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

10.7554/eLife.23644
CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin
Cited by: 112
Author(s): Katharina van Pee, Alexander Neuhaus, Edoardo D’Imprima, Deryck J. Mills, Werner Kühlbrandt, Özkan Yıldız
Software Mentions: 2
Published: over 7 years ago
10.7554/eLife.09832
Dna2 nuclease-helicase structure, mechanism and regulation by Rpa
Cited by: 89
Author(s): Chun Zhou, Sergei Pourmal, Nikola P. Pavletich
Software Mentions: 2
Published: about 9 years ago
10.7554/eLife.21829
Structure of the transporter associated with antigen processing trapped by herpes simplex virus
Cited by: 80
Author(s): Michael L. Oldham, Nikolaus Grigorieff, Jue Chen
Software Mentions: 2
Published: almost 8 years ago
10.7554/eLife.01496
Crystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803
Cited by: 66
Author(s): Yuval Mazor, Daniel Nataf, Hila Toporik, Nathan Nelson
Software Mentions: 2
Published: almost 11 years ago
10.7554/eLife.41848
An unexpected INAD PDZ tandem-mediated plcβ binding in Drosophila photo receptors
Cited by: 9
Author(s): Fei Ye, Yuguang Huang, J. Li, Yinfa Ma, Chensu Xie, Zexu Liu, Xiǎoyīng Dèng, Jun Wan, Tian Xue, Wei Liu, Mingjie Zhang
Software Mentions: 2
Published: almost 6 years ago
10.7554/eLife.01456
Collaboration gets the most out of software
Cited by: 807
Author(s): Andrew Morin, Ben Eisenbraun, Jason Key, Paul C. Sanschagrin, Michael A Timony, Michelle Ottaviano, Piotr Sliz
Software Mentions: 2
Published: about 11 years ago
10.7554/eLife.10034
Structural determinants of nuclear export signal orientation in binding to exportin CRM1
Cited by: 68
Author(s): Ho Yee Joyce Fung, Szu Chin Fu, Chad A. Brautigam, Yuh Min Chook
Software Mentions: 2
Published: about 9 years ago
10.7554/eLife.02674
Drastic changes in conformational dynamics of the antiterminator M2-1 regulate transcription efficiency in Pneumovirinae
Cited by: 39
Author(s): C. Leyrat, Max Renner, K. Harlos, Juha T. Huiskonen, Jonathan M. Grimes
Software Mentions: 2
Published: over 10 years ago
10.7554/eLife.39611
Multiple serine transposase dimers assemble the transposon-end synaptic complex during IS607-family transposition
Cited by: 6
Author(s): Wenyang Chen, Sridhar Mandali, S.P. Hancock, Pramod Kumar, Michael Collazo, Duilio Cascio, Reid C. Johnson
Software Mentions: 2
Published: about 6 years ago
10.7554/eLife.46986
Cryo-EM structures and functional characterization of murine Slc26a9 reveal mechanism of uncoupled chloride transport
Cited by: 83
Author(s): Justin D. Walter, Marta Sawicka, Raimund Dutzler
Software Mentions: 2
Published: over 5 years ago
10.7554/eLife.57870
High-resolution structures of multiple 5-HT3AR-setron complexes reveal a novel mechanism of competitive inhibition
Cited by: 26
Author(s): Sandip Basak, Arvind Kumar, Steven Ramsey, Eric Gibbs, Anoop Kapoor, Marta Filizola, Sudha Chakrapani
Software Mentions: 2
Published: about 4 years ago
10.7554/eLife.41140
Mechanisms of opening and closing of the bacterial replicative helicase
Cited by: 15
Author(s): Jillian Chase, Andrew Catalano, Alex J. Noble, Edward T. Eng, Paul Dominic B. Olinares, Kelly R. Molloy, Danaya Pakotiprapha, Martin A. Samuels, Brian T. Chait, Amédée des Georges, David Jeruzalmi
Software Mentions: 2
Published: almost 6 years ago
10.7554/eLife.39213
Cryo-EM structure of respiratory complex I at work
Cited by: 90
Author(s): Kristian Parey, Ulrich Brandt, Hao Xie, Deryck J. Mills, Karin Siegmund, Janet Vonck, Werner Kühlbrandt, Volker Zickermann
Software Mentions: 2
Published: about 6 years ago
10.7554/eLife.32660
Intracellular antibody signalling is regulated by phosphorylation of the Fc receptor TRIM21
Cited by: 53
Author(s): Claire F. Dickson, Adam J. Fletcher, Marina Vaysburd, Ji‐Chun Yang, Donna L. Mallery, Jingwei Zeng, Christopher M. Johnson, Stephen H. McLaughlin, Mark Skehel, Sarah Maslen, James Cruickshank, Nicolas Huguenin‐Dezot, Jason W. Chin, David Neuhaus, Leo C. James
