cran: PHENIX | Projects | Ecosyste.ms: Papers

10.1016/j.str.2017.01.002

Crystal Structure of the Heterotrimeric Integrin-Binding Region of Laminin-111
Cited by: 28
Author(s): David Pulido, Sadaf-Ahmahni Hussain, Erhard Hohenester
Software Mentions: 3
Published: over 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 6 years ago

10.1371/journal.ppat.1004795

The Aspartate-Less Receiver (ALR) Domains: Distribution, Structure and Function
Cited by: 25
Author(s): Andrew J. Maule, David P. Wright, Joshua Weiner, Lu Han, Francis C. Peterson, Brian F. Volkman, N.R. Silvaggi, Andrew T. Ulijasz
Software Mentions: 3
Published: over 11 years ago

10.1107/S1744309113012931

Structure of PatF fromProchloron didemni
Cited by: 26
Author(s): Andrew F. Bent, Jesko Koehnke, Wael E. Houssen, Margaret Caroline MacHin Smith, Marcel Jaspars, James H. Naismith
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.ppat.1005165

Structure Elucidation of Coxsackievirus A16 in Complex with GPP3 Informs a Systematic Review of Highly Potent Capsid Binders to Enteroviruses
Cited by: 19
Author(s): Luigi De Colibus, Xiangxi Wang, Aloys Tijsma, Johan Neyts, John A. B. Spyrou, Jingshan Ren, Jonathan M. Grimes, Gerhard Puerstinger, Pieter Leyssen, Elizabeth E. Fry, Zihe Rao, David I. Stuart
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.ppat.1009016

Structural insights into loss of function of a pore forming toxin and its role in pneumococcal adaptation to an intracellular lifestyle
Cited by: 10
Author(s): Dilip Badgujar, Anjali Anil, Angharad E Green, Manalee Vishnu Surve, Shilpa Madhavan, Alison J. Beckett, Ian A. Prior, Barsa Kanchan Jyotshna Godsora, Sanket B. Patil, Prachi More, Shruti Guha Sarkar, Andrea M. Mitchell, Rinti Banerjee, Prashant S. Phale, Timothy J. Mitchell, Daniel R. Neill, Prasenjit Bhaumik, Anirban Banerjee
Software Mentions: 3
Published: almost 6 years ago

10.1107/S2053230X15018336

Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I
Cited by: 8
Author(s): Mathias Enderle, A.A. McCarthy, Karthik S. Paithankar, Martin Grininger
Software Mentions: 3
Published: almost 11 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 11 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: about 6 years ago

10.1107/S0907444910052224

Recent advances in theCRANKsoftware suite for experimental phasing
Cited by: 79
Author(s): Navraj S. Pannu, Willem Jan Waterreus, Pavol Skubák, Irakli Sikharulidze, Jan Pieter Abrahams, R. A. G. de Graaff
Software Mentions: 3
Published: over 15 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 8 years ago

10.1038/s41598-018-30154-w

Genome-wide association study and genomic prediction using parental and breeding populations of Japanese pear (Pyrus pyrifolia Nakai)
Cited by: 44
Author(s): Mai F. Minamikawa, Norio Takada, Shingo Terakami, Toshihiro Saito, Akio Onogi, Hiromi Kajiya‐Kanegae, Takeshi Hayashi, Takatsugu Yamamoto, Hiroyoshi Iwata
Software Mentions: 3
Published: about 8 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 7 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: about 11 years ago

10.1080/14756366.2021.1931862

Structure-based virtual screening of highly potent inhibitors of the nematode chitinase CeCht1
Cited by: 7
Author(s): Wei Chen, Qi Chen, Ashutosh Kumar, Xi Jiang, Kam Y. J. Zhang, Qing Yang
Software Mentions: 3
Published: almost 6 years ago

10.1107/S1399004715005210

In meso in situ serial X-ray crystallography of soluble and membrane proteins
Cited by: 98
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Ezequiel Panepucci, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 3
Published: over 11 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 6 years ago

10.1016/j.jbc.2021.100743

From integrative structural biology to cell biology
Cited by: 38
Author(s): Andrej Šali
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.str.2017.12.005

Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa
Cited by: 27
Author(s): Osman Salih, Shaoda He, Sara Planamente, Lasse Stach, James T. MacDonald, Eleni Manoli, S.H.W. Scheres, Alain Filloux, Paul S. Freemont
Software Mentions: 3
Published: over 8 years ago

10.1107/S0907444912001308

Towards automated crystallographic structure refinement with phenix.refine
Cited by: 4,334
Author(s): Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Nathaniel Echols, Jeffrey J. Headd, Nigel W. Moriarty, Marat Mustyakimov, Thomas C. Terwilliger, Alexandre Urzhumtsev, Peter H. Zwart, Paul D. Adams
Software Mentions: 3
Published: over 14 years ago

10.1016/j.str.2020.08.004

Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics
Cited by: 14
Author(s): D E. Nicholson, Thomas A. Edwards, Alex J. O’Neill, Neil A. Ranson
Software Mentions: 3
Published: about 6 years ago

10.1074/jbc.RA119.010697

Structural basis of cell-surface signaling by a conserved sigma regulator in Gram-negative bacteria
Cited by: 3
Author(s): Jaime L. Jensen, Beau D. Jernberg, Sangita C. Sinha, Christopher L. Colbert
Software Mentions: 3
Published: over 6 years ago

10.1107/S090744491104978X

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum
Cited by: 26
Author(s): Axel T. Brunger, Debanu Das, Ashley M. Deacon, Joanna C Grant, Thomas C. Terwilliger, Randy J. Read, Paul D. Adams, Michael Levitt, Gunnar F. Schröder
Software Mentions: 3
Published: over 14 years ago

10.1016/j.jbc.2021.100927

Beyond PKA: Evolutionary and structural insights that define a docking and dimerization domain superfamily
Cited by: 3
Author(s): Heather R. Dahlin, Ning Zheng, John D. Scott
Software Mentions: 3
Published: about 5 years ago

10.1107/S2052252519007668

Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder
Cited by: 10
Author(s): Jeong Kuk Park, Keon Young Kim, Yeo Won Sim, Young Dong Kim, Jin Kyun Kim, Cheol Lee, Jeongran Han, Chae Un Kim, J. Eugene Lee, SangYoun Park
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.ppat.1002957

De novo GTP Biosynthesis Is Critical for Virulence of the Fungal Pathogen Cryptococcus neoformans
Cited by: 53
Author(s): Carl A. Morrow, Eugene Valkov, Anna Stamp, Eve W. L. Chow, I. Russel Lee, Ania Wronski, Simon J. Williams, Jennifer Hill, Julianne T. Djordjevic, Ulrike Kappler, Boštjan Kobe, James S. Fraser
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.ppat.1009775

Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses
Cited by: 10
Author(s): Sofia Banchenko, Ferdinand Krupp, Christine Gotthold, Jörg Bürger, Andrea Graziadei, Francis J. O’Reilly, Ludwig Sinn, Olga Ruda, Juri Rappsilber, C.M.T. Spahn, Thorsten Mielke, Ian A. Taylor, David Schwefel
Software Mentions: 3
Published: about 5 years ago

10.1074/jbc.M116.730382

Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases
Cited by: 14
Author(s): Marco Igor Valencia-Sánchez, Annia Rodríguez‐Hernández, Ruben Ferreira, Hugo A. Santamaría-Suárez, Marcelino Arciniega, Anne-Catherine Dock-Brégeon, Dino Moras, Brice Beinsteiner, Haydyn D. T. Mertens, Dmitri I. Svergun, Luis G. Brieba, Morten Grøtli, Alfredo Torres‐Larios
Software Mentions: 3
Published: over 10 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 11 years ago

10.7554/eLife.56889

An ER translocon for multi-pass membrane protein biogenesis
Cited by: 68
Author(s): Philip T. McGilvray, S. Anghel, Arunkumar Sundaram, Frank Zhong, Michael J. Trnka, James R. Fuller, Hong Yu Hu, Alma L. Burlingame, Robert J. Keenan
Software Mentions: 3
Published: about 6 years ago

