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

10.1111/febs.15514
Structure‐based design of peptides that trigger <i>Streptococcus pneumoniae</i> cell death
Cited by: 11
Author(s): Sung-Min Kang, Chun Jin, Do-Hee Kim, Sung Jean Park, Sang-Woo Han, Bong-Jin Lee
Software Mentions: 3
Published: about 4 years ago
10.1186/s13104-015-1760-1
Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation
Cited by: 6
Author(s): Noriko Inoguchi, Kittichai Chaiseeda, Mamoru Yamanishi, Moon Ki Kim, Yunho Jang, M. Bajaj, Catherine P. Chia, Donald F. Becker, Hideaki Moriyama
Software Mentions: 3
Published: almost 9 years ago
10.3389/fmolb.2021.652530
Cryo-EM Map–Based Model Validation Using the False Discovery Rate Approach
Cited by: 4
Author(s): Mateusz Olek, Agnel Praveen Joseph
Software Mentions: 3
Published: over 3 years ago
10.3389/fpls.2021.668897
The Plastid-Encoded RNA Polymerase-Associated Protein PAP9 Is a Superoxide Dismutase With Unusual Structural Features
Cited by: 8
Author(s): Adrien Favier, Pierre Gans, Elisabetta Erba, Luca Signor, Soumiya Sankari Muthukumar, Thomas Pfannschmidt, Robert Blanvillain, David Cobessi
Software Mentions: 3
Published: over 3 years ago
10.1128/JB.00115-20
A Novel Growth-Based Selection Strategy Identifies New Constitutively Active Variants of the Major Virulence Regulator PrfA in Listeria monocytogenes
Cited by: 4
Author(s): S. Hansen, Michael Hall, C. Grundström, Kristoffer Brännström, A. Elisabeth Sauer‐Eriksson, Jörgen Johansson
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.ppat.1005265
The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases
Cited by: 25
Author(s): D.S. Ferrero, M. Buxaderas, José F. Rodrı́guez, N. Verdaguer
Software Mentions: 3
Published: almost 9 years ago
10.1371/journal.ppat.1008848
Chaperone-tip adhesin complex is vital for synergistic activation of CFA/I fimbriae biogenesis
Cited by: 1
Author(s): Libang He, Hao Wang, Yang Liu, Mei Kang, Tao Li, Changcheng Li, Aiping Tong, Yuanfeng Zhu, Yingjie Song, Stephen J. Savarino, Michael G. Prouty, Di Xia, Rui Bao
Software Mentions: 3
Published: about 4 years ago
10.1073/pnas.1911776116
Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection
Cited by: 14
Author(s): Fiona Whelan, Aleix Lafita, Samuel C. Griffiths, R.E.M. Cooper, J.L. Whittingham, J.P. Turkenburg, Iain W. Manfield, Alexander N. St John, Emanuele Paci, Alex Bateman, Jennifer R. Potts
Software Mentions: 3
Published: almost 5 years ago
10.1126/sciadv.abh0250
X-ray free-electron laser studies reveal correlated motion during isopenicillin <i>N</i> synthase catalysis
Cited by: 19
Author(s): Patrick Rabe, Jos J. A. G. Kamps, Kyle D. Sutherlin, J. Linyard, Pierre Aller, Cindy C. Pham, Hiroki Makita, I.J. Clifton, M.A. McDonough, T.M. Leissing, Denis Shutin, Pauline A. Lang, A. Butryn, Jürgen Brem, Sheraz Gul, Franklin D. Fuller, In-Sik Kim, Mun Hon Cheah, Thomas Fransson, Asmit Bhowmick, I.D. Young, Lee J. O’Riordan, Aaron S. Brewster, Ilaria Pettinati, Margaret Doyle, Yasumasa Joti, Shigeki Owada, Kensuke Tono, A. Batyuk, Mark S. Hunter, Roberto Alonso-Mori, Uwe Bergmann, R.L. Owen, Nicholas K. Sauter, Timothy D. W. Claridge, Carol V. Robinson, Vittal K. Yachandra, Junko Yano, Jan Kern, Allen M. Orville, Christopher J. Schofield
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-018-29058-6
Structural determinants of specificity and regulation of activity in the allosteric loop network of human KLK8/neuropsin
Cited by: 7
Author(s): Mekdes Debela, Viktor Magdolen, Wolfgang Skala, Brigitta Elsässer, Eric L. Schneider, Charles S. Craik, Martin L. Biniossek, Oliver Schilling, Wolfram Bode, Hans Brandstetter, Peter Goettig