Software Mentions: 2
Published: over 6 years ago
10.7554/eLife.14294
Structural basis for DNA 5´-end resection by RecJ
Cited by: 49
Author(s): Kaiying Cheng, Hong Xu, Xuanyi Chen, Liangyan Wang, Bing Teng, Ye Zhao, Yuejin Hua
Software Mentions: 2
Published: over 8 years ago
10.7554/eLife.41124
Structures in multiple conformations reveal distinct transition metal and proton pathways in an Nramp transporter
Cited by: 45
Author(s): Aaron T. Bozzi, Christina M. Zimanyi, John M. Nicoludis, Brandon K Lee, Casey H Zhang, Rachelle Gaudet
Software Mentions: 2
Published: almost 6 years ago
10.7554/eLife.48120
Cryo-EM structures of the human glutamine transporter SLC1A5 (ASCT2) in the outward-facing conformation
Cited by: 44
Author(s): Xiaodi Yu, Olga Plotnikova, Paul D. Bonin, Timothy A. Subashi, Thomas J. McLellan, Darren S. Dumlao, Ye Che, Yin Dong, E.P. Carpenter, Graham M. West, Xiayang Qiu, Jeffrey S. Culp, Seungil Han
Software Mentions: 2
Published: about 5 years ago
10.7554/eLife.70871
Regulation of human mTOR complexes by DEPTOR
Cited by: 11
Author(s): Matthias Wälchli, Karolin Berneiser, Francesca Mangia, Stefan Imseng, Louise-Marie Craigie, Edward Stuttfeld, Michael N. Hall, Timm Maier
Software Mentions: 2
Published: about 3 years ago
10.7554/eLife.38958
Unified mechanisms for self-RNA recognition by RIG-I Singleton-Merten syndrome variants
Cited by: 24
Author(s): Charlotte Lässig, Katja Lammens, Jacob Lucián Gorenflos López, Sebastian Michalski, Olga Fettscher, Karl‐Peter Hopfner
Software Mentions: 2
Published: over 6 years ago
10.7554/eLife.51898
Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon–anticodon pairing
Cited by: 25
Author(s): Eric D. Hoffer, Sung Il Hong, S. Sunita, Tatsuya Maehigashi, Ruben L Gonzalez, Paul C. Whitford, C.M. Dunham
Software Mentions: 2
Published: about 4 years ago
10.7554/eLife.22311
Structural basis for the hijacking of endosomal sorting nexin proteins by Chlamydia trachomatis
Cited by: 53
Author(s): Blessy Paul, Hyunsung Kim, Markus C. Kerr, Wilhelmina M. Huston, Rohan D. Teasdale, Brett M. Collins
Software Mentions: 2
Published: almost 8 years ago
10.7554/eLife.57127
Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity
Cited by: 20
Author(s): L.M. Langer, Yair Gat, Fabien Bonneau, Elena Conti
Software Mentions: 2
Published: over 4 years ago
10.7554/eLife.35677
Specific Eph receptor-cytoplasmic effector signaling mediated by SAM–SAM domain interactions
Cited by: 30
Author(s): Yue Wang, Yuan Shang, Jianchao Li, Weidi Chen, Gang Li, Jun Wan, Wei Liu, Mingjie Zhang
Software Mentions: 2
Published: over 6 years ago
10.7554/eLife.36307
An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering
Cited by: 106
Author(s): D.A. Keedy, Z.B. Hill, J.T. Biel, Emily L. Kang, T.J. Rettenmaier, J. Brandão-Neto, Nicholas M. Pearce, Frank von Delft, James A. Wells, James S. Fraser
Software Mentions: 2
Published: over 6 years ago
10.7554/eLife.48822
Crystal structure of dopamine receptor D4 bound to the subtype selective ligand, L745870
Cited by: 19
Author(s): Ye Zhou, Chuanai Cao, Lingli He, Xianping Wang, Xuejun C. Zhang
Software Mentions: 2
Published: about 5 years ago
10.7554/eLife.22709
Chlamydia interfere with an interaction between the mannose-6-phosphate receptor and sorting nexins to counteract host restriction
Cited by: 58
Author(s): Cherilyn A. Elwell, Nadine Czudnochowski, John Von Dollen, Jeffrey R. Johnson, Rachel Nakagawa, Kathleen M. Mirrashidi, Nevan J. Krogan, Joanne N. Engel, Oren S. Rosenberg
Software Mentions: 2
Published: over 7 years ago
10.7554/eLife.62117
Structural basis for transcription complex disruption by the Mfd translocase
Cited by: 31
Author(s): Jin Young Kang, Eliza Llewellyn, James Chen, Paul Dominic B. Olinares, Joshua Brewer, Brian T. Chait, Elizabeth A. Campbell, Seth A. Darst
Software Mentions: 2