10.1074/jbc.M117.776476

Allosteric mechanism of action of the therapeutic anti-IgE antibody omalizumab
Cited by: 57
Author(s): Anna M. Davies, Elizabeth G. Allan, Anthony H. Keeble, Jean Delgado, Benjamin P. Cossins, A.N. Mitropoulou, M.O.Y. Pang, Tom Ceska, Andrew J. Beavil, Graham Craggs, Marta Westwood, Alistair J. Henry, James M. McDonnell, Brian J. Sutton
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.46417

Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
Cited by: 58
Author(s): Gregory M. Martin, Min Woo Sung, Zhongying Yang, Laura Innes, Krishnaswamy Balamurugan, Larry L. David, Craig Yoshioka, Show Ling Shyng
Software Mentions: 3
Published: about 7 years ago

10.1107/S2059798317017235

DIALS: 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: over 8 years ago

10.7554/eLife.48907

Two new polymorphic structures of human full-length alpha-synuclein fibrils solved by cryo-electron microscopy
Cited by: 191
Author(s): Ricardo C. Guerrero-Ferreira, Nicholas M. I. Taylor, Ana-Andreea Arteni, Pratibha Kumari, Daniel Mona, Philippe Ringler, Markus Britschgi, Matthias E. Lauer, Ali Makky, Joeri Verasdonck, Roland Riek, Ronald Melki, Beat H. Meier, Anja Böckmann, Luc Bousset, Henning Stahlberg
Software Mentions: 3
Published: almost 7 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: about 6 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: about 5 years ago

10.1074/jbc.M117.806893

Negatively charged residues in the first extracellular loop of the L-type CaV1.2 channel anchor the interaction with the CaVα2δ1 auxiliary subunit
Cited by: 16
Author(s): Benoîte Bourdin, Julie Briot, Marie-Philippe Tétreault, Rémy Sauvé, Lucie Parent
Software Mentions: 3
Published: about 9 years ago

10.1107/S1399004714025875

Data Exploration Toolkitfor serial diffraction experiments
Cited by: 27
Author(s): Oliver B. Zeldin, Aaron S. Brewster, Johan Hattne, Monarin Uervirojnangkoorn, A.Y. Lyubimov, Qiuhong Zhou, Minglei Zhao, William I. Weis, Nicholas K. Sauter, Axel T. Brunger
Software Mentions: 3
Published: over 11 years ago

10.1107/S1399004715000383

Brickworxbuilds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps
Cited by: 8
Author(s): Grzegorz Chojnowski, Tomasz Waleń, Paweł Piątkowski, Wojciech Potrzebowski, Janusz M. Bujnicki
Software Mentions: 3
Published: over 11 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: almost 8 years ago

10.1107/S1399004715004514

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams
Cited by: 112
Author(s): Nicolas Coquelle, Aaron S. Brewster, U. Kapp, Anastasya Shilova, Britta Weinhausen, Manfred Burghammer, J.P. Colletier
Software Mentions: 3
Published: over 11 years ago

10.1038/s41421-019-0103-0

Molecular basis for hierarchical histone de-β-hydroxybutyrylation by SIRT3
Cited by: 64
Author(s): Xingrun Zhang, Ruili Cao, Jinrong Niu, Sen Yang, Huida Ma, Shuai Zhao, Haitao Li
Software Mentions: 3
Published: over 7 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: over 12 years ago

10.1016/j.cell.2021.02.045

Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling
Cited by: 18
Author(s): R.A. Robinson, Samuel C. Griffiths, Lieke L van de Haar, Tomas Malinauskas, Eljo Y. van Battum, Pavol Zelina, Rebekka A. Schwab, Dimple Karia, L. Malinauskaite, Sara Brignani, Marleen H. van den Munkhof, O. Dudukcu, A.A. De Ruiter, Dianne M.A. van den Heuvel, B. Bishop, J. Elegheert, A. Radu Aricescu, R. Jeroen Pasterkamp, Christian Siebold
Software Mentions: 3
Published: over 5 years ago

10.1107/S2059798320000418

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction
Cited by: 13
Author(s): Nicholas K. Sauter, Jan Kern, Junko Yano, James M. Holton
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0156344

