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: almost 7 years ago
1 dependent package
161 downloads last month
Papers Mentioning PHENIX 2,287
10.1074/jbc.RA120.012444
Pterocarpan synthase (PTS) structures suggest a common quinone methide–stabilizing function in dirigent proteins and proteins with dirigent-like domainsCited by: 15
Author(s): Meng Qing, Syed G. A. Moinuddin, Sungjin Kim, Diana L. Bedgar, Michael A. Costa, Dennis Thomas, Robert P. Young, Clyde A. Smith, John Cort, Laurence B. Davin, Norman G. Lewis
Software Mentions: 1
Published: almost 4 years ago
10.1016/j.str.2014.11.020
Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular ReplacementCited by: 19
Author(s): G. Bunkóczi, Björn Wallner, Randy J. Read
Software Mentions: 1
Published: over 9 years ago
10.1084/jem.20191957
Metabolic bifunctionality of Rv0812 couples folate and peptidoglycan biosynthesis in <i>Mycobacterium tuberculosis</i>Cited by: 4
Author(s): Katherine A. Black, Lei Duan, Lungelo Mandyoli, Bruna Pelegrim Selbach, Weizhen Xu, Sabine Ehrt, James C. Sacchettini, Kyu Y. Rhee
Software Mentions: 1
Published: about 3 years ago
10.7554/eLife.01030
Bub3 reads phosphorylated MELT repeats to promote spindle assembly checkpoint signalingCited by: 196
Author(s): Ivana Primorac, John R. Weir, Elena Chiroli, Fridolin Groß, Ingrid Hoffmann, Suzan van Gerwen, Andrea Ciliberto, Andrea Musacchio
Software Mentions: 1
Published: over 10 years ago
10.1074/jbc.RA120.013998
Biochemical and biophysical analyses of hypoxia sensing prolyl hydroxylases from Dictyostelium discoideum and Toxoplasma gondiiCited by: 6
Author(s): Tongri Liu, Martine I. Abboud, Rasheduzzaman Chowdhury, Anthony Tumber, Adam P. Hardy, Kerstin Lippl, Christopher T. Lohans, Elisabete Pires, James Wickens, Michael A. McDonough, Christopher M. West, Christopher J. Schofield
Software Mentions: 1
Published: over 3 years ago
10.1016/j.chembiol.2014.03.009
Synthetic Inositol Phosphate Analogs Reveal that PPIP5K2 Has a Surface-Mounted Substrate Capture Site that Is a Target for Drug DiscoveryCited by: 45
Author(s): Huanchen Wang, H. Yasmin Godage, Andrew M. Riley, Jeremy D. Weaver, Stephen B. Shears, Barry V. L. Potter
Software Mentions: 1
Published: about 10 years ago
10.1186/s13045-021-01032-2
Recurrent XPO1 mutations alter pathogenesis of chronic lymphocytic leukemiaCited by: 25
Author(s): J. T. Walker, Zachary A. Hing, Bonnie K. Harrington, J.M. Baumhardt, Hatice Gülçin Özer, Amy Lehman, Brian Giacopelli, Larry Beaver, Katie Williams, Jordan Skinner, Casey B. Cempre, Qingxiang Sun, Sharon Shacham, Benjamin R. Stromberg, Matthew K. Summers, Lynne V. Abruzzo, Laura Z. Rassenti, Thomas J. Kipps, Sameer A. Parikh, Neil E. Kay, Kerry A. Rogers, Jennifer A. Woyach, Vincenzo Coppola, Yuh Min Chook, Christopher C. Oakes, John C. Byrd, Rosa Lapalombella
Software Mentions: 1
Published: over 3 years ago
10.1074/jbc.RA120.016106
In crystallo screening for proline analog inhibitors of the proline cycle enzyme PYCR1Cited by: 21
Author(s): Emily M. Christensen, Alexandra N Bogner, Anke Vandekeere, Gabriela S. Tam, Sagar M. Patel, Donald F. Becker, Sarah-Maria Fendt, John J. Tanner
Software Mentions: 1
Published: over 3 years ago
10.1074/jbc.RA120.016019
Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition, and intersubunit electron transferCited by: 14
Author(s): Mussa Quareshy, Muralidharan Shanmugam, Eleanor Townsend, Eleanor Jameson, Timothy D. H. Bugg, Alexander D. Cameron, Yin Chen
Software Mentions: 1
Published: over 3 years ago
10.1074/jbc.RA120.015853
The molecular basis of the nonprocessive elongation mechanism in levansucrasesCited by: 11
Author(s): Enrique Raga-Carbajal, A. Diaz-Vilchis, S.P. Rojas-Trejo, E. Rudiño-Piñera, Clarita Olvera
Software Mentions: 1
Published: over 3 years ago
10.1016/j.ijpddr.2016.02.001
The Ascaris suum nicotinic receptor, ACR-16, as a drug target: Four novel negative allosteric modulators from virtual screeningCited by: 15
Author(s): Fudan Zheng, Alan P. Robertson, Melanie Abongwa, Edward Yu, R. J. Martin
Software Mentions: 1
Published: about 8 years ago
10.1016/j.jbc.2021.100263
Mammalian-like type II glutaminyl cyclases in Porphyromonas gingivalis and other oral pathogenic bacteria as targets for treatment of periodontitisCited by: 9
Author(s): Nadine Taudte, Miriam Linnert, Jens‐Ulrich Rahfeld, Anke Piechotta, Daniel Ramsbeck, Mirko Buchholz, Petr Kolenko, C. Parthier, John A. Houston, Florian Veillard, Sigrun Eick, Jan Potempa, Stephan Schilling, Hans‐Ulrich Demuth, Milton T. Stubbs
Software Mentions: 1
Published: over 3 years ago
10.4049/jimmunol.1303142
Mutational and Structural Analysis of KIR3DL1 Reveals a Lineage-Defining Allotypic Dimorphism That Impacts Both HLA and Peptide SensitivityCited by: 46
Author(s): Geraldine M. O’Connor, J.P. Vivian, Jacqueline M.L. Widjaja, John S. Bridgeman, Emma Gostick, Bernard A. P. Lafont, Stephen Anderson, David A. Price, Andrëw G. Brööks, Jamie Rossjohn, Daniel W. McVicar
Software Mentions: 1
Published: about 10 years ago
10.1074/jbc.RA120.015735
Affinity maturation of the RLIP76 Ral binding domain to inform the design of stapled peptides targeting the Ral GTPasesCited by: 5
Author(s): Catherine Hurd, P. Brear, Jefferson D. Revell, Sarah J. Ross, Helen R. Mott, Darerca Owen
Software Mentions: 1
Published: over 3 years ago
10.1074/jbc.RA120.016461
Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl–enzyme conformational dynamics to extend antibiotic resistanceCited by: 20
Author(s): C.L. Tooke, P. Hinchliffe, Robert A. Bonomo, Christopher J. Schofield, Adrian J. Mulholland, James Spencer
Software Mentions: 1
Published: over 3 years ago
10.1016/j.chembiol.2015.10.015
Unraveling the B. pseudomallