published: almost 11 years ago
10.1007/s13238-014-0108-2
Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases
Cited by: 49
Author(s): Chunmei Jia, Mei Li, Jianjun Li, Jingjing Zhang, Hongmei Zhang, Peng Cao, Xiaowei Pan, Xuefeng Lü, Wenrui Chang
Software Mentions: 1
Published: about 10 years ago
10.1007/s13238-015-0181-1
Molecular basis for the inhibition of β-hydroxyacyl-ACP dehydratase HadAB complex from Mycobacterium tuberculosis by flavonoid inhibitors
Cited by: 25
Author(s): Yuhui Dong, Xinwei Qiu, Neil Shaw, Yueyang Xu, Yuna Sun, Xuemei Li, Jun Li, Zihe Rao
Software Mentions: 1
Published: over 9 years ago
10.1007/s13238-016-0289-y
An unusual UMP C-5 methylase in nucleoside antibiotic polyoxin biosynthesis
Cited by: 7
Author(s): Wenqing Chen, Yan Li, Jie Li, Lian Wu, Yan Li, Renxiao Wang, Zixin Deng, Jiahai Zhou
Software Mentions: 1
Published: over 8 years ago
10.1007/s13238-019-00671-z
Structural insights into substrate recognition by the type VII secretion system
Cited by: 23
Author(s): Shuhui Wang, Kaixuan Zhou, Xiaolin Yang, Bing Zhang, Yao Zhao, Yu Xiao, Xiuna Yang, Haitao Yang, Luke W. Guddat, Jun Li, Zihe Rao
Software Mentions: 1
Published: about 5 years ago
10.1007/s13238-021-00871-6
An ultrapotent pan-β-coronavirus lineage B (β-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope
Cited by: 18
Author(s): Zezhong Liu, Wei Xu, Zhenguo Chen, Wangyang Fu, Wuqiang Zhan, Yidan Gao, Jie Zhou, Yunjiao Zhou, Jianbo Wu, Qin Wang, Xiang Zhang, Aihua Hao, Wei Wu, Qianqian Zhang, Yaming Li, Kaiyue Fan, Ruihong Chen, Qiaochu Jiang, Christian T. Mayer, Till Schoofs, Youhua Xie, Shibo Jiang, Yumei Wen, Zhenghong Yuan, Kang Wang, Lu Lu, Lei Sun, Qiao Wang
Software Mentions: 1
Published: about 3 years ago
10.1093/protein/gzu007
Adhiron: a stable and versatile peptide display scaffold for molecular recognition applications
Cited by: 132
Author(s): Christian Tiede, Anna A Tang, Sarah E. Deacon, Upasana Mandal, Joanne E. Nettleship, R.L. Owen, Suja E. George, David J. Harrison, Raymond J. Owens, Darren C. Tomlinson, Michael J. McPherson
Software Mentions: 1
Published: over 10 years ago
10.1002/pro.3439
X-ray crystal structures of the type IVb secretion system DotB ATPases
Cited by: 14
Author(s): Marie S. Prevost, Gabriel Waksman
Software Mentions: 1
Published: over 6 years ago
10.1002/pro.3955
Iris: Interactive all‐in‐one graphical validation of <scp>3D</scp> protein model iterations
Cited by: 5
Author(s): William Rochira, Jon Agirre
Software Mentions: 1
Published: about 4 years ago
10.34133/2019/5641746
Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System
Cited by: 9
Author(s): Seung-Joo Lee, Rou-Jia Sung, Gregory L. Verdine
Software Mentions: 1
Published: almost 6 years ago
10.34133/2019/2602414
Crystal Structure of 4-Hydroxyphenylpyruvate Dioxygenase in Complex with Substrate Reveals a New Starting Point for Herbicide Discovery
Cited by: 55
Author(s): Hong‐Yan Lin, Xi Chen, Jianan Chen, Dawei Wang, Feng-Xu Wu, Song-Yun Lin, Zhan Chen, Jiawei Wu, Wen‐Chao Yang, Guang‐Fu Yang