A Novel Phenanthridionone Based Scaffold As a Potential Inhibitor of the BRD2 Bromodomain: Crystal Structure of the Complex
Cited by: 11
Author(s): Shailesh Tripathi, Shruti Mathur, Prashant Deshmukh, R Manjula, Balasundaram Padmanabhan
Software Mentions: 3
Published: over 10 years ago

10.1038/cddis.2017.487

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2
Cited by: 20
Author(s): M. Merski, Cátia Moreira, Rui M.V. Abreu, María J. Ramos, Pedro A. Fernandes, L. Miguel Martins, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro
Software Mentions: 3
Published: about 9 years ago

10.1074/jbc.RA118.004469

Discovery of peptide ligands targeting a specific ubiquitin-like domain–binding site in the deubiquitinase USP11
Cited by: 24
Author(s): Anastasios Spiliotopoulos, Lia Blokpoel Ferreras, Ruth M Densham, Simon G. Caulton, Ben C. Maddison, Joanna R. Morris, James E. Dixon, Kevin C. Gough, Ingrid Dreveny
Software Mentions: 3
Published: almost 8 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 7 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 11 years ago

10.1371/journal.pone.0039550

On the Structure and Function of the Phytoene Desaturase CRTI from Pantoea ananatis, a Membrane-Peripheral and FAD-Dependent Oxidase/Isomerase
Cited by: 74
Author(s): Patrick Schaub, Qiuju Yu, Sandra Gemmecker, Pierre Poussin-Courmontagne, J. Mailliot, A.G. McEwen, Sandro Ghisla, Salim Al‐Babili, Jean Cavarelli, Peter Beyer
Software Mentions: 3
Published: over 14 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 13 years ago

10.1107/S2059798316007695

Ab initiophasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus
Cited by: 3
Author(s): Masato Yoshimura, Nai Chi Chen, Hongbing Guan, Phimonphan Chuankhayan, Chi‐Chang Lin, Atsushi Nakagawa, Chun‐Jung Chen
Software Mentions: 3
Published: over 10 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: about 15 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 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 6 years ago

10.1371/journal.pone.0077995

Structural and Enzymatic Characterization of the Phosphotriesterase OPHC2 from Pseudomonas pseudoalcaligenes
Cited by: 52
Author(s): Guillaume Gotthard, Julien Hiblot, Daniel H. González, Mikael Elias, Éric Chabrière
Software Mentions: 3
Published: almost 13 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 9 years ago

10.1371/journal.pone.0233689

The crystal structures of Thermus thermophilus CMP kinase complexed with a phosphoryl group acceptor and donor
Cited by: 3
Author(s): Ryosuke Mega, Noriko Nakagawa, Seiki Kuramitsu, Ryoji Masui
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0214440

A DNA aptamer reveals an allosteric site for inhibition in metallo-β-lactamases
Cited by: 17
Author(s): Nazmul H Khan, Anthony A. Bui, Yang Xiao, R. Bryan Sutton, Robert W. Shaw, Benjamin J. Wylie, Michael P. Latham
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pntd.0008091

Trypanosomatid selenophosphate synthetase structure, function and interaction with selenocysteine lyase
Cited by: 4
Author(s): Marco Túlio Alves da Silva, Ivan Rosa e Silva, Lívia Maria Faim, Natália Karla Bellini, Murilo Leão Pereira, Ana Laura Lima, Teresa Cristina Leandro de Jesus, Fernanda Cristina Costa, Tatiana F. Watanabe, H.M. Pereira, Sandro Roberto Valentini, Cleslei Fernando Zanelli, Júlio César Borges, Márcio Vinícius Bertacini Dias, Júlia Pinheiro Chagas da Cunha, Bidyottam Mittra, Norma W. Andrews, Otávio Henrique Thiemann
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0115082

Ethenoguanines Undergo Glycosylation by Nucleoside 2′-Deoxyribosyltransferases at Non-Natural Sites
Cited by: 10
Author(s): Wenjie Ye, Debajyoti Paul, Lina Gao, Jolita Šečkutė, R. Sangaiah, K. Jayaraj, Zhenfa Zhang, P.A. Kaminski, S.E. Ealick, Avram Gold, Louise M. Ball
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0080210