Published: almost 4 years ago
10.7554/eLife.22679
Evolution of substrate specificity in a retained enzyme driven by gene loss
Cited by: 21
Author(s): Ana Lilia Juárez-Vázquez, Janaka N. Edirisinghe, E.A. Verduzco-Castro, K. Michalska, Chenggang Wu, Lianet Noda-García, G. Babnigg, M. Endres, Sofía Medina-Ruiz, Julián Santoyo-Flores, Mauricio Carrillo‐Tripp, Hung Ton‐That, A. Joachimiak, Christopher S. Henry, Francisco Barona‐Gómez
Software Mentions: 2
Published: over 7 years ago
10.7554/eLife.60482
Structure of the bacterial ribosome at 2 Å resolution
Cited by: 125
Author(s): Zoe L Watson, Fred R. Ward, Raphaël Méheust, Omer Ad, Alanna Schepartz, Jillian F. Banfield, Jamie H. D. Cate
Software Mentions: 2
Published: about 4 years ago
10.7554/eLife.42400
DNA translocation mechanism of an XPD family helicase
Cited by: 32
Author(s): Kaiying Cheng, Dale B. Wigley
Software Mentions: 2
Published: almost 6 years ago
10.7554/eLife.03579
Structure and substrate ion binding in the sodium/proton antiporter PaNhaP
Cited by: 82
Author(s): David Wöhlert, Werner Kühlbrandt, Özkan Yıldız
Software Mentions: 2
Published: about 10 years ago
10.7554/eLife.21510
Structural insights into the mechanism of the DEAH-box RNA helicase Prp43
Cited by: 75
Author(s): M.J. Tauchert, Jean‐Baptiste Fourmann, Reinhard Lührmann, Ralf Ficner
Software Mentions: 2
Published: almost 8 years ago
10.7554/eLife.28020
A novel central nervous system-penetrating protease inhibitor overcomes human immunodeficiency virus 1 resistance with unprecedented aM to pM potency
Cited by: 39
Author(s): Manabu Aoki, Hironori Hayashi, Kalapala Venkateswara Rao, Debananda Das, Nobuyo Higashi-Kuwata, Haydar Bulut, Hiromi Aoki-Ogata, Yuki Takamatsu, Ravikiran S. Yedidi, David A. Davis, Shin Hattori, Noriko Nishida, Kazuya Hasegawa, Nobutoki Takamune, Prasanth R. Nyalapatla, Heather L. Osswald, Hirofumi Jono, Hideyuki Saya, Robert Yarchoan, Shogo Misumi, Arun K. Ghosh, Hiroaki Mitsuya
Software Mentions: 2
Published: about 7 years ago
10.7554/eLife.57887
The architecture of EMC reveals a path for membrane protein insertion
Cited by: 72
Author(s): John P. O’Donnell, Ben P. Phillips, Yuichi Yagita, Szymon Juszkiewicz, Armin Wagner, Duccio Malinverni, Robert J. Keenan, Elizabeth A. Miller, Ramanujan S. Hegde
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms130810010
Effects of a Buried Cysteine-To-Serine Mutation on Yeast Triosephosphate Isomerase Structure and Stability
Cited by: 6
Author(s): Alejandra Hernández-Santoyo, Lenin Domínguez-Ramírez, César A. Reyes-López, Edith González-Mondragón, Andrés Hernández‐Arana, Adela Rodrı́guez-Romero
Software Mentions: 2
Published: over 12 years ago
10.3390/ijms17040446
Structure of the PLP-Form of the Human Kynurenine Aminotransferase II in a Novel Spacegroup at 1.83 Å Resolution
Cited by: 13
Author(s): Alireza Nematollahi, Guorong Sun, S.J. Harrop, Jane R. Hanrahan, W. Bret Church
Software Mentions: 2
Published: over 8 years ago
10.3390/ijms18071336
Quinolin-6-Yloxyacetamides Are Microtubule Destabilizing Agents That Bind to the Colchicine Site of Tubulin
Cited by: 9
Author(s): Ashwani Sharma, Gonzalo Sáez-Calvo, Natacha Olieric, Francisco de Asís Balaguer, Isabel Barasoaín, Clemens Lamberth, J. Fernando Díaz, Michel O. Steinmetz
Software Mentions: 2
Published: over 7 years ago
10.3390/ijms20061392
Crystal Structure of the Cyclostreptin-Tubulin Adduct: Implications for Tubulin Activation by Taxane-Site Ligands
Cited by: 23
Author(s): Francisco de Asís Balaguer, Tobias Mühlethaler, Juan Estévez-Gallego, Enrique Calvo, Juan F. Giménez-Abián, April L. Risinger, Erik J. Sorensen, Christopher D. Vanderwal, Karl‐Heinz Altmann, Susan L. Mooberry, Michel O. Steinmetz, M.A. Oliva, A.E. Prota, J. Fernando Díaz
Software Mentions: 2
Published: over 5 years ago
10.3390/ijms20071533
The Molecular and Structural Basis of O-methylation Reaction in Coumarin Biosynthesis in Peucedanum praeruptorum Dunn