Software Mentions: 3
Published: over 6 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
10.1038/s41598-019-40432-w
Reactive centre loop dynamics and serpin specificity
Cited by: 28
Author(s): Emilia M. Marijanovic, James Fodor, Blake T. Riley, Benjamin T. Porebski, Maurício G. S. Costa, Itamar Kass, David E. Hoke, Sheena McGowan, Ashley M. Buckle
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-020-68419-y
Enzymatic reaction mechanism of cis-aconitate decarboxylase based on the crystal structure of IRG1 from Bacillus subtilis
Cited by: 8
Author(s): Hye Lin Chun, So Yeon Lee, Sung Hoon Lee, Chang Sup Lee, Hyun Ho Park
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.ppat.1008394
Structural and functional insights into a novel two-component endolysin encoded by a single gene in Enterococcus faecalis phage
Cited by: 21
Author(s): Biao Zhou, Xiangkai Zhen, Huan Zhou, Feiyang Zhao, Chao Fan, Vanja Perčulija, Yigang Tong, Zhiqiang Mi, Songying Ouyang
Software Mentions: 3
Published: over 4 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
10.1038/s42003-020-01123-9
Structure and function of a malaria transmission blocking vaccine targeting Pfs230 and Pfs230-Pfs48/45 proteins
Cited by: 34
Author(s): Kavita Singh, Martin Burkhardt, Sofia Nakuchima, Raúl Herrera, Olga Muratova, Apostolos G. Gittis, Emily Kelnhofer, Karine Reiter, Margery Smelkinson, Daniel Veltri, Bruce J. Swihart, Richard L. Shimp, Vu Nguyen, Baoshan Zhang, Nicholas J. MacDonald, Patrick E. Duffy, David N. Garboczi, David L. Narum
Software Mentions: 3
Published: over 4 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
10.1016/j.jmb.2015.08.023
Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain
Cited by: 9
Author(s): Nora Cronin, Jing Yang, Ziguo Zhang, Kiran Kulkarni, Leifu Chang, Hiroyuki Yamano, David Barford
Software Mentions: 3
Published: about 9 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
10.1371/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
10.1107/S1399004715004241
Using support vector machines to improve elemental ion identification in macromolecular crystal structures
Cited by: 4
Author(s): Nader Morshed, Nathaniel Echols, Paul D. Adams
Software Mentions: 3
Published: over 9 years ago
10.1111/cea.12230
Human <scp>I</scp> g <scp>E</scp> against the major allergen <scp>B</scp> et v 1 – defining an epitope with limited cross‐reactivity between different <scp>PR</scp> ‐10 family proteins
Cited by: 20
Author(s): Mattias Levin, Anna M. Davies, Maria Liljekvist, Fredrika Carlsson, Hannah J. Gould, Brian J. Sutton, Mats Ohlin
Software Mentions: 3
Published: almost 11 years ago
10.15252/embj.2021107985
Neutralization of SARS‐CoV‐2 by highly potent, hyperthermostable, and mutation‐tolerant nanobodies
Cited by: 56
Author(s): Thomas Güttler, Metin Aksu, Antje Dickmanns, Kim M. Stegmann, Kathrin Gregor, Renate Rees, Waltraud Taxer, Oleh Rymarenko, Jürgen Schünemann, Christian Dienemann, Philip Gunkel, Bianka Mußil, Jens Krull, Ulrike Teichmann, Uwe Groß, Volker C. Cordes, Matthias Dobbelstein, Dirk Görlich
Software Mentions: 3
Published: 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: over 11 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
10.1371/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
10.1371/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
10.3390/ijms22083812
Crystal Structure of the Epo1-Bem3 Complex for Bud Growth
Cited by: 0
Author(s): Jin Wang, Lei Li, Zhenhua Ming, Lijie Wu, Liming Yan