Comparative Sequence, Structure and Redox Analyses of Klebsiella pneumoniae DsbA Show That Anti-Virulence Target DsbA Enzymes Fall into Distinct Classes
Cited by: 25
Author(s): Fabian Kurth, Kieran Rimmer, Lakshmanane Premkumar, Biswaranjan Mohanty, Wilko Duprez, Maria A. Halili, Stephen R. Shouldice, Begoña Heras, David P. Fairlie, M.J. Scanlon, Jennifer L. Martin
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0241513

Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX
Cited by: 12
Author(s): Linda Yingqi Lin, Sawyer McCarthy, Barrett M. Powell, Yanti Manurung, Irene M. Xiang, William L. Dean, Brad Chaires, Liliya A. Yatsunyk
Software Mentions: 3
Published: almost 6 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 10 years ago

10.1371/journal.pone.0036297

Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (PPAR) γ Activators and Pan-PPAR Partial Agonists
Cited by: 163
Author(s): M.V. Liberato, Alessandro S. Nascimento, Steven D. Ayers, Jean Z. Lin, Aleksandra Čvoro, Rodrigo L. Silveira, Leandro Martı́nez, Paulo C. T. Souza, Daniel Menezes Saidemberg, Tuo Deng, Angela Angelica Amato, Marie Togashi, Willa A. Hsueh, Kevin J. Phillips, Mário Sérgio Palma, Francisco de Assis Rocha Neves, Munir S. Skaf, Paul Webb, Igor Polikarpov
Software Mentions: 3
Published: over 14 years ago

10.1107/S2059798318006678

Engineering glycoside hydrolase stability by the introduction of zinc binding
Cited by: 1
Author(s): Thomas L. Ellinghaus, J.H. Pereira, R.P. McAndrew, Ditte Hededam Welner, Andy DeGiovanni, Joel M. Guenther, Huu M. Tran, Taya Feldman, Blake A. Simmons, Kenneth L. Sale, Paul D. Adams
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pbio.3000958

Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome
Cited by: 14
Author(s): Kai Ehrenbolger, Nathan Jespersen, Himanshu Sharma, Yuliya Y. Sokolova, Yuri S. Tokarev, Charles R. Vossbrinck, Jonas Barandun
Software Mentions: 3
Published: almost 6 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: about 7 years ago

10.1371/journal.pbio.1001994

Thermodynamic System Drift in Protein Evolution
Cited by: 74
Author(s): Kathryn M. Hart, Michael J. Harms, Bryan H. Schmidt, Carolyn Elya, Joseph W. Thornton, Susan Marqusee
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pbio.1001669

An RNA-Binding Complex Involved in Ribosome Biogenesis Contains a Protein with Homology to tRNA CCA-Adding Enzyme
Cited by: 32
Author(s): Jinzhong Lin, Jing Lü, Yingang Feng, Mengyi Sun, Keqiong Ye
Software Mentions: 3
Published: about 13 years ago

10.1007/s11103-020-01052-5

Structural insights into Arabidopsis ethylene response factor 96 with an extended N-terminal binding to GCC box
Cited by: 12
Author(s): Chun‐Yen Chen, Pei‐Hsuan Lin, Kun-Hung Chen, Yi-Sheng Cheng
Software Mentions: 3
Published: about 6 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 13 years ago

10.7717/peerj.4728

Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain from Mycobacterium tuberculosis
Cited by: 5
Author(s): Mingjing Yu, Chao Dou, Yijun Gu, Wei Cheng
Software Mentions: 3
Published: over 8 years ago

10.1107/S0907444909022707

Polarizable atomic multipole X-ray refinement: application to peptide crystals
Cited by: 48
Author(s): Michael J. Schnieders, Timothy D. Fenn, Vijay S. Pande, Axel T. Brunger
Software Mentions: 3
Published: about 17 years ago

10.1016/j.molmet.2020.101015

The type 2 diabetes gene product STARD10 is a phosphoinositide-binding protein that controls insulin secretory granule biogenesis
Cited by: 20
Author(s): Gaëlle Carrat, Elizabeth Haythorne, Alejandra Tomás, Leena Haataja, Andreas Müller, Peter Arvan, Alexandra Piunti, Kaiying Cheng, Mutian Huang, Timothy J. Pullen, Eleni Georgiadou, Theodoros Stylianides, Nur Shabrina Amirruddin, Victoria Salem, Walter Distaso, Andrew Cakebread, Kate J Heesom, Philip A. Lewis, David J. Hodson, Linford J.B. Briant, Annie Fung, Richard B. Sessions, Fabien Alpy, Alice Pik‐Shan Kong, Peter I. Benke, Federico Torta, Adrian Kee Keong Teo, Isabelle Leclerc, Michele Solimena, Dale B. Wigley, Guy A. Rutter
Software Mentions: 3
Published: about 6 years ago

10.3390/cancers13133317

A Novel Nanobody Precisely Visualizes Phosphorylated Histone H2AX in Living Cancer Cells under Drug-Induced Replication Stress
Cited by: 12
Author(s): Eric Moeglin, Dominique Desplancq, Audrey Stoessel, Christian Massute, Jeremy Ranniger, A.G. McEwen, Gabrielle Zeder‐Lutz, Mustapha Oulad‐Abdelghani, Manuela Chiper, Pierre Lafaye, Barbara Di Ventura, Pascal Didier, Arnaud Poterszman, Étienne Weiss
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pbio.1001512

Conformational Change-Induced Repeat Domain Expansion Regulates Rap Phosphatase Quorum-Sensing Signal Receptors
Cited by: 56
Author(s): Vijay Parashar, Philip D. Jeffrey, Matthew B. Neiditch
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pcbi.1003478

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor
Cited by: 69
Author(s): Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, Brian M. Baker
Software Mentions: 3
Published: over 12 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 7 years ago

10.1038/celldisc.2016.51

Structural mechanism for the arginine sensing and regulation of CASTOR1 in the mTORC1 signaling pathway
Cited by: 33
Author(s): Zhongchao Gai, Qian Wang, Can Yang, Lei Wang, Wei Deng, Geng Wu
Software Mentions: 3
Published: almost 10 years ago

10.1016/j.molcel.2017.09.027

A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants
Cited by: 54
Author(s): Mads Gabrielsen, Lori Buetow, Mark A. Nakasone, Syed Feroj Ahmed, Gary Sibbet, Brian O. Smith, Wei Zhang, Sachdev S. Sidhu, Danny T. Huang
Software Mentions: 3
Published: about 9 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 5 years ago

10.1016/j.molcel.2019.07.022

Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk
Cited by: 140
Author(s): James A. Letts, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, L.A. Sazanov
Software Mentions: 3
Published: about 7 years ago

10.15252/embj.2018100825

Diverse roles of TssA‐like proteins in the assembly of bacterial type VI secretion systems
Cited by: 34
Author(s): Johannes Schneider, Sergey Nazarov, Ricardo Adaixo, Martina Liuzzo, Peter David Ringel, Henning Stahlberg, Marek Basler
Software Mentions: 3
Published: about 7 years ago

10.1107/S0108767310039140

Geometric properties of nucleic acids with potential for autobuilding
Cited by: 11
Author(s): Tim Gruene, George M. Sheldrick
Software Mentions: 3
Published: almost 16 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: about 5 years ago

10.1107/S0907444910000302

Rapid model building of β-sheets in electron-density maps
Cited by: 4
Author(s): Thomas C. Terwilliger
Software Mentions: 3
Published: over 16 years ago

10.1074/jbc.M115.705863

Inhibition of PRL-2·CNNM3 Protein Complex Formation Decreases Breast Cancer Proliferation and Tumor Growth
Cited by: 38
Author(s): Elie Kostantin, Serge Hardy, William C. Valinsky, Andreas Kompatscher, Jeroen H. F. de Baaij, Yevgen Zolotarov, Mélissa Landry, Noriko Uetani, Luis Alfonso Martínez-Cruz, Joost G. J. Hoenderop, Alvin Shrier, Michel L. Tremblay
Software Mentions: 3
Published: over 10 years ago