Cited by: 13
Author(s): Yucheng Zhao, Nana Wang, Ziwei Sui, C.H. Huang, Zhixiong Zeng, Ling‐Yi Kong
Software Mentions: 2
Published: over 5 years ago
10.3390/ijms20205085
Crystal Structure-Based Exploration of Arginine-Containing Peptide Binding in the ADP-Ribosyltransferase Domain of the Type III Effector XopAI Protein
Cited by: 5
Author(s): Jyung-Hurng Liu, Jun-Yi Yang, Duen-Wei Hsu, Yi-Hua Lai, Yun-Pei Li, Yi-Rung Tsai, Ming-Hon Hou
Software Mentions: 2
Published: about 5 years ago
10.3390/ijms20246279
Structural Insights into the Intracellular Region of the Human Magnesium Transport Mediator CNNM4
Cited by: 13
Author(s): Paula Giménez-Mascarell, Iker Oyenarte, Irene González‐Recio, Carmen Fernández‐Rodríguez, María Ángeles Corral-Rodríguez, Igone Campos-Zarraga, Jorge Simón, Elie Kostantin, Serge Hardy, Antonio Díaz-Quintana, Mara Zubillaga Lizeaga, Nekane Merino, Tammo Diercks, Francisco J. Blanco, Irene Dίaz–Moreno, María Luz Martínez‐Chantar, Michel L. Tremblay, Dominik Müller, Dritan Siliqi, Luis Alfonso Martínez-Cruz
Software Mentions: 2
Published: almost 5 years ago
10.3390/ijms21010083
The Structure of Sucrose-Soaked Levansucrase Crystals from Erwinia tasmaniensis reveals a Binding Pocket for Levanbiose
Cited by: 14
Author(s): Ivan Polsinelli, Rosanna Caliandro, Nicola Demitri, Stefano Benini
Software Mentions: 2
Published: almost 5 years ago
10.3390/ijms21072600
Structural Characterization of an ACP from Thermotoga maritima: Insights into Hyperthermal Adaptation
Cited by: 8
Author(s): Yeongjoon Lee, Ahjin Jang, Min‐Cheol Jeong, Nuri Park, Jungwoo Park, Woo Cheol Lee, Chaejoon Cheong, Yangmee Kim
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms21093332
Polysaccharide-Based Injection Matrix for Serial Crystallography
Cited by: 25
Author(s): Ki Hyun Nam
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms21155277
Biophysical Characterization of Cancer-Related Carbonic Anhydrase IX
Cited by: 4
Author(s): Katarina Koruza, Akilah B. Murray, Brian P. Mahon, Jesse B. Hopkins, Wolfgang Knecht, Robert McKenna, S.Z. Fisher
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms21165915
Biochemical Characterization and Crystal Structure of a Novel NAD+-Dependent Isocitrate Dehydrogenase from Phaeodactylum tricornutum
Cited by: 5
Author(s): Shiping Huang, Luchun Zhou, Bin Wen, Peng Wang
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms21197081
Impact of HLA-DR Antigen Binding Cleft Rigidity on T Cell Recognition
Cited by: 5
Author(s): Christopher Szeto, Joseph Bloom, Hannah Sloane, Christian A. Lobos, James Fodor, Dhilshan Jayasinghe, D.S.M. Chatzileontiadou, Emma J. Grant, Ashley M. Buckle, Stéphanie Gras
Software Mentions: 2
Published: about 4 years ago
10.3390/ijms22063219
Crystal Structure of a Phospholipase D from the Plant-Associated Bacteria Serratia plymuthica Strain AS9 Reveals a Unique Arrangement of Catalytic Pocket
Cited by: 7
Author(s): Fanghua Wang, Siyu Liu, Xuejing Mao, Ruiguo Cui, Bo Yang, Yonghua Wang
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms22094769
Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity
Cited by: 4
Author(s): Pablo Maturana, Marı́a S. Orellana, Sixto M. Herrera, Ignacio Martı́nez, Maximiliano Figueroa, José Martínez‐Oyanedel, Víctor Castro‐Fernández, Elena Uribe
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms22136830
‘All That Glitters Is Not Gold’: High-Resolution Crystal Structures of Ligand-Protein Complexes Need Not Always Represent Confident Binding Poses
Cited by: 6
Author(s): Sohini Chakraborti, Kaushik Hatti, Narayanaswamy Srinivasan
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms22136859
Sub-3 Å Cryo-EM Structures of Necrosis Virus Particles via the Use of Multipurpose TEM with Electron Counting Camera
Cited by: 1
Author(s): Chun-Hsiung Wang, Donghua Chen, Shih-Hsin Huang, Yimin A. Wu, Yiyun Chen, Y. Hwu, David Bushnell, Roger D. Kornberg, Wen Ho Chang