Software Mentions: 3
Published: over 3 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
10.1098/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
10.1093/aobpla/plw042
Experimental assessment of factors mediating the naturalization of a globally invasive tree on sandy coastal plains: a case study from Brazil
Cited by: 10
Author(s): Thalita Gabriella Zimmermann, Antônio Carlos Silva de Andrade, David M. Richardson
Software Mentions: 3
Published: over 9 years ago
10.1107/S090744491301576X
Complex structure of type VI peptidoglycan muramidase effector and a cognate immunity protein
Cited by: 17
Author(s): Tianyu Wang, Jingjin Ding, Ying Zhang, Dacheng Wang, Wei Liu
Software Mentions: 3
Published: about 11 years ago
10.1107/S2059798317017235
<i>DIALS</i>: implementation and evaluation of a new integration package
Cited by: 750
Author(s): Graeme Winter, David Waterman, James M. Parkhurst, Aaron S. Brewster, Richard J. Gildea, Markus Gerstel, Luis Fuentes-Montero, M. Vollmar, Tara Michels-Clark, I.D. Young, Nicholas K. Sauter, Gwyndaf Evans
Software Mentions: 3
Published: almost 7 years ago
10.1038/s41598-019-39641-0
Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H
Cited by: 13
Author(s): Chang Woo Lee, Sun Ha Park, Chang-Sung Jeong, Sun Mi Shin, Hyun Park, Jun Hyuck Lee
Software Mentions: 3
Published: over 5 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
10.1186/s13068-017-0944-4
Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity
Cited by: 29
Author(s): Bruno Luan Mello, Anna Alessi, Diego Mauricio Riaño‐Pachón, Eduardo R. deAzevedo, Francisco Eduardo Gontijo Guimarães, Melissa C. Espirito Santo, Simon J. McQueen‐Mason, Neil C. Bruce, Igor Polikarpov
Software Mentions: 3
Published: about 7 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: almost 11 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
10.1371/journal.ppat.1008736
Recognition of a highly conserved glycoprotein B epitope by a bivalent antibody neutralizing HCMV at a post-attachment step
Cited by: 14
Author(s): Xiaohua Ye, Hang Su, Daniel Wrapp, Daniel C. Freed, Fengsheng Li, Zihao Yuan, Aimin Tang, Leike Li, Zhiqiang Ku, Wei Xiong, Dabbu Kumar Jaijyan, Hua Zhu, Dai Wang, Jason S. McLellan, Ningyan Zhang, Tong-Ming Fu, Zhiqiang An
Software Mentions: 3
Published: over 4 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
10.1107/S1399004714001308
Automated identification of elemental ions in macromolecular crystal structures
Cited by: 37
Author(s): Nathaniel Echols, Nader Morshed, Pavel V. Afonine, Airlie J. McCoy, Mitchell D. Miller, Randy J. Read, Jane S. Richardson, Thomas C. Terwilliger, Paul D. Adams
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0167763
Crystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting Signal
Cited by: 21
Author(s): Michele D. Kattke, Albert H. Chan, Andrew Duong, Danielle L. Sexton, M.R. Sawaya, Duilio Cascio, Marie A. Elliot, Robert T. Clubb
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0096198
Structural Basis for the Site-Specific Incorporation of Lysine Derivatives into Proteins
Cited by: 16
Author(s): Veronika Flügel, Milan Vrábel, Sabine Schneider
Software Mentions: 2
Published: over 10 years ago
10.1107/S2053230X15003337
High-resolution crystal structure of a polyextreme GH43 glycosidase from<i>Halothermothrix orenii</i>with α-<scp>L</scp>-arabinofuranosidase activity
Cited by: 7
Author(s): Noor Hassan, Lokesh D. Kori, Rosaria Gandini, Bharat K. C. Patel, Christina Divne, T.C. Tan
Software Mentions: 2
Published: almost 10 years ago
