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

10.1107/S0907444913023512
Improved estimates of coordinate error for molecular replacement
Cited by: 41
Author(s): Robert D. Oeffner, G. Bunkóczi, Airlie J. McCoy, Randy J. Read
Software Mentions: 1
Published: about 11 years ago
10.1107/S0909049513022164
Creation and structure determination of an artificial protein with three complete sequence repeats
Cited by: 2
Author(s): Motoyasu Adachi, R Shimizu, Ryota Kuroki, Michael Blaber
Software Mentions: 1
Published: about 11 years ago
10.7554/eLife.08504
Structure of a bacterial RNA polymerase holoenzyme open promoter complex
Cited by: 185
Author(s): Byungchan Bae, Andrey Feklístov, Agnieszka Lass-Napiorkowska, Robert Landick, Seth A. Darst
Software Mentions: 1
Published: about 9 years ago
10.1007/s10858-019-00278-w
Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser
Cited by: 6
Author(s): Jienv Ding, Monalisa Swain, Ping Yü, Jason R. Stagno, Yun‐Xing Wang
Software Mentions: 1
Published: about 5 years ago
10.1083/jcb.201709092
A Numb–Mdm2 fuzzy complex reveals an isoform-specific involvement of Numb in breast cancer
Cited by: 33
Author(s): Ivan N. Colaluca, Andrea Basile, Lee Freiburger, Veronica D'Uva, Davide Disalvatore, Manuela Vecchi, Stefano Confalonieri, Daniela Tosoni, Valentina Cecatiello, Maria Grazia Malabarba, Chun Jiun Yang, Masatsune Kainosho, Michael Sattler, Marina Mapelli, Salvatore Pece, Pier Paolo Di Fiore
Software Mentions: 1
Published: almost 7 years ago
10.7554/eLife.28619
Structural basis of host recognition and biofilm formation by Salmonella Saf pili
Cited by: 20
Author(s): Longhui Zeng, Li Zhang, Pengran Wang, Guoyu Meng
Software Mentions: 1
Published: about 7 years ago
10.1107/S1399004714017040
Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data
Cited by: 26
Author(s): Thomas C. Terwilliger, G. Bricogne
Software Mentions: 1
Published: about 10 years ago
10.1186/s13321-016-0119-5
11th German Conference on Chemoinformatics (GCC 2015)
Cited by: 0
Author(s): Uli Fechner, Chris de Graaf, Andrew E. Torda, Stefan Güssregen, A. M. J. Evers, Hans Eberhard Matter, Gerhard Heßler, Nicola J. Richmond, Peter Schmidtke, Marwin Segler, Mark P. Waller, Stefanie Pleik, Joan‐Emma Shea, Zachary A. Levine, Ryan Mullen, Karina van den Broek, Matthias Epple, Hubert Kuhn, Andreas Truszkowski, Achim Zielesny, Johannes Hans Fraaije, Rubèn Serral Gracià, Stefan M. Kast, Krishna C. Bulusu, Andreas Bender, Abraham Yosipof, Oren E. Nahum, Timo Krotzky, Robert Schulz, Gerhard Wolber, Stefan Bietz, Matthias Rarey, Markus O. Zimmermann, Andreas Lange, Manuel Ruff, Johannes Heidrich, Ionut Onlia, Thomas E. Exner, Frank M. Boeckler, Marcel Bermudez, Dzmitry S. Firaha, Oldamur Hollóczki, Barbara Kirchner, Christofer S. Tautermann, Andrea Volkamer, Sameh Eid, Samo Turk, Friedrich Rippmann, Simone Fulle, Noureldin Saleh, Giorgio Saladino, Francesco Luigi Gervasio, Elke Haensele, Lee Banting, David C. Whitley, Jana Sopková−de Oliveira Santos, Ronan Bureau, Timothy W.I. Clark, Achim Sandmann, Harald Lanig, Patrick Kibies, Jochen Heil, Franziska Hoffgaard, Roland Frach, Julian Engel, Steven Smith, Debjit Basu, Daniel Rauh, Oliver Kohlbacher, Jonathan W. Essex, Michael S. Bodnarchuk, Gregory A. Ross, Arndt R. Finkelmann, Andreas H. Göller, Gisbert Schneider, Tamara Husch, Christoph Schütter, Andrea Balducci, Martin Korth, Fidele Ntie‐Kang, Stefan Günther, Wolfgang Sippl, Luc Meva’a Mbaze, Conrad V. Simoben, Lydia L. Lifongo, Philip N. Judson, J. Barilla, M. Lokajíček, H. Pisaková, Pavel Šimr, Natalia Kireeva, Alexandre Petrov, Denis Ostroumov, В.П. Соловьев, В. С. Первов, Nils-Ole Friedrich, Kai Sommer, Johannes Kirchmair, Eugen Proschak, Júlia Wéber, Daniel Moser, Lena Kalinowski, Janosch Achenbach, Mark Mackey, Tim Cheeseright, Gerrit Renner, Torsten Schmidt, J.A.J.M. Schram, Marion Egelkraut-Holtus, Albert van Oeyen, Tuomo Kalliokoski, Denis Fourches, Akachukwu Ibezim, Chika J Mbah, Umale M Adikwu, Ngozi Justina Nwodo, Alexander Steudle, Brian B. Masek, Stephan Nagy, David Baker, Fred Soltanshahi, Roman Dorfman, Karen Dubrucq, Hitesh Patel, Oliver Koch, Florian Mrugalla, Qurrat Ul Ain, Julian E. Fuchs, Robert M. Owen, Kiyoyuki Omoto, R. Torella, David C. Pryde, Robert C. Glen, Petr Hošek, Vojtěch Spiwok, I. Barrett, Mike Firth, David C. Murray, Lisa McWilliams, Qing Cao, Ola Engkvist, Dawid Warszycki, Marek Śmieja, Andrzej J. Bojarski, Natália Aniceto, Alex Canal Freitas, Taravat Ghafourian, Guido Herrmann, Valentina Eigner-Pitto, Alexandra Naß, Rafał Kurczab, Marcel B Günther, Susanne Hennig, Felix Michael Büttner, C. Schall, Adrian Sievers‐Engler, Francesco Ansideri, Pierre Koch, Thilo Stehle, Stefan Laufer, Frank M Böckler, Barbara Zdrazil, Floriane Montanari, Gerhard Ecker, Christoph Grebner, Anders Hogner, Johan Ulander, K. A. P. Edman, Vı́ctor Guallar, Christian Tyrchan, Wolfgang Klute, Fredrik Bergström, Christian Krämer, Quốc Đạt Nguyễn, Steven Strohfeldt, Saraphina Böttcher, Tim Pongratz, Dominik Horinek, Bernd Rupp, Raed Al-Yamori, Michael Lisurek, Ronald Kühne, Filipe Furtado, Ludger A. Wessjohann, Miriam Mathea, Knut Baumann, Siti Zuraidah Mohamad-Zobir, Xinping Fu, Tai-Ping Fan, Maximilian Kühn, Christoph A. Sotriffer, Azédine Zoufir, Xitong Li, Lewis Mervin, Ellen van den Berg, Mark A. Polokoff, Wolf‐D. Ihlenfeldt, Jette Pretzel, Zayan Alhalabi, Robert Fraczkiewicz, Marvin Waldman, Robert D. Clark, Neem Shaikh, Prabha Garg, Alexander J. Kos, Hans-Jürgen Himmler, Christophe Jardin, Heinrich Sticht, Thomas Steinbrecher, Markus Dahlgren, Daniel Cappel, T. D. Lin, Lingle Wang, Goran Krilov, Robert B. Abel, Richard A. Friesner, Woody Sherman, Ina Pöhner, Joanna Panecka, Rebecca C. Wade, Karen T. Schomburg, Matthias Hilbig, Christian Jäger, Vivien Wieczorek, Lance M. Westerhoff, O.Y. Borbulevych, Hans‐Ulrich Demuth, Mirko Buchholz, Denis Schmidt, Thomas Rickmeyer, Peter Kolb, Sumit Mittal, Elsa Sánchez-García, Mauro S. Nogueira, Tiago Bernadon de Oliveira, Fernando Bastos Costa, Thomas J. Schmidt
Software Mentions: 1
Published: over 8 years ago
10.1007/s10822-020-00354-6
The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design
Cited by: 15
Author(s): O.Y. Borbulevych, Roger I. Martin, Lance M. Westerhoff
Software Mentions: 1
Published: about 4 years ago
10.1155/2016/6179635
Sulfatide Preserves Insulin Crystals Not by Being Integrated in the Lattice but by Stabilizing Their Surface
Cited by: 7
Author(s): Karsten Buschard, A.W. Bracey, Daniel L. McElroy, Andrew T. Magis, Thomas Østerbye, Mark A. Atkinson, Kate Bailey, Amanda L. Posgai, David A. Ostrov
Software Mentions: 1
Published: almost 9 years ago
10.7554/eLife.39979
BRCT domains of the DNA damage checkpoint proteins TOPBP1/Rad4 display distinct specificities for phosphopeptide ligands
Cited by: 32
Author(s): Matthew Day, Mathieu Rappas, Katie Ptasińska, Dominik Boos, Antony W. Oliver, Laurence H. Pearl
Software Mentions: 1
Published: about 6 years ago
10.1080/14756366.2021.1906663
Discovery of the natural product 3',4',7,8-tetrahydroxyflavone as a novel and potent selective BRD4 bromodomain 2 inhibitor
Cited by: 9
Author(s): Jiao Li, Wei Zou, Koukou Yu, Bing Liu, Weifeng Liang, Lisha Wang, Yin Lu, Zhaoyi Jiang, Aiyun Wang, Jiapeng Zhu
Software Mentions: 1
Published: almost 4 years ago
10.1107/S1399004713032987
The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition
Cited by: 14
Author(s): Isha Singh, Yajun Lian, Lei Li, Millie M. Georgiadis
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.ppat.1000186
Prevention of Cytotoxic T Cell Escape Using a Heteroclitic Subdominant Viral T Cell Determinant
Cited by: 14
Author(s): Noah S. Butler, A. Theodossis, Andrew I. Webb, Roza Nastovska, Sri H. Ramarathinam, Michelle Anne Dunstone, Jamie Rossjohn, Anthony W. Purcell, Stanley Perlman
Software Mentions: 1
Published: about 16 years ago
10.1371/journal.ppat.1000259
A Novel Co-Crystal Structure Affords the Design of Gain-of-Function Lentiviral Integrase Mutants in the Presence of Modified PSIP1/LEDGF/p75
Cited by: 141
Author(s): S. Hare, Ming-Chieh Shun, Saikat Das Gupta, Eugene Valkov, Alan Engelman, Peter Cherepanov
Software Mentions: 1
Published: almost 16 years ago
10.3390/ijms21113940
The Structural Basis of the Binding of Various Aminopolycarboxylates by the Periplasmic EDTA-Binding Protein EppA from Chelativorans sp. BNC1
Cited by: 3
Author(s): K.M. Lewis, C.L. Greene, S.A. Sattler, BuHyun Youn, Luying Xun, ChulHee Kang
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.ppat.1000751
Structural and Biochemical Characterization of SrcA, a Multi-Cargo Type III Secretion Chaperone in Salmonella Required for Pathogenic Association with a Host
Cited by: 44
Author(s): Colin A. Cooper, Kun Zhang, Sara N. Andres, Yuan Fang, Natalia A. Kaniuk, Mandy Hannemann, John H. Brumell, Leonard J. Foster, M.S. Junop, Brian K. Coombes
Software Mentions: 1
Published: almost 15 years ago
10.1016/j.yjsbx.2020.100021
Cryo-EM structure of the prefusion state of canine distemper virus fusion protein ectodomain
Cited by: 4
Author(s): David Kalbermatter, Neeta Shrestha, Flavio M. Gall, Marianne Wyss, Rainer Riedl, Philippe Plattet, Dimitrios Fotiadis
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.ppat.1002011
Novel Escape Mutants Suggest an Extensive TRIM5α Binding Site Spanning the Entire Outer Surface of the Murine Leukemia Virus Capsid Protein
Cited by: 53
Author(s): Sadayuki Ohkura, David C. Goldstone, Melvyn W. Yap, Kate Holden-Dye, Ian A. Taylor, Jonathan P. Stoye
Software Mentions: 1
Published: over 13 years ago
10.1371/journal.ppat.1002034
Structural Insights into Viral Determinants of Nematode Mediated Grapevine fanleaf virus Transmission
Cited by: 41
Author(s): Pascale Schellenberger, Claude Sauter, Bernard Lorber, Patrick Bron, Stefano Trapani, Marc Bergdoll, Aurélie Marmonier, Corinne Schmitt-Keichinger, Olivier Lemaire, Gérard Demangeat, Christophe Ritzenthaler
Software Mentions: 1
Published: over 13 years ago
10.7554/eLife.59407
Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter
Cited by: 26
Author(s): Julia Steiner, L.A. Sazanov
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.ppat.1002162
Structural Basis of Chemokine Sequestration by CrmD, a Poxvirus-Encoded Tumor Necrosis Factor Receptor
Cited by: 34
Author(s): Xiaoguang Xue, Qingyu Lu, Hui Wei, Dongli Wang, Dongwei Chen, Guang‐Jun He, Li Huang, Hanzhong Wang, Xinquan Wang
Software Mentions: 1
Published: over 13 years ago
10.1371/journal.ppat.1002294
Biochemical and Structural Insights into the Mechanisms of SARS Coronavirus RNA Ribose 2′-O-Methylation by nsp16/nsp10 Protein Complex
Cited by: 279
Author(s): Yu Chen, Ceyang Su, Manzhu Ke, Xu Jin, Lirong Xu, Zhou Zhang, Andong Wu, Yan Sun, Zhouning Yang, Po Tien, Tero Ahola, Yi Liang, Xinqi Liu, Deyin Guo
Software Mentions: 1
Published: about 13 years ago
10.1371/journal.ppat.1002249
Structural and Functional Analysis of Laninamivir and its Octanoate Prodrug Reveals Group Specific Mechanisms for Influenza NA Inhibition
Cited by: 131
Author(s): Christopher J. Vavricka, Qing Li, Yan Wu, Jianxun Qi, Mingyang Wang, Yue Liu, Feng Gao, Jun Li, Eryin Feng, Jianhua He, Jinfang Wang, Hong Liu, Hualiang Jiang, George F. Gao
Software Mentions: 1
Published: about 13 years ago
10.1371/journal.ppat.1002524
Specialized Peptidoglycan Hydrolases Sculpt the Intra-bacterial Niche of Predatory Bdellovibrio and Increase Population Fitness
Cited by: 69
Author(s): Thomas R. Lerner, Andrew L. Lovering, Nhat Khai Bui, Kaoru Uchida, Shin‐Ichi Aizawa, Waldemar Vollmer, R. Elizabeth Sockett
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.ppat.1002531
Structural and Functional Insights into the Pilotin-Secretin Complex of the Type II Secretion System
Cited by: 44
Author(s): Shuang Gu, Saima Rehman, Xiaohui Wang, Vladimir E. Shevchik, Richard W. Pickersgill
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.ppat.1002550
The Ebola Virus Interferon Antagonist VP24 Directly Binds STAT1 and Has a Novel, Pyramidal Fold
Cited by: 123
Author(s): Adrianna P. P. Zhang, Zachary A. Bornholdt, Tong Liu, Dafna M. Abelson, David E. Lee, Sheng Li, Virgil L. Woods, Erica Ollmann Saphire
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.ppat.1002528
Structural Insights into a Unique Legionella pneumophila Effector LidA Recognizing Both GDP and GTP Bound Rab1 in Their Active State
Cited by: 46
Author(s): Wei Cheng, Kun Yin, Defen Lu, Bingqing Li, Deyu Zhu, Yuzhen Chen, Hao Zhang, Sujuan Xu, Jijie Chai, Lichuan Gu
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.ppat.1002559
Differential Function of Lip Residues in the Mechanism and Biology of an Anthrax Hemophore
Cited by: 41
Author(s): MarCia T. Ekworomadu, Catherine B. Poor, Cedric P. Owens, Miriam Balderas, Marián Fabián, John S. Olson, F.V. Murphy, Erol Balkabasi, Erin S. Honsa, Chuan He, Celia W. Goulding, Anthony W. Maresso
Software Mentions: 1
Published: over 12 years ago
10.7554/eLife.36615
Electron cryo-microscopy structure of the canonical TRPC4 ion channel
Cited by: 83
Author(s): Deivanayagabarathy Vinayagam, Thomas Mager, Amir Apelbaum, Arne Bothe, Felipe Merino, Oliver Hofnagel, Christos Gatsogiannis, Stefan Raunser
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.ppat.1002633
Loss of Anti-Viral Immunity by Infection with a Virus Encoding a Cross-Reactive Pathogenic Epitope
Cited by: 28
Author(s): Alex T. Chen, Markus Cornberg, Stéphanie Gras, Carole Guillonneau, Jamie Rossjohn, Andrew Trees, Sébastien Emonet, Juan Carlos de la Torre, Raymond M. Welsh, Liisa K. Selin
Software Mentions: 1
Published: over 12 years ago
10.7554/eLife.49110
Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a
Cited by: 40
Author(s): Gavin J. Knott, Brady F. Cress, Jun Jie Liu, Brittney W. Thornton, Rachel J. Lew, Basem Al-Shayeb, Daniel Rosenberg, Michal Hammel, Benjamin A. Adler, Marco Lobba, Michael Xu, Adam P. Arkin, Christof Fellmann, Jennifer A. Doudna
Software Mentions: 1
Published: over 5 years ago
10.1016/j.yjsbx.2021.100049
Structural characterization of two solute-binding proteins for N,N′-diacetylchitobiose/N,N′,N′′-triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7
Cited by: 0
Author(s): Takafumi Itoh, Misaki Yaguchi, Akari Nakaichi, Moe Yoda, Takao Hibi, Hisashi Kimoto
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.ppat.1002876
A Unique Bivalent Binding and Inhibition Mechanism by the Yatapoxvirus Interleukin 18 Binding Protein
Cited by: 25
Author(s): Brian E. Krumm, Xiangzhi Meng, Zhixin Wang, Yan Xiang, Junpeng Deng
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.ppat.1002958
Molecular Basis for Genetic Resistance of Anopheles gambiae to Plasmodium: Structural Analysis of TEP1 Susceptible and Resistant Alleles
Cited by: 36
Author(s): Binh M. Le, Marni Williams, Shankar Logarajah, Richard H. G. Baxter
Software Mentions: 1
Published: about 12 years ago
10.7554/eLife.20383
Structure of the malaria vaccine candidate antigen CyRPA and its complex with a parasite invasion inhibitory antibody
Cited by: 46
Author(s): Paola Favuzza, Elena Guffart, Marco Tamborrini, Bianca Scherer, Anita M. Dreyer, Arne C. Rufer, Johannes Erny, Joerg Hoernschemeyer, Ralf Thoma, Georg Schmid, Bernard Gsell, Araceli Lamelas, J. Benz, Catherine Joseph, Hugues Matile, Gerd Pluschke, M.G. Rudolph
Software Mentions: 1
Published: almost 8 years ago
10.1107/S0907444912027965
The structure of the ternary Eg5–ADP–ispinesib complex
Cited by: 40
Author(s): Sandeep K. Talapatra, Alexander W. Schüttelkopf, Frank Kozielski
Software Mentions: 1
Published: about 12 years ago
10.1371/journal.ppat.1003121
A Pathogen Type III Effector with a Novel E3 Ubiquitin Ligase Architecture
Cited by: 78
Author(s): A.U. Singer, Sebastian Schulze, T. Skarina, Xiaohui Xu, Hong Cui, Lennart Eschen‐Lippold, Monique Egler, Tharan Srikumar, Brian Raught, Justin Lee, Dierk Scheel, Alexei Savchenko, Ulla Bonas
Software Mentions: 1
Published: almost 12 years ago
10.1107/S090744491300958X
Microcrystal manipulation with laser tweezers
Cited by: 16
Author(s): Armin Wagner, Ramona Duman, Bob Stevens, Andrew D. Ward
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.ppat.1003307
A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly
Cited by: 77
Author(s): Julien R. C. Bergeron, L.J. Worrall, Nikolaos G. Sgourakis, Frank DiMaio, Richard A. Pfuetzner, Heather B. Felise, M. Vuckovic, Angel C. Y. Yu, Samuel I. Miller, David Baker, N.C.J. Strynadka
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.ppat.1003342
Broadly Neutralizing Antibody PGT121 Allosterically Modulates CD4 Binding via Recognition of the HIV-1 gp120 V3 Base and Multiple Surrounding Glycans
Cited by: 266
Author(s): Jean-Philippe Julien, Devin Sok, Reza Khayat, Jeong Hyun Lee, Katie J. Doores, Laura M. Walker, Alejandra Ramos, Devan Diwanji, Robert Pejchal, Albert Cupo, Umesh Katpally, Rafael S. Depetris, Robyn L. Stanfield, Ryan McBride, Andre J. Marozsan, James C. Paulson, Rogier W. Sanders, John P. Moore, Dennis R. Burton, Pascal Poignard, Andrew B. Ward, Ian A. Wilson
Software Mentions: 1
Published: over 11 years ago
10.3390/ijms21175977
Lard Injection Matrix for Serial Crystallography
Cited by: 25
Author(s): Ki Hyun Nam
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.ppat.1003352
Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5α Specificity
Cited by: 27
Author(s): K. McCarthy, Aaron Schmidt, Andrea Kirmaier, Allison L. Wyand, Ruchi M. Newman, Welkin E. Johnson
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.ppat.1003390
Structural and Functional Basis for Inhibition of Erythrocyte Invasion by Antibodies that Target Plasmodium falciparum EBA-175
Cited by: 54
Author(s): Edwin Chen, May M. Paing, Nichole D. Salinas, B. Kim Lee Sim, Niraj H. Tolia
Software Mentions: 1
Published: over 11 years ago
10.7554/eLife.43584
Heparin-induced tau filaments are polymorphic and differ from those in Alzheimer’s and Pick’s diseases
Cited by: 270
Author(s): W Zhang, Benjamin Falcon, Alexey G. Murzin, Jiaqin Fan, R. Anthony Crowther, Michel Goedert, Sjors H.W. Scheres
Software Mentions: 1
Published: almost 6 years ago
10.1107/S0909049513021572
Structural studies of haemoglobin from pisces species shortfin mako shark (<i>Isurus oxyrinchus)</i>at 1.9 Å resolution
Cited by: 5
Author(s): Ramesh Pandian, S. Sundaresan, Pon. Sathya Moorthy, Mahalingam Balasubramanian, M. N. Ponnuswamy
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.ppat.1003684
Crystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a Potent Cross-Reactive Neutralizing Human Monoclonal Antibody
Cited by: 48
Author(s): Kai Xu, Barry Rockx, Yihu Xie, Blair L. DeBuysscher, Deborah L Fusco, Zhongyu Zhu, Yee-Peng Chan, Yan Xu, Truong Luu, Regina Z. Cer, Heinz Feldmann, Vishwesh Mokashi, Dimiter S. Dimitrov, Kimberly A. Bishop‐Lilly, Christopher C. Broder, Dimitar B. Nikolov
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.ppat.1003690
Structure of a Bimodular Botulinum Neurotoxin Complex Provides Insights into Its Oral Toxicity
Cited by: 98
Author(s): Kwangkook Lee, Shenyan Gu, Lei Jin, Thi Tuc Nghi Le, Luisa W. Cheng, Jasmin Strotmeier, Anna Magdalena Kruel, Guorui Yao, Kay Perry, Andreas Rummel, Rongsheng Jin
Software Mentions: 1
Published: about 11 years ago
10.1107/S1399004713032112
Crystal structure and conformational flexibility of the unligated FK506-binding protein FKBP12.6
Cited by: 4
Author(s): Hui Chen, Sourajit M. Mustafi, David M. LeMaster, Zhong Li, A. Héroux, Hongmin Li, Griselda Hernández
Software Mentions: 1
Published: almost 11 years ago
10.1107/S0907444909021933
Averaged kick maps: less noise, more signal…and probably less bias
Cited by: 58
Author(s): Jure Pražnikar, Pavel V. Afonine, Gregor Gunčar, Paul D. Adams, Dušan Turk
Software Mentions: 1
Published: over 15 years ago
10.1371/journal.ppat.1003837
Pfit Is a Structurally Novel Crohn's Disease-Associated Superantigen
Cited by: 4
Author(s): Lihui Liu, Hui Chen, Michael Brecher, Zhong Li, Bo-Bo Wei, Bisweswar Nandi, Jing Zhang, Hua Ling, Gary M. Winslow, Jonathan Braun, Hongmin Li
Software Mentions: 1
Published: almost 11 years ago
10.7554/eLife.31473
Hepatitis B virus core protein allosteric modulators can distort and disrupt intact capsids
Cited by: 74
Author(s): Christopher John Schlicksup, Joseph Che Yen Wang, Samson Francis, Balasubramanian Venkatakrishnan, William W. Turner, Michael S. VanNieuwenhze, Adam Zlotnick
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.ppat.1004316
Structure of CfaA Suggests a New Family of Chaperones Essential for Assembly of Class 5 Fimbriae
Cited by: 8
Author(s): Rui Bao, April Fordyce, Chen Yuxing, Annette L. McVeigh, Stephen J. Savarino, Di Xia
Software Mentions: 1
Published: over 10 years ago
10.3390/ijms21197166
Repurposing Benzbromarone for Familial Amyloid Polyneuropathy: A New Transthyretin Tetramer Stabilizer
Cited by: 15
Author(s): Ellen Y Cotrina, Â. Oliveira, José P. Leite, Jordi Llop, Luı́s Gales, Jordi Quintana, Isabel Cardoso, Gemma Arsequell
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.ppat.1004401
A Sialic Acid Binding Site in a Human Picornavirus
Cited by: 41
Author(s): Georg Zocher, Nitesh Mistry, Martin Frank, Irmgard Hähnlein-Schick, Jens‐Ola Ekström, Niklas Arnberg, Thilo Stehle
Software Mentions: 1
Published: about 10 years ago
10.1107/S1399004713034718
The structures of cytosolic and plastid-located glutamine synthetases from<i>Medicago truncatula</i>reveal a common and dynamic architecture
Cited by: 21
Author(s): Eva Torreira, Ana R. Seabra, Helen M. Marriott, Min Zhou, Óscar Llorca, Carol V. Robinson, Helena Carvalho, Carlos Fernández‐Tornero, Pedro José Barbosa Pereira
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.ppat.1004512
Crystal Structure of Cytomegalovirus IE1 Protein Reveals Targeting of TRIM Family Member PML via Coiled-Coil Interactions
Cited by: 53
Author(s): Myriam Scherer, Stefan Klingl, Madhumati Sevvana, Victoria Otto, Eva-Maria Schilling, Joachim D. Stump, Regina Müller, Nina Reuter, Heinrich Sticht, Yves A. Muller, Thomas Stamminger
Software Mentions: 1
Published: about 10 years ago
10.3390/ijms21197375
Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2
Cited by: 45
Author(s): Annika Rogstam, Maria Nyblom, Steffan Wittrup Christensen, C. Sele, V. Talibov, Therese Lindvall, Anna Andersson Rasmussen, Ingemar André, S.Z. Fisher, Wolfgang Knecht, Frank Kozielski
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.ppat.1004682
A Crystal Structure of the Dengue Virus NS5 Protein Reveals a Novel Inter-domain Interface Essential for Protein Flexibility and Virus Replication
Cited by: 174
Author(s): Yongxiang Zhao, Tingjin Sherryl Soh, Jie Zheng, Kitti Wing Ki Chan, Wint Wint Phoo, Chin Chin Lee, Moon Y. F. Tay, Kunchithapadam Swaminathan, Tobias Cornvik, Siew Pheng Lim, Pei–Yong Shi, Julien Lescar, Subhash G. Vasudevan, Dahai Luo
Software Mentions: 1
Published: over 9 years ago
10.1038/srep13133
Structural basis for the neutralization of MERS-CoV by a human monoclonal antibody MERS-27
Cited by: 59
Author(s): Xintong Yu, Senyan Zhang, Liwei Jiang, Ye Cui, Dongxia Li, Dongli Wang, Nianshuang Wang, Lili Fu, Xuanlin Shi, Ziqiang Li, Linqi Zhang, Xinquan Wang
Software Mentions: 1
Published: over 9 years ago
10.1038/srep13028
Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy
Cited by: 32
Author(s): Xiaoyan Zhu, Yun Zhu, Sheng Ye, Qian Wang, Wei Xu, Shan Su, Zhiwu Sun, Fei Yu, Qi Liu, Chao Wang, Tianhong Zhang, Zhenqing Zhang, Xiaoyan Zhang, Jianqing Xu, Lanying Du, Keliang Liu, Lu Lu, Rongguang Zhang, Shibo Jiang
Software Mentions: 1
Published: over 9 years ago
10.1038/srep15808
Structural evidence for the role of polar core residue Arg175 in arrestin activation
Cited by: 33
Author(s): Joachim Granzin, Andreas M. Stadler, Anneliese Cousin, Ramona Schlesinger, Renu Batra‐Safferling
Software Mentions: 1
Published: about 9 years ago
10.7554/eLife.50155
Structural model for differential cap maturation at growing microtubule ends
Cited by: 42
Author(s): Juan Estévez-Gallego, Fernando Josa-Prado, Siou Ku, Rubén M. Buey, Francisco A Balaguer, A.E. Prota, Daniel Lucena‐Agell, Christina S. Kamma-Lorger, Toshiki Yagi, Hiroyuki Iwamoto, Laurence Duchesne, Isabel Barasoaín, Michel O. Steinmetz, Denis Chrétien, Shinji Kamimura, J. Fernando Díaz, M.A. Oliva
Software Mentions: 1
Published: over 4 years ago
10.1038/srep16470
Structural insights into HetR−PatS interaction involved in cyanobacterial pattern formation
Cited by: 27
Author(s): Hai-Xi Hu, Yong-Liang Jiang, Mingyang Zhao, Kun Cai, Sanling Liu, Bin Wen, Pei Lv, Yonghui Zhang, Junhui Peng, Hui Zhong, Gino Yu, Yan-Min Ren, Zhiyong Zhang, Changlin Tian, Qingfa Wu, Mikael Oliveberg, Cheng‐Cai Zhang, Yuxing Chen, Cong‐Zhao Zhou
Software Mentions: 1
Published: about 9 years ago
10.7554/eLife.59038
Molecular principles of assembly, activation, and inhibition in epithelial sodium channel
Cited by: 33
Author(s): Sigrid Noreng, Richard Posert, Arpita Bharadwaj, Alexandra Houser, Isabelle Baconguis
Software Mentions: 1
Published: over 4 years ago
10.1038/srep16915
Structural insights into YfiR sequestering by YfiB in Pseudomonas aeruginosa PAO1
Cited by: 14
Author(s): Shanshan Li, Tingting Li, Yueyang Xu, Qionglin Zhang, Wei Zhang, Shiyou Che, Ruihua Liu, Yingying Wang, Mark Bartlam
Software Mentions: 1
Published: about 9 years ago
10.1038/srep17216
Structure of the Human Factor VIII C2 Domain in Complex with the 3E6 Inhibitory Antibody
Cited by: 5
Author(s): Michelle E. Wuerth, Rebecca K. Cragerud, P. Clint Spiegel
Software Mentions: 1
Published: about 9 years ago
10.1038/srep17204
Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation
Cited by: 64
Author(s): Masatoshi Wakamori, Yuki Fujii, Noriyuki Suka, Mikako Shirouzu, Kensaku Sakamoto, Takashi Umehara, Shigeyuki Yokoyama
Software Mentions: 1
Published: about 9 years ago
10.1038/srep17144
Structure of Mycobacterium thermoresistibile GlgE defines novel conformational states that contribute to the catalytic mechanism
Cited by: 3
Author(s): V. Mendes, M. Błaszczyk, Ana Maranha, Nuno Empadinhas, Tom L. Blundell
Software Mentions: 1
Published: almost 9 years ago
10.1107/S1399004714021099
Enzyme–adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface
Cited by: 14
Author(s): Adele Kim Williamson, U. Rothweiler, Hanna‐Kirsti S. Leiros
Software Mentions: 1
Published: about 10 years ago
10.3390/ijms21207787
High-Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase from Chlamydomonas reinhardtii—An Enzyme Involved in the Photosynthetic Calvin-Benson Cycle
Cited by: 3
Author(s): Théo Le Moigne, Pierre Crozet, Stéphane D. Lemaire, Julien Henri
Software Mentions: 1
Published: about 4 years ago
10.1038/srep19211
Peptides in headlock – a novel high-affinity and versatile peptide-binding nanobody for proteomics and microscopy
Cited by: 97
Author(s): Michael B. Braun, Bjoern Traenkle, Philipp Alexander Koch, Felix Emele Emele, F. T. Weiss, Oliver Poetz, Thilo Stehle, Ulrich Rothbauer
Software Mentions: 1
Published: almost 9 years ago
10.1038/srep19565
Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 μ homology domain
Cited by: 12
Author(s): Akira Shimada, Atsuko Yamaguchi, Daisuke Kohda
Software Mentions: 1
Published: almost 9 years ago
10.1107/S1399004715008548
Structure of protease-cleaved<i>Escherichia coli</i>α-2-macroglobulin reveals a putative mechanism of conformational activation for protease entrapment
Cited by: 11
Author(s): Cameron David Fyfe, Rhys Grinter, Inokentijs Josts, Khédidja Mosbahi, A.W. Roszak, Richard J. Cogdell, Daniel M. Wall, Richard Burchmore, Olwyn Byron, Daniel Walker
Software Mentions: 1
Published: over 9 years ago
10.1038/srep20161
Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain
Cited by: 15
Author(s): Eerappa Rajakumara, Naveen Kumar Nakarakanti, M. Angel Nivya, Mutyala Satish
Software Mentions: 1
Published: almost 9 years ago
10.1038/srep21581
Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation
Cited by: 65
Author(s): Chien Hao Chiang, Cédric Grauffel, Wu Li, Pan Hsien Kuo, L.G. Doudeva, Carmay Lim, Che Kun James Shen, Hanna S. Yuan
Software Mentions: 1
Published: almost 9 years ago
10.7554/eLife.56427
Chemical and structural investigation of the paroxetine-human serotonin transporter complex
Cited by: 46
Author(s): Jonathan A. Coleman, Vikas Navratna, Daniele Antermite, Dongxue Yang, James A. Bull, Eric Gouaux
Software Mentions: 1
Published: over 4 years ago
10.1038/srep22475
Characterization of heat induced spherulites of lysozyme reveals new insight on amyloid initiation
Cited by: 25
Author(s): Pankaj Sharma, Neha Verma, Pradip Kumar Singh, Suresh Korpole, . Ashish
Software Mentions: 1
Published: over 8 years ago
10.1038/srep23600
Crystal structure of the vicilin from Solanum melongena reveals existence of different anionic ligands in structurally similar pockets
Cited by: 18
Author(s): A. C. Jain, Ashish Kumar, Dinakar M. Salunke
Software Mentions: 1
Published: over 8 years ago
10.1038/srep23784
Human DNA polymerase α in binary complex with a DNA:DNA template-primer
Cited by: 33
Author(s): Javier Pardo de Santayana y Coloma, Robert E. Johnson, Louise Prakash, Satya Prakash, Aneel K. Aggarwal
Software Mentions: 1
Published: over 8 years ago
10.1107/S1399004714000091
Partial rotational lattice order–disorder in stefin B crystals
Cited by: 9
Author(s): M. Renko, Ajda Taler‐Verčič, Marko Mihelič, Eva Žerovnik, Dušan Turk
Software Mentions: 1
Published: over 10 years ago
10.1038/srep24979
Crystal structure and MD simulation of mouse EndoV reveal wedge motif plasticity in this inosine-specific endonuclease
Cited by: 9
Author(s): Meh Sameen Nawaz, Erik Sebastian Vik, Mia Elise Ronander, Anne Marthe Solvoll, Pernille Blicher, Magnar Bjørås, Ingrun Alseth, Bjørn Dalhus
Software Mentions: 1
Published: over 8 years ago
10.1038/srep24788
The structural basis of chicken, swine and bovine CD8αα dimers provides insight into the co-evolution with MHC I in endotherm species
Cited by: 9
Author(s): Yanjie Liu, Xin Li, Jianxun Qi, Nianzhi Zhang, Chun Xia
Software Mentions: 1
Published: over 8 years ago
10.1038/srep25961
X-Ray Structure and Inhibition of 3C-like Protease from Porcine Epidemic Diarrhea Virus
Cited by: 11
Author(s): Sarah E. St. John, Brandon Anson, Andrew D. Mesecar
Software Mentions: 1
Published: over 8 years ago
10.1128/AAC.02260-16
Cyclic Boronates Inhibit All Classes of β-Lactamases
Cited by: 89
Author(s): Samuel T. Cahill, Ricky Cain, David Y. Wang, Christopher T. Lohans, David W. Wareham, Henry Oswin, J Manna Mohammed, James Spencer, Colin W. G. Fishwick, M.A. McDonough, Christopher J. Schofield, Jürgen Brem
Software Mentions: 1
Published: over 7 years ago
10.1038/srep27498
Structural and biochemical characterization of the cell fate determining nucleotidyltransferase fold protein MAB21L1
Cited by: 33
Author(s): Carina C. de Oliveira Mann, R. Kiefersauer, Gregor Witte, Karl‐Peter Hopfner
Software Mentions: 1
Published: over 8 years ago
10.3390/antiox10030389
Structural Insights into a Bifunctional Peptide Methionine Sulfoxide Reductase MsrA/B Fusion Protein from Helicobacter pylori
Cited by: 3
Author(s): Sulhee Kim, Kitaik Lee, Sun Ha Park, Geun Hee Kwak, Min Seok Kim, Hwa Young Kim, Kwang Yeon Hwang
Software Mentions: 1
Published: over 3 years ago
10.3390/antiox7100142
Mitochondrial Arabidopsis thaliana TRXo Isoforms Bind an Iron–Sulfur Cluster and Reduce NFU Proteins In Vitro
Cited by: 21
Author(s): Flavien Zannini, Thomas Roret, Jonathan Przybyla-Toscano, Tiphaine Dhalleine, Nicolas Rouhier, Jérémy Couturier
Software Mentions: 1
Published: about 6 years ago
10.3390/antiox8100461
C-terminal Redox Domain of Arabidopsis APR1 is a Non-Canonical Thioredoxin Domain with Glutaredoxin Function
Cited by: 4
Author(s): Fang‐Fang Chen, Chia‐Yu Chien, Chao-Cheng Cho, Yi‐Chung Chang, Chun‐Hua Hsu
Software Mentions: 1
Published: about 5 years ago
10.1128/AAC.02073-20
Structural Investigations of the Inhibition of Escherichia coli AmpC β-Lactamase by Diazabicyclooctanes
Cited by: 8
Author(s): Pauline A. Lang, T.M. Leissing, Malcolm G. P. Page, Christopher J. Schofield, Jürgen Brem
Software Mentions: 1
Published: almost 4 years ago
10.7554/eLife.17063
Crystal structure of an HIV assembly and maturation switch
Cited by: 119
Author(s): Jonathan M. Wagner, Kaneil K. Zadrozny, Jakub Chrustowicz, Michael D. Purdy, Mark Yeager, Barbie K. Ganser‐Pornillos, Owen Pornillos
Software Mentions: 1
Published: over 8 years ago
10.1007/s00253-020-10960-x
Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods
Cited by: 19
Author(s): Sanni Voutilainen, Markus Heinonen, Martina Andberg, Emmi Jokinen, Hannu Maaheimo, J. Paakkonen, Nina Hakulinen, Juha Rouvinen, Harri Lähdesmäki, Samuel Kaski, Juho Rousu, Merja Penttilä, Anu Koivula
Software Mentions: 1
Published: about 4 years ago
10.7554/eLife.03275
Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks
Cited by: 73
Author(s): Suwen Zhao, A. Sakai, Xinshuai Zhang, M.W. Vetting, Ritesh Kumar, B. Hillerich, Brian San Francisco, José O. Solbiati, Adam Steves, Shoshana D. Brown, Eyal Akiva, Alan E. Barber, R.D. Seidel, Patricia C. Babbitt, Steven C. Almo, J.A. Gerlt, Matthew P. Jacobson
Software Mentions: 1
Published: over 10 years ago
10.1038/srep28664
New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit
Cited by: 17
Author(s): Priyanka Chaurasia, Shivendra Pratap, Ingemar von Ossowski, Airi Palva, Vengadesan Krishnan
Software Mentions: 1
Published: over 8 years ago
10.1080/15548627.2020.1822629
RAB33B recruits the ATG16L1 complex to the phagophore via a noncanonical RAB binding protein
Cited by: 16
Author(s): Supansa Pantoom, Georgios Konstantinidis, Stephanie Voß, Han Hong-mei, Oliver Hofnagel, Zhiyu Li, Yao‐Wen Wu
Software Mentions: 1
Published: about 4 years ago
10.1080/15548627.2016.1226736
Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex
Cited by: 50
Author(s): Yohei Ohashi, Nicolas Soler, Miguel García Ortegón, Lufei Zhang, Marie L. Kirsten, Olga Perišić, Glenn R. Masson, John E. Burke, Arjen J. Jakobi, Apostolos A. Apostolakis, Christopher M. Johnson, Maki Ohashi, Nicholas T. Ktistakis, Carsten Sachse, Roger L. Williams
Software Mentions: 1
Published: about 8 years ago
10.1186/s12858-017-0082-4
Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase LdtMt2 by biapenem and tebipenem
Cited by: 39
Author(s): M.A. Bianchet, Ying Pan, Leighanne A. Brammer Basta, Harry Saavedra, Evan P. Lloyd, Priyanka Kumar, Rohini Mattoo, Craig A. Townsend, Gyanu Lamichhane
Software Mentions: 1
Published: over 7 years ago
10.1107/S1399004714012917
Mapping the conformational space accessible to catechol-<i>O</i>-methyltransferase
Cited by: 30
Author(s): A. Ehler, Jörg Benz, Daniel Schlatter, M.G. Rudolph
Software Mentions: 1
Published: over 10 years ago
10.1038/srep29457
Dual thio-digalactoside-binding modes of human galectins as the structural basis for the design of potent and selective inhibitors
Cited by: 66
Author(s): T.J. Hsieh, Hsien Ya Lin, Zhijay Tu, Ting Chien Lin, Shang-Chuen Wu, Yu Yao Tseng, Fu‐Tong Liu, Shang-Te Danny Hsu, Chun Hung Lin
Software Mentions: 1
Published: over 8 years ago
10.3390/ijms21218186
Structural Insight on Functional Regulation of Human MINERVA Protein
Cited by: 1
Author(s): Hyunggu Hahn, Dong‐Eun Lee, Dong Man Jang, Jiyoun Kim, Yeon Lee, Heesun Cheong, Byung Woo Han, Hyoun Sook Kim
Software Mentions: 1
Published: about 4 years ago