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms22179140
Structural and Functional Characterizations of Cancer Targeting Nanoparticles Based on Hepatitis B Virus Capsid
Cited by: 0
Author(s): Yunseok Heo, Hyomin Jeong, Youngki Yoo, Ji-Hye Yun, Bumhan Ryu, Young-je Cha, Boram Lee, Ye-Eun Jeon, Jongmin Kim, S.-H. Jeong, Eunji Jo, Jae Sung Woo, Jeewon Lee, Hyun-Soo Cho, Weontae Lee
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms221910640
Trop2 Forms a Stable Dimer with Significant Structural Differences within the Membrane-Distal Region as Compared to EpCAM
Cited by: 10
Author(s): Miha Pavšič
Software Mentions: 2
Published: about 3 years ago
10.3390/ijms221910862
Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis
Cited by: 7
Author(s): Carolina Rodrigues, Patrícia T. Borges, Magalí F. Scocozza, Diogo Silva, André Taborda, Vânia Brissos, Carlos Frazão, Lı́gia O. Martins
Software Mentions: 2
Published: about 3 years ago
10.1186/s12951-019-0512-0
Design and site-directed compartmentalization of gold nanoclusters within the intrasubunit interfaces of ferritin nanocage
Cited by: 16
Author(s): Jiachen Zang, Bowen Zheng, Xiuqing Zhang, Paolo Arosio, Guanghua Zhao
Software Mentions: 2
Published: over 5 years ago
10.18632/oncotarget.21652
Structural basis of the therapeutic anti-PD-L1 antibody atezolizumab
Cited by: 54
Author(s): Fei Zhang, Xiaoqiang Qi, Xiaoxiao Wang, Diyang Wei, Jiawei Wu, Lingling Feng, Haiyan Cai, Yugang Wang, Naiyan Zeng, Ting Xu, Aiwu Zhou, Ying Zheng
Software Mentions: 2
Published: about 7 years ago
10.1155/2017/4342789
Identification, Characterization, and Structure of Tm16 from<i>Trichuris muris</i>
Cited by: 10
Author(s): Zhuyun Liu, Alan Kelleher, Shanii Tabb, Junfei Wei, Jeroen Pollet, Peter J. Hotez, María Elena Bottazzi, Bin Zhan, Oluwatoyin A. Asojo
Software Mentions: 2
Published: almost 8 years ago
10.1098/rsob.120142
Structure and function of cytidine monophosphate kinase from <i>Yersinia pseudotuberculosis</i> , essential for virulence but not for survival
Cited by: 11
Author(s): Nicola Walker, Elizabeth A. Clark, Donna C. Ford, Helen L. Bullifent, Erin V. McAlister, Melanie Duffield, K. Ravi Acharya, Petra C. F. Oyston
Software Mentions: 2
Published: almost 12 years ago
10.1098/rsob.150128
Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA
Cited by: 22
Author(s): Akihisa Osakabe, Fumiya Adachi, Yasuhiro Arimura, Kazuhira Maehara, Yasuyuki Ohkawa, Hitoshi Kurumizaka
Software Mentions: 2
Published: about 9 years ago
10.1098/rsob.160053
Structure of astrotactin-2: a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development
Cited by: 28
Author(s): Ni Tien, K. Harlos, Robert J.C. Gilbert
Software Mentions: 2
Published: over 8 years ago
10.1098/rsob.160090
Structural and biochemical analyses of monoubiquitinated human histones H2B and H4
Cited by: 32
Author(s): Shuichi Machida, Satoshi Sekine, Yuka Nishiyama, Naoki Horikoshi, Hitoshi Kurumizaka
Software Mentions: 2
Published: over 8 years ago
10.1098/rsob.160127
Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A
Cited by: 24
Author(s): Naoki Horikoshi, Yasuhiro Arimura, Hiroyuki Taguchi, Hitoshi Kurumizaka
Software Mentions: 2
Published: over 8 years ago
10.1098/rsob.160157
Exploring the active site of the <i>Streptococcus pneumoniae</i> topoisomerase IV–DNA cleavage complex with novel 7,8-bridged fluoroquinolones
Cited by: 18
Author(s): Ivan Laponogov, Xiao Su Pan, D. A. Veselkov, Ryan T. Cirz, Allan S. Wagman, Heinz Moser, L. Mark Fisher, Mark Sanderson
Software Mentions: 2
Published: about 8 years ago
10.1016/j.jsb.2015.08.009
Polyhedra structures and the evolution of the insect viruses
Cited by: 23
Author(s): Xiaoyun Ji, Danny Axford, Robin L. Owen, Gwyndaf Evans, H. Ginn, Geoff Sutton, David I. Stuart
Software Mentions: 2
Published: about 9 years ago