10.1107/S2053230X16017891
The crystal structure of the endoglucanase Cel10, a family 8 glycosyl hydrolase from<i>Klebsiella pneumoniae</i>
Cited by: 9
Author(s): Ayman Attigani, Lifang Sun, Qing Wang, Yadan Liu, Ding-Ping Bai, Shengping Li, Xiaohong Huang
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0026021
Structural and Biochemical Studies of Human 4-hydroxy-2-oxoglutarate Aldolase: Implications for Hydroxyproline Metabolism in Primary Hyperoxaluria
Cited by: 49
Author(s): Travis J. Riedel, Lynnette C. Johnson, John Knight, Roy R. Hantgan, Ross P. Holmes, W. Todd Lowther
Software Mentions: 2
Published: about 13 years ago
10.1371/journal.pone.0080298
Diversification of Fungal Specific Class A Glutathione Transferases in Saprotrophic Fungi
Cited by: 37
Author(s): Yann Mathieu, P. Prosper, F. Favier, Luc Harvengt, Claude Didierjean, Jean‐Pierre Jacquot, Mélanie Morel‐Rouhier, Éric Gelhaye
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pone.0081904
New Conformational State of NHERF1-CXCR2 Signaling Complex Captured by Crystal Lattice Trapping
Cited by: 10
Author(s): Yuanyuan Jiang, Guorong Lu, Laura Trescott, Yuning Hou, Xiaoqing Guan, Shuo Wang, Angelique Stamenkovich, J.S. Brunzelle, Nualpun Sirinupong, Chunying Li, Zhe Yang
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0004656
Unusual Armadillo Fold in the Human General Vesicular Transport Factor p115
Cited by: 25
Author(s): Harald Striegl, Yvette Roske, Daniel Kümmel, Udo Heinemann
Software Mentions: 2
Published: over 15 years ago
10.1107/S1399004714019725
Structural characterization of the virulence factor nuclease A from<i>Streptococcus agalactiae</i>
Cited by: 7
Author(s): A.F. Moon, Philippe Gaudu, Lars C. Pedersen
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pntd.0004132
Structural and Functional Characterization of the Enantiomers of the Antischistosomal Drug Oxamniquine
Cited by: 18
Author(s): Alexander B. Taylor, Livia Pica‐Mattoccia, C. Polcaro, Enrica Donati, Xiaoguang Cao, Annalisa Basso, Алессандра Гуиди, Anastasia R. Rugel, S. Holloway, Timothy J. Anderson, P. John Hart, Donato Cioli, Philip T. LoVerde
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.pone.0033524
Carbohydrate Recognition by an Architecturally Complex α-N-Acetylglucosaminidase from Clostridium perfringens
Cited by: 42
Author(s): E. Ficko-Blean, C.P. Stuart, M.D.L. Suits, Melissa Cid, Matthew B. Tessier, Robert J. Woods, A.B. Boraston
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0242383
The crystal structure of mouse IRG1 suggests that cis-aconitate decarboxylase has an open and closed conformation
Cited by: 4
Author(s): Hye Lin Chun, So Yeon Lee, Ki-Hwa Kim, Chang Sup Lee, Tae‐Jin Oh, Hyun Ho Park
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0146457
The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex
Cited by: 14
Author(s): N. Silva-Martin, María I. Daudén, Sebastian Glatt, N.A. Hoffmann, Panagiotis L. Kastritis, Peer Bork, Martin Beck, Christoph W. Müller
Software Mentions: 2
Published: almost 9 years ago
10.1107/S1399004713033841
Structural characteristics of an insect group I chitinase, an enzyme indispensable to moulting
Cited by: 46
Author(s): Lei Chen, Tian Liu, Yong Zhou, Qi Chen, Xu Shen, Qing Yang
Software Mentions: 2
Published: over 10 years ago
10.1107/S0907444911007888
Structure of HLA-A*0301 in complex with a peptide of proteolipid protein: insights into the role of HLA-A alleles in susceptibility to multiple sclerosis
Cited by: 27
Author(s): Róisín M. McMahon, Lone Smidstrup Friis, Christian Siebold, Manuel A. Friese, Lars Fugger, E Y Jones