10.1074/jbc.RA118.006045

Structural insights into non-covalent ubiquitin activation of the cIAP1-UbcH5B∼ubiquitin complex
Cited by: 12
Author(s): Amrita Patel, Gary Sibbet, Danny T. Huang
Software Mentions: 3
Published: almost 8 years ago

10.1074/jbc.RA119.007709

Structure and interactions of the archaeal motility repression module ArnA–ArnB that modulates archaellum gene expression in Sulfolobus acidocaldarius
Cited by: 15
Author(s): Lena Hoffmann, Katrin Anders, Lisa Franziska Bischof, Xing Ye, Julia Reimann, Sunia Khadouma, Trong Khoa Pham, Chris van der Does, Phillip C. Wright, Lars‐Oliver Essen, Sonja‐Verena Albers
Software Mentions: 3
Published: over 7 years ago

10.1074/jbc.RA120.012788

Small molecule AX-024 reduces T cell proliferation independently of CD3ϵ/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain
Cited by: 10
Author(s): Kirsten Richter, Arne C. Rufer, Magali Muller, Dominique Burger, Fabio Casagrande, Tabea Grossenbacher, Sylwia Huber, Melanie N. Hug, Philipp Koldewey, Andrea D’Osualdo, Daniel Schlatter, Theodor Stoll, M.G. Rudolph
Software Mentions: 3
Published: over 6 years ago

10.1016/j.jbc.2021.100700

ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis
Cited by: 8
Author(s): Jitender Mehla, George W. Liechti, Randy M. Morgenstein, J. Harry Caufield, Ali Hosseinnia, Alla Gagarinova, Sadhna Phanse, Norman Goodacre, Mary R. Brockett, Neha Sakhawalkar, Mohan Babu, Rong Xiao, Gaetano T. Montelione, S.M. Vorobiev, T. den Blaauwen, J.F. Hunt, Peter Uetz
Software Mentions: 3
Published: almost 6 years ago

10.3390/life5021264

The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets
Cited by: 14
Author(s): Birgit Märtens, G.A. Bezerra, Mathias Josef Kreuter, Irina Grishkovskaya, Andrea Manica, Valentina Arkhipova, Kristina Djinović-Carugo, Udo Bläsi
Software Mentions: 3
Published: over 11 years ago

10.1016/j.jbc.2021.101061

A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase
Cited by: 7
Author(s): Emily Chen, Krystle Reiss, Dilip Shah, R Manjula, Brandon Allen, Eva Murphy, James W. Murphy, Víctor S. Batista, Vineet Bhandari, Elias Lolis, George P. Lisi
Software Mentions: 3
Published: about 5 years ago

10.1016/j.molimm.2017.11.022

Crystal structures of murine and human Histamine-Releasing Factor (HRF/TCTP) and a model for HRF dimerisation in mast cell activation
Cited by: 12
Author(s): K.A. Dore, Jun‐ichi Kashiwakura, James M. McDonnell, Hannah Gould, Toshiaki Kawakami, Brian J. Sutton, Anna M. Davies
Software Mentions: 3
Published: almost 9 years ago

10.3390/biom10050744

Structure–Activity Relationship Study Reveals the Molecular Basis for Specific Sensing of Hydrophobic Amino Acids by the Campylobacter jejuni Chemoreceptor Tlp3
Cited by: 13
Author(s): Mohammad Firoz Khan, Mayra A. Machuca, Mohammad Mizanur Rahman, Cengiz Koç, Raymond S. Norton, Brian J. Smith, Anna Roujeinikova
Software Mentions: 3
Published: over 6 years ago

10.1107/S1399004714027011

Three-dimensional structures ofPlasmodium falciparumspermidine synthase with bound inhibitors suggest new strategies for drug design
Cited by: 12
Author(s): J. Sprenger, Bo Svensson, J.C. Halander, Jannette Carey, Lo Persson, Salam Al-Karadaghi
Software Mentions: 3
Published: over 11 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 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: almost 9 years ago

Projects: cran: PHENIX

Science Score: 75/100

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Papers Mentioning PHENIX 2,287