10.1016/j.jsb.2014.12.002
Seeing tobacco mosaic virus through direct electron detectors
Cited by: 82
Author(s): Simon A. Fromm, Tanmay A. M. Bharat, Arjen J. Jakobi, Wim J. H. Hagen, Carsten Sachse
Software Mentions: 2
Published: almost 10 years ago
10.1016/j.jsb.2016.08.006
Structures of type IV pilins from Thermus thermophilus demonstrate similarities with type II secretion system pseudopilins
Cited by: 11
Author(s): V. Karuppiah, Angela Thistlethwaite, Jeremy P. Derrick
Software Mentions: 2
Published: almost 8 years ago
10.1016/j.jsb.2016.01.016
Easy mammalian expression and crystallography of maltose-binding protein-fused human proteins
Cited by: 31
Author(s): Marcel Bokhove, Hamed Sadat Al Hosseini, Takako Saitô, Elisa Dioguardi, Katharina Gegenschatz‐Schmid, Kaoru Nishimura, Isha Raj, Daniele de Sanctis, Ling Han, Luca Jovine
Software Mentions: 2
Published: over 8 years ago
10.1016/j.yjsbx.2020.100028
A complex between the Zika virion and the Fab of a broadly cross-reactive neutralizing monoclonal antibody revealed by cryo-EM and single particle analysis at 4.1 Å resolution
Cited by: 3
Author(s): Anu Tyagi, Tofayel Ahmed, Jing Shi, Shashi Bhushan
Software Mentions: 2
Published: almost 5 years ago
10.1016/j.yjsbx.2020.100024
Cryo-electron microscopic and X-ray crystallographic analysis of the light-driven proton pump proteorhodopsin reveals a pentameric assembly
Cited by: 4
Author(s): Stephan Hirschi, David Kalbermatter, Zöhre Ucurum, Dimitrios Fotiadis
Software Mentions: 2
Published: almost 5 years ago
10.1016/j.yjsbx.2020.100030
Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii
Cited by: 3
Author(s): Yuta Sato, Takashi Yabuki, Naruhiko Adachi, Toshio Moriya, T. Arakawa, Masato Kawasaki, Chihaya Yamada, Toshiya Senda, Shinya Fushinobu, Takayoshi Wakagi
Software Mentions: 2
Published: almost 5 years ago
10.1007/s10969-015-9193-6
A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNACys
Cited by: 1
Author(s): Takatoshi Yanagisawa, Ryohei Ishii, Yasushi Hikida, Ryuya Fukunaga, Toru Sengoku, S. Sekine, Shigeyuki Yokoyama
Software Mentions: 2
Published: almost 10 years ago
10.1107/S1600577518010354
High-speed raster-scanning synchrotron serial microcrystallography with a high-precision piezo-scanner
Cited by: 18
Author(s): Yuan Gao, Weihe Xu, Wuxian Shi, Alexei S. Soares, Jean Jakoncic, Stuart Myers, Bruno Martins, John M. Skinner, Qun Li, H. J. Bernstein, Seán McSweeney, Evgeny Nazaretski, Martin R. Fuchs
Software Mentions: 2
Published: over 6 years ago
10.1107/S1600577514026289
Radiation damage to nucleoprotein complexes in macromolecular crystallography
Cited by: 20
Author(s): C.S. Bury, Elspeth F. Garman, H. Ginn, Raimond B. G. Ravelli, Ian Carmichael, Geoff Kneale, J.E. McGeehan
Software Mentions: 2
Published: almost 10 years ago
10.1107/S1600577520014599
High-resolution macromolecular crystallography at the FemtoMAX beamline with time-over-threshold photon detection
Cited by: 0
Author(s): Mikael Jensen, Viktor Ahlberg Gagnér, Juan Sanchez, Anders Bengtsson, Johanna Ekström, Tinna Björg Úlfarsdóttir, María-José García-Bonete, Andrius Jurgilaitis, David Kroon, Van Tuong Pham, Stefano Checcia, Hélène Coudert-Alteirac, Siawosch Schewa, Manfred Rößle, Helena Rodilla, Jan Stake, Vitali Zhaunerchyk, Jörgen Larsson, Gergely Katona
Software Mentions: 2
Published: almost 4 years ago
10.1107/S0909049513020803
High-resolution crystal structure of<i>Streptococcus pyogenes</i>β-NAD<sup>+</sup>glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface
Cited by: 4
Author(s): Ji Young Yoon, Doo Ri An, Hye Jin Yoon, Hyoun Sook Kim, Sang Jae Lee, Ha Na Im, Jun Young Jang, Se Won Suh
Software Mentions: 2
Published: about 11 years ago
10.1107/S0909049513020773
Structural fluctuation observed in Z-DNA d(CGCGCG)<sub>2</sub>in the absence of divalent metal cations and polyamines
Cited by: 5
Author(s): Toshiyuki Chatake
Software Mentions: 2