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pgen.1004533
The TRIM-NHL Protein LIN-41 Controls the Onset of Developmental Plasticity in Caenorhabditis elegans
Cited by: 59
Author(s): Cristina Tocchini, J.J. Keusch, Sarah Miller, Susanne Finger, H. Gut, Michael Stadler, Rafal Ciosk
Software Mentions: 2
Published: about 10 years ago
10.1107/S1399004715002308
Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array
Cited by: 67
Author(s): A.Y. Lyubimov, Thomas D. Murray, Antoine Koehl, Ismail Emre Araci, Monarin Uervirojnangkoorn, Oliver B. Zeldin, Aina E. Cohen, S. Michael Soltis, E.L. Baxter, Aaron S. Brewster, Nicholas K. Sauter, Axel T. Brunger, James M. Berger
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pbio.2005160
DENR–MCTS1 heterodimerization and tRNA recruitment are required for translation reinitiation
Cited by: 30
Author(s): Yasar Luqman Ahmed, Sibylle Schleich, Jonathan Bohlen, Nicolas Mandel, Bernd Simon, Irmgard Sinning, Aurelio A. Teleman
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pbio.3001209
Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes
Cited by: 31
Author(s): Dan Fu, Guangshun Zhang, Yuhui Wang, Zheng Zhang, Hengrui Hu, Shū Shěn, Jun Wu, Bo Li, Xin Li, Yaohui Fang, Jia Liu, Qiao Wang, Yunjiao Zhou, Wei Wang, Yufeng Li, Zhonghua Lu, Xiaoxiao Wang, Cui Nie, Yujie Tian, Da Chen, Yuan Wang, Xuan Zhou, Qisheng Wang, Feng Yu, Chen Zhang, Changjing Deng, Liang Zhou, Guang-kuo Guan, Ningsheng Shao, Zhiyong Lou, Fei Deng, Hongkai Zhang, Xinwen Chen, Manli Wang, Louis Liu, Zihe Rao, Yu Guo
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pgen.1002484
Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1
Cited by: 22
Author(s): Takehiro Nishimura, Guillaume Molinard, Tom J. Petty, Larissa Broger, Caroline Gabus, Thanos D. Halazonetis, Stéphane Thore, Jerzy Paszkowski
Software Mentions: 2
Published: almost 13 years ago
10.1107/S1399004714022755
Structural implications of the C-terminal tail in the catalytic and stability properties of manganese peroxidases from ligninolytic fungi
Cited by: 33
Author(s): Elena Fernández‐Fueyo, Sandra Acebes, Francisco J. Ruíz-Dueñas, Marı́a Jesús Martı́nez, Antonio Romero, F.J. Medrano, Vı́ctor Guallar, Ángel T. Martı́nez
Software Mentions: 2
Published: almost 10 years ago
10.1107/S1399004715009438
High-resolution crystal structures of the solubilized domain of porcine cytochrome<i>b</i><sub>5</sub>
Cited by: 3
Author(s): Yu Hirano, Shigenobu Kimura, Taro Tamada
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pbio.3000277
Structural insights into histone chaperone Chz1-mediated H2A.Z recognition and histone replacement
Cited by: 17
Author(s): Yunyun Wang, Sheng Liu, Lu Sun, Ning Xu, Shan Shan, Fei Wu, Xiaoping Liang, Yingzi Huang, Ed Luk, Carl Wu, Zheng Zhou
Software Mentions: 2
Published: over 5 years ago
10.1107/S2059798316016910
Strategies for carbohydrate model building, refinement and validation
Cited by: 45
Author(s): Jon Agirre
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pbio.1001776
Segmental Helical Motions and Dynamical Asymmetry Modulate Histidine Kinase Autophosphorylation
Cited by: 97
Author(s): A.E. Mechaly, Nathalie Sassoon, Jean‐Michel Betton, Pedro M. Alzari
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pbio.3001386
Structural characterization of the Plasmodium falciparum lactate transporter PfFNT alone and in complex with antimalarial compound MMV007839 reveals its inhibition mechanism
Cited by: 9
Author(s): Xi Peng, Nan Wang, Angqi Zhu, Hanwen Xu, Jialu Li, Yanxia Zhou, Chen Wang, Qi Xiao, Li Guo, Fei Liu, Zhijun Jia, Huaichuan Duan, Jianping Hu, Weidan Yuan, Jia Geng, Chuangye Yan, Xin Jiang, Dong Deng
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pntd.0005374
Structure of SALO, a leishmaniasis vaccine candidate from the sand fly Lutzomyia longipalpis
Cited by: 10
Author(s): Oluwatoyin A. Asojo, Alan Kelleher, Zhuyun Liu, Jeroen Pollet, Elissa M. Hudspeth, Wanderson Rezende, Mallory Jo Groen, Christopher A. Seid, Maha Abdeladhim, Shannon E. Townsend, Waldionê de Castro, Antonio Ferreira Mendes-Sousa, Daniella Castanheira Bartholomeu, Ricardo Toshio Fujiwara, María Elena Bottazzi, Peter J. Hotez, Bin Zhan, Fabiano Oliveira, Shaden Kamhawi, Jesús G. Valenzuela
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0032070
Recognition of Anesthetic Barbiturates by a Protein Binding Site: A High Resolution Structural Analysis
Cited by: 13
Author(s): Simon Oakley, L.S. Vedula, Weiming Bu, Qing Cheng Meng, Xi Jin, Renyu Liu, Roderic G. Eckenhoff, Patrick J. Loll
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pbio.1000589
Structural Basis of Response Regulator Dephosphorylation by Rap Phosphatases
Cited by: 86
Author(s): Vijay Parashar, Nicolas Mirouze, David Dubnau, Matthew B. Neiditch
Software Mentions: 2
Published: almost 14 years ago
10.1107/S1399004715000152
Structure of Csd3 from<i>Helicobacter pylori</i>, a cell shape-determining metallopeptidase
Cited by: 17
Author(s): Doo Ri An, Hyoun Sook Kim, Jieun Kim, Ha Na Im, Hye Jin Yoon, Ji Young Yoon, Jun Young Jang, Dušan Hesek, Mijoon Lee, Shahriar Mobashery, Soon-Jong Kim, Byung Il Lee, Se Won Suh
Software Mentions: 2
Published: over 9 years ago
10.3390/v13081495
Crystal Structure of a Retroviral Polyprotein: Prototype Foamy Virus Protease-Reverse Transcriptase (PR-RT)
Cited by: 3
Author(s): Jerry Joe Ebow Kingsley Harrison, Steve Tuske, Kalyan Kumar Das, Francesc Xavier Ruiz, J.D. Bauman, Paul L. Boyer, Jeffrey J. DeStefano, Stephen H. Hughes, Eddy Arnold
Software Mentions: 2
Published: over 3 years ago
10.1107/S1399004714018732
Structural basis for the recognition of muramyltripeptide by<i>Helicobacter pylori</i>Csd4, a<scp>D</scp>,<scp>L</scp>-carboxypeptidase controlling the helical cell shape
Cited by: 19
Author(s): Hyoun Sook Kim, Jieun Kim, Ha Na Im, Doo Ri An, Mijoon Lee, Dušan Hesek, Shahriar Mobashery, Jin Young Kim, Kun Cho, Hye Jin Yoon, Byung Woo Han, Byung Il Lee, Se Won Suh
Software Mentions: 2
Published: about 10 years ago
10.20411/pai.v4i2.338
Crystal Structure and Immunogenicity of the DS-Cav1-Stabilized Fusion Glycoprotein From Respiratory Syncytial Virus Subtype B
Cited by: 24
Author(s): Michael Joyce, Amy Bao, Man Chen, Ivelin S. Georgiev, Li Ou, Tatsiana Bylund, Aliaksandr Druz, Wing-Pui Kong, Dongjun Peng, E.J. Rundlet, Joseph G. Van Galen, Shuishu Wang, Yongping Yang, Baoshan Zhang, Gwo-Yu Chuang, Jason S. McLellan, Barney S. Graham, John R. Mascola, Peter D. Kwong
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pbio.1002480
The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation
Cited by: 39
Author(s): Sohail Khoshnevis, Isabel Askenasy, Matthew C. Johnson, Maria D. Dattolo, Crystal L. Young-Erdos, M. Elizabeth Stroupe, Katrin Karbstein
Software Mentions: 2
Published: over 8 years ago
10.1107/S2059798318005764
From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation
Cited by: 6
Author(s): Pavel V. Afonine, Paul D. Adams, Alexandre Urzhumtsev
Software Mentions: 2
Published: over 6 years ago
10.1107/S090744491302252X
Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2
Cited by: 53
Author(s): Naoki Horikoshi, Koichi Sato, Keisuke Shimada, Yasuhiro Arimura, Akihisa Osakabe, Hiroaki Tachiwana, Yoko Hayashi‐Takanaka, W. Iwasaki, Wataru Kagawa, Masahiko Harata, Hiroshi Kimurâ, Hitoshi Kurumizaka
Software Mentions: 2
Published: about 11 years ago
10.1107/S205979831801519X
Iron–sulfur clusters have no right angles
Cited by: 15
Author(s): Nigel W. Moriarty, Paul D. Adams
Software Mentions: 2
Published: almost 6 years ago
10.3390/v13061101
The Molecular Basis for Escherichia coli O157:H7 Phage FAHEc1 Endolysin Function and Protein Engineering to Increase Thermal Stability
Cited by: 7
Author(s): Michael J. Love, David Coombes, Sarah H. Manners, Gayan S. Abeysekera, Craig Billington, Renwick C. J. Dobson
Software Mentions: 2
Published: over 3 years ago
10.1107/S2059798318013347
Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space
Cited by: 23
Author(s): Brendan Sullivan, Rick Archibald, Patricia S. Langan, Holger Dobbek, Martin Bommer, Robert L. McFeeters, Leighton Coates, Xiaoping Wang, Franz X. Gallmeier, J.M. Carpenter, V. E. Lynch, Paul Langan
Software Mentions: 2
Published: about 6 years ago
10.1107/S2059798319006831
Structural and functional characterization of CMP-<i>N</i>-acetylneuraminate synthetase from<i>Vibrio cholerae</i>
Cited by: 1
Author(s): Sucharita Bose, Debayan Purkait, Deepthi Joseph, Vinod Nayak, Ramaswamy Subramanian
Software Mentions: 2
Published: over 5 years ago
10.1107/S0907444912040590
Nearest-cell: a fast and easy tool for locating crystal matches in the PDB
Cited by: 13
Author(s): Varun Ramraj, Gwyndaf Evans, Jonathan M. Diprose, Robert Esnouf
Software Mentions: 2
Published: about 12 years ago
10.1107/S139900471501857X
Native sulfur/chlorine SAD phasing for serial femtosecond crystallography
Cited by: 50
Author(s): Takanori Nakane, Changyong Song, Mamoru Suzuki, Eriko Nango, Jun Kobayashi, Tetsuya Masuda, Shiro Inoue, Eiichi Mizohata, Toru Nakatsu, Tomoyuki Tanaka, Rie Tanaka, Tatsuro Shimamura, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, So Iwata, Michihiro Sugahara
Software Mentions: 2
Published: almost 9 years ago
10.3390/v12121346
Structural Basis of Zika Virus Specific Neutralization in Subsequent Flavivirus Infections
Cited by: 7
Author(s): Madhumati Sevvana, Thomas F. Rogers, Andrew Miller, Feng Long, Thomas Klose, Nathan Beutler, Yu-Cheng Lai, Mara Parren, Laura M. Walker, Geeta Buda, Dennis R. Burton, Michael G. Rossmann, Richard Kühn
Software Mentions: 2
Published: almost 4 years ago
10.1007/s11120-017-0450-3
Crystal structure of Psb27 from Arabidopsis thaliana determined at a resolution of 1.85 Å
Cited by: 7
Author(s): Xingxing Cheng, Jiuyang Liu, Huan Zhang, Fudong Li, Zhang Shuya, Min Xu, Ke Ruan, Yuhua Wang, Aigen Fu
Software Mentions: 2
Published: about 7 years ago
10.3390/v13040663
Structural Characterization of a Minimal Antibody against Human APOBEC3B
Cited by: 1
Author(s): Heng Tang, Özlem Demir, Fredy Kurniawan, William L. Brown, Ke Shi, Nicholas H. Moeller, Michael A. Carpenter, Christopher Belica, Kayo Orellana, Guocheng Du, Aaron M. LeBeau, Rommie E. Amaro, Reuben S. Harris, Hideki Aihara
Software Mentions: 2
Published: over 3 years ago
10.3390/v13071374
Structural Investigation of Orf Virus Bcl-2 Homolog ORFV125 Interactions with BH3-Motifs from BH3-Only Proteins Puma and Hrk
Cited by: 3
Author(s): Chathura D. Suraweera, Mark G. Hinds, Marc Kvansakul
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pbio.1001226
Structural Basis of Response Regulator Inhibition by a Bacterial Anti-Activator Protein