Software Mentions: 1
Published: almost 6 years ago
10.1186/s12977-019-0489-7
Characterization of resistance to a potent d-peptide HIV entry inhibitor
Cited by: 5
Author(s): Amanda R. Smith, Matthew T. Weinstock, Amanda E. Siglin, Frank G. Whitby, James N. Francis, Christopher P. Hill, Debra M. Eckert, Michael J. Root, Michael S. Kay
Software Mentions: 1
Published: about 5 years ago
10.1177/2472555220960428
Discovery of Drug-Like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3
Cited by: 30
Author(s): Rajdeep S Virdi, Robert Bavisotto, Nicholas C Hopper, Nemanja Vuksanovic, Trevor R Melkonian, N.R. Silvaggi, David N. Frick
Software Mentions: 1
Published: about 4 years ago
10.1016/j.xpro.2021.100642
Protocol for improving diffraction quality of leucyl-tRNA synthetase 1 with methylation and post-crystallization soaking and cooling in cryoprotectants
Cited by: 0
Author(s): Sulhee Kim, Ina Yoon, Sung Hoon Kim, Kwang Yeon Hwang
Software Mentions: 1
Published: over 3 years ago
10.1016/j.xpro.2021.100686
Protocol for the use of focused ion-beam milling to prepare crystalline lamellae for microcrystal electron diffraction (MicroED)
Cited by: 7
Author(s): Michael W. Martynowycz, Tamir Gonen
Software Mentions: 1
Published: over 3 years ago
10.1126/sciadv.aax8855
Cryo–electron microscopy structure and analysis of the P-Rex1–Gβγ signaling scaffold
Cited by: 28
Author(s): Jennifer N. Cash, Sarah Urata, Sheng Li, Sandeep K. Ravala, Larisa Avramova, Michael D. Shost, J. Silvio Gutkind, John J.G. Tesmer, Michael A. Cianfrocco
Software Mentions: 1
Published: about 5 years ago
10.1126/sciadv.aax1836
Allosteric modulation of nucleoporin assemblies by intrinsically disordered regions
Cited by: 12
Author(s): Bartlomiej J. Blus, Junseock Koh, Aleksandra Królak, Hyuk‐Soo Seo, Elias Coutavas, Günter Blobel
Software Mentions: 1
Published: about 5 years ago
10.1126/sciadv.abe2631
Structures of <i>Rhodopseudomonas palustris</i> RC-LH1 complexes with open or closed quinone channels
Cited by: 37
Author(s): David J. K. Swainsbury, Pu Qian, Philip J. Jackson, Kaitlyn M. Faries, Dariusz M. Niedzwiedzki, Elizabeth C. Martin, David A. Farmer, Lorna A. Malone, Rebecca Thompson, Neil A. Ranson, Daniel P. Canniffe, Mark J. Dickman, Dewey Holten, Christine Kirmaier, Andrew Hitchcock, C. Neil Hunter
Software Mentions: 1
Published: almost 4 years ago
10.1126/sciadv.abg9676
Genetic prion disease–related mutation E196K displays a novel amyloid fibril structure revealed by cryo-EM
Cited by: 24
Author(s): Liqiang Wang, Kun Zhao, Han-Ye Yuan, Xiangning Li, Hai-Bin Dang, Yeyang Ma, Qiang Wang, Chen Wang, Yunpeng Sun, Jie Chen, Dan Li, Delin Zhang, Ping Yin, Cong Liu, Yi Liang
Software Mentions: 1
Published: over 3 years ago
10.1038/s41597-019-0010-0
MHz data collection of a microcrystalline mixture of different jack bean proteins
Cited by: 4