Published: about 11 years ago
10.1128/JVI.01560-20
Orsay Virus CP-δ Adopts a Novel β-Bracelet Structural Fold and Incorporates into Virions as a Head Fiber
Cited by: 0
Author(s): Yusong R. Guo, Yingying Fan, Ying Zhou, Miao Jin, Jim L. Zhang, Hongbing Jiang, Matthew V. Holt, Tao Wang, Nicolas L. Young, David Wang, Weiwei Zhong, Yizhi Jane Tao
Software Mentions: 2
Published: about 4 years ago
10.1128/JVI.00723-19
GII.13/21 Noroviruses Recognize Glycans with a Terminal β-Galactose via an Unconventional Glycan Binding Site
Cited by: 7
Author(s): Cong Xu, Xiaoman Sun, Jianxun Qi, Han-Bo Li, Wengang Chai, Qing Zhang, Hong Wang, Xiangyu Kong, Jiao Song, Lili Pang, Miao Jin, Dan-di Li, Ming Tan, Zhaojun Duan
Software Mentions: 2
Published: over 5 years ago
10.1128/JVI.01253-17
NS3 from Hepatitis C Virus Strain JFH-1 Is an Unusually Robust Helicase That Is Primed To Bind and Unwind Viral RNA
Cited by: 11
Author(s): Ting Zhou, Xiao‐Ming Ren, Rebecca L. Adams, Anna Marie Pyle
Software Mentions: 2
Published: almost 7 years ago
10.1128/JVI.00694-16
Crystal Structure of the Human Astrovirus Capsid Protein
Cited by: 32
Author(s): Yukimatsu Toh, Justin Harper, Kelly A. Dryden, Mark Yeager, Carlos F. Arias, Ernesto Méndez, Yizhi Jane Tao
Software Mentions: 2
Published: about 8 years ago
10.1128/mBio.00280-20
The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site
Cited by: 34
Author(s): Jérémie Prévost, W.D. Tolbert, Halima Medjahed, Rebekah Sherburn, Navid Madani, Daria Zoubchenok, Gabrielle Gendron‐Lepage, Althea Gaffney, Melissa C. Grenier, Sharon Kirk, Natasha Gupta Vergara, Changze Han, Brendan T. Mann, Agnès Laurence Chenine, Adel Ahmed Rashad Ahmed, Irwin M. Chaiken, Frank Kirchhoff, Beatrice H. Hahn, Hillel Haim, Cameron F. Abrams, Amos B. Smith, Joseph Sodroski, Marzena Pazgier, Andrés Finzi
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0065080
Mycobacterium tuberculosis Rv3406 Is a Type II Alkyl Sulfatase Capable of Sulfate Scavenging
Cited by: 17
Author(s): Kimberly M. Sogi, Zev J. Gartner, Mark A. Breidenbach, Mason J. Appel, Michael W. Schelle, Carolyn R. Bertozzi
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0112873
Crystal Structure of Escherichia coli-Expressed Haloarcula marismortui Bacteriorhodopsin I in the Trimeric Form
Cited by: 14
Author(s): Vitaly Shevchenko, Ivan Gushchin, Vitaly Polovinkin, Ekaterina Round, Valentin Borshchevskiy, P. Utrobin, А. Н. Попов, Taras Balandin, Georg Büldt, Valentin Gordeliy
Software Mentions: 1
Published: almost 10 years ago
10.1371/journal.pone.0044934
Mechanistic Insights into Validoxylamine A 7'-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex
Cited by: 18
Author(s): Michael C. Cavalier, Young Sun Yim, Shumpei Asamizu, David Neau, Khaled H. Almabruk, Taifo Mahmud, Yong-Hwan Lee
Software Mentions: 1
Published: about 12 years ago
10.1128/mBio.01303-20
Structure and Multitasking of the c-di-GMP-Sensing Cellulose Secretion Regulator BcsE
Cited by: 12
Author(s): Samira Zouhir, W. Abidi, M. Caleechurn, Petya V. Krasteva
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0063010
The Carboxy-Terminal αN Helix of the Archaeal XerA Tyrosine Recombinase Is a Molecular Switch to Control Site-Specific Recombination
Cited by: 22
Author(s): Marie-Claude Serre, Toufic El Arnaout, Mark A. Brooks, Dominique Durand, Johnny Lisboa, Noureddine Lazar, Bertrand Raynal, Herman van Tilbeurgh, Sophie Quevillon‐Chéruel
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0131788
Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington’s Disease (HD) and Spinocerebellar Ataxias (SCAs)
Cited by: 25
Author(s): Arpita Tawani, Amit Kumar
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pone.0052890
Crystal Structure of Proteus mirabilis Lipase, a Novel Lipase from the Proteus/Psychrophilic Subfamily of Lipase Family I.1
Cited by: 22
Author(s): Tyler P. Korman, James U. Bowie