Cited by: 52
Author(s): Melinda D. Baker, Matthew B. Neiditch
Software Mentions: 2
Published: almost 13 years ago
10.1186/1743-422X-7-359
Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives
Cited by: 40
Author(s): Timothy C. Mueser, Jennifer M. Hinerman, Juliette M. Devos, Ryan A Boyer, Kandace J. Williams
Software Mentions: 2
Published: almost 14 years ago
10.1107/S0907444910001502
Detection and correction of underassigned rotational symmetry prior to structure deposition
Cited by: 12
Author(s): Billy K. Poon, Ralf W. Grosse‐Kunstleve, Peter H. Zwart, Nicholas K. Sauter
Software Mentions: 2
Published: over 14 years ago
10.3390/v7122946
Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone
Cited by: 43
Author(s): Carmela Garcia-Doval, José R. Castón, Daniel Luque, Meritxell Granell, José M. Otero, Antonio L. Llamas‐Saiz, Madalena Renouard, P. Boulanger, Mark J. van Raaij
Software Mentions: 2
Published: almost 9 years ago
10.1107/S2059798319008933
Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data
Cited by: 0
Author(s): Laurel Jones, Michael Tynes, Paul Smith
Software Mentions: 2
Published: over 5 years ago
10.1111/mmi.12656
The structure, function and properties of sirohaem decarboxylase - an enzyme with structural homology to a transcription factor family that is part of the alternative haem biosynthesis pathway
Cited by: 14
Author(s): David J. Palmer, Susanne Schroeder, Andrew D. Lawrence, Evelyne Deery, Susana A.L. Lobo, Lı́gia M. Saraiva, Kirsty J. McLean, Andrew W. Munro, Stuart J. Ferguson, Richard W. Pickersgill, David G. Brown, Martin J. Warren
Software Mentions: 2
Published: over 10 years ago
10.3390/v9110321
Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction
Cited by: 6
Author(s): Nikéa Pittman, Adam Misseldine, Lorena Geilen, Sujata Halder, J. W. G. Smith, Justin Kurian, Paul R. Chipman, Mandy E.W. Janssen, Robert McKenna, Timothy S. Baker, Anthony D’Abramo, Susan F. Cotmore, Peter Tattersall, Mavis Agbandje‐McKenna
Software Mentions: 2
Published: about 7 years ago
10.1107/S2053230X19012172
Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking
Cited by: 3
Author(s): Eric Montemayor, Johanna M Virta, Lauren D. Hagler, Steven C. Zimmerman, Samuel E. Butcher
Software Mentions: 2
Published: about 5 years ago
10.1107/S1399004714027114
Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes
Cited by: 12
Author(s): S.O. Dahms, Magnus C. Mayer, Dirk Roeser, Gerd Multhaup, Manuel E. Than
Software Mentions: 2
Published: over 9 years ago
10.1107/S2053230X18002236
Crystal structure of theMSMEG_4306gene product fromMycobacterium smegmatis
Cited by: 1
Author(s): Adarsh Kumar, Subramanian Karthikeyan
Software Mentions: 2
Published: over 6 years ago
10.1107/S2053230X14003355
A range of C∊3–C∊4 interdomain angles in IgE Fc accommodate binding to its receptor CD23
Cited by: 13
Author(s): B. Dhaliwal, M.O.Y. Pang, Daopeng Yuan, Andrew J. Beavil, Brian J. Sutton
Software Mentions: 2
Published: almost 11 years ago
10.1107/S2059798319010027
Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX
Cited by: 11
Author(s): Katarina Koruza, Bénédicte Lafumat, Maria Nyblom, Brian P. Mahon, Wolfgang Knecht, Robert McKenna, S.Z. Fisher
Software Mentions: 2
Published: over 5 years ago
10.1107/S2059798315023116
Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects
Cited by: 11
Author(s): Christian Reichen, Chaithanya Madhurantakam, Simon Hansen, Markus G. Grütter, Andreas Plückthun, Peer R. E. Mittl
Software Mentions: 2
Published: almost 9 years ago