Author(s): Marie Luise Grünbein, Johan Bielecki, A. Gorel, M. Stricker, Richard Bean, Marco Cammarata, Katerina Dörner, Lars Fröhlich, Elisabeth Hartmann, Steffen Hauf, M. Hilpert, Yoonhee Kim, Marco Kloos, Romain Letrun, Marc Messerschmidt, Grant Mills, Gabriela Nass Kovács, Marco Ramilli, C.M. Roome, Tokushi Sato, Matthias Scholz, Michel Sliwa, J. Sztuk-Dambietz, Martin H. Weik, Britta Weinhausen, Nasser Al-Qudami, Djelloul Boukhelef, Sándor Brockhauser, Wajid Ehsan, Moritz Emons, Sergey Esenov, Hans Fangohr, A. Kaukher, Thomas Kluyver, Max Lederer, Luis Maia, Maurizio Manetti, Thomas Michelat, A. Münnich, Florent Pallas, Guido Palmer, Gianpietro Previtali, Natascha Raab, A. Silenzi, J. Szuba, Sandhya Venkatesan, K. Wrona, Jun Zhu, R. Bruce Doak, Robert L. Shoeman, L. Foucar, J.P. Colletier, Adrian P. Mancuso, T.R.M. Barends, Claudiu A. Stan, Ilme Schlichting
Software Mentions: 1
Published: over 5 years ago
10.1038/srep09878
Auto-inhibitory Mechanism of the Human Mitochondrial RNase P Protein Complex
Cited by: 26
Author(s): Fengzhi Li, Xiaofen Liu, Weihong Zhou, Xue Yang, Yuequan Shen
Software Mentions: 1
Published: over 9 years ago
10.1038/srep09762
Protein stabilization utilizing a redefined codon
Cited by: 33
Author(s): Kazumasa Ohtake, Atsushi Yamaguchi, Takahito Mukai, Hiroki Kashimura, Nobutaka Hirano, Mitsuru Haruki, Sosuke Kohashi, Kazumasa Yamagishi, Kazutaka Murayama, Yuri Tomabechi, Takashi Itagaki, Ryogo Akasaka, Masahito Kawazoe, Chie Takemoto, Mikako Shirouzu, Shigeyuki Yokoyama, Kensaku Sakamoto
Software Mentions: 1
Published: over 9 years ago
10.1038/srep10451
A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering
Cited by: 106
Author(s): Philip Roedig, Ismo Vartiainen, Ramona Duman, S. Panneerselvam, Nicolas Stübe, O. Lorbeer, Martin Warmer, Geoff Sutton, David I. Stuart, E. Weckert, Christian Dávid, Armin Wagner, A. Meents
Software Mentions: 1
Published: over 9 years ago
10.1038/srep12830
Crystal structures of Mycobacterium tuberculosis GlgE and complexes with non-covalent inhibitors
Cited by: 12
Author(s): Jared Lindenberger, Sri Kumar Veleti, Brittney N. Wilson, Steven J. Sucheck, Donald R. Ronning
Software Mentions: 1
Published: over 9 years ago
10.1038/s41598-018-28599-0
Understanding the indirect DNA read-out specificity of I-CreI Meganuclease
Cited by: 12
Author(s): Jesús Prieto, Pilar Negrete Redondo, Blanca López-Méndez, Marco D’Abramo, Nekane Merino, Francisco J. Blanco, P. Duchateau, Guillermo Montoya, Rafael Molina
Software Mentions: 1
Published: over 6 years ago
10.1038/s41598-018-28783-2
A V-to-F substitution in SK2 channels causes Ca2+ hypersensitivity and improves locomotion in a C. elegans ALS model
Cited by: 12
Author(s): Young‐Woo Nam, Sabia N. Baskoylu, Dimitris Gazgalis, Razan Orfali, Meng Cui, Anne C. Hart, Miao Zhang
Software Mentions: 1
Published: over 6 years ago
10.1038/s41598-018-29182-3
Electrostatic Tuning of the Ligand Binding Mechanism by Glu27 in Nitrophorin 7
Cited by: 4
Author(s): Stefania Abbruzzetti, Alessandro Allegri, Axel Bidon‐Chanal, Hideaki Ogata, Giancarlo Soavi, Giulio Cerullo, Stefano Bruno, Chiara Montali, F. Javier Luque, Cristiano Viappiani
Software Mentions: 1
Published: over 6 years ago