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pone.0148909
Computing Molecular Devices in L.major through Transcriptome Analysis: Structured Simulation Approach
Cited by: 1
Author(s): Pruthvi Raj Bejugam, Shailza Singh
Software Mentions: 1
Published: almost 9 years ago
10.1128/mBio.01488-20
Structural Characterization of the Essential Cell Division Protein FtsE and Its Interaction with FtsX in Streptococcus pneumoniae
Cited by: 10
Author(s): Martín Alcorlo, Daniel Straume, Joe Lutkenhaus, Leiv Sigve Håvarstein, J.A. Hermoso
Software Mentions: 1
Published: about 4 years ago
10.1128/mBio.02012-20
Molecular Deceleration Regulates Toxicant Release to Prevent Cell Damage in Pseudomonas putida S16 (DSM 28022)
Cited by: 4
Author(s): Hongzhi Tang, Kunzhi Zhang, Haiyang Hu, Geng Wu, Weiwei Wang, Xiongyu Zhu, Gongquan Liu, Ping Xu
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pone.0127733
A New Family of HEAT-Like Repeat Proteins Lacking a Critical Substrate Recognition Motif Present in Related DNA Glycosylases
Cited by: 8
Author(s): E.A. Mullins, Rongxin Shi, Lyle A. Kotsch, Brandt F. Eichman
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pone.0146164
A Streamlined, Automated Protocol for the Production of Milligram Quantities of Untagged Recombinant Rat Lactate Dehydrogenase A Using ÄKTAxpressTM
Cited by: 7
Author(s): Matthew W. Nowicki, Elizabeth A. Blackburn, I.W. McNae, Martin A. Wear
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.pone.0113224
Electrostatic Effects in the Folding of the SH3 Domain of the c-Src Tyrosine Kinase: pH-Dependence in 3D-Domain Swapping and Amyloid Formation
Cited by: 24
Author(s): Julio Bacarizo, Sergio Martínez‐Rodríguez, José M. Martín-García, Montserrat Andújar‐Sánchez, Emilia Ortiz‐Salmerón, José L. Neira, A. Cámara-Artigas
Software Mentions: 1
Published: almost 10 years ago
10.7554/eLife.16309
Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5α
Cited by: 77
Author(s): Jonathan M. Wagner, Marcin D. Roganowicz, Katarzyna Skorupka, Steven L. Alam, Devin E. Christensen, Ginna Doss, Yuqing Wan, Gabriel A. Frank, Barbie K. Ganser‐Pornillos, Wesley I. Sundquist, Owen Pornillos
Software Mentions: 1
Published: over 8 years ago
10.1107/S2059798319001426
Challenge data set for macromolecular multi-microcrystallography
Cited by: 4
Author(s): James M. Holton
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pone.0074735
The Inhibitory Helix Controls the Intramolecular Conformational Switching of the C-Terminus of STIM1
Cited by: 36
Author(s): Boyang Cui, Xue Yang, Siwei Li, Zhijie Lin, Wang Zheng, Dong Cheng, Yuequan Shen
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pone.0187701
Structural and biochemical analysis of atypically low dephosphorylating activity of human dual-specificity phosphatase 28
Cited by: 3
Author(s): Bonsu Ku, Won Pyo Hong, Chae Won Keum, Myeongbin Kim, Hyunyeol Ryu, Donghwan Jeon, Hang‐Sik Shin, Jae-Hoon Kim, Seung Jun Kim, Seong Eon Ryu
Software Mentions: 1
Published: about 7 years ago
10.1371/journal.pone.0248385
Characterization of a broadly specific cadaverine N-hydroxylase involved in desferrioxamine B biosynthesis in Streptomyces sviceus
Cited by: 2
Author(s): Lesley-Ann Giddings, G.T. Lountos, Kang Woo Kim, Matthew Brockley, D. Needle, Scott Cherry, Joseph E. Tropea, David S. Waugh
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0101036
A Linear Relationship between Crystal Size and Fragment Binding Time Observed Crystallographically: Implications for Fragment Library Screening Using Acoustic Droplet Ejection
Cited by: 13
Author(s): Krystal Cole, Christian G. Roessler, Elizabeth A. Mulé, Emma J. Benson-Xu, John D. Mullen, Benjamin A. Le, Alanna M. Tieman, Claire Birone, María Brown, Jesús Hernández, Sherry Neff, Daniel E. Williams, Marc Allaire, Allen M. Orville, Robert M. Sweet, Alexei S. Soares
Software Mentions: 1
Published: over 10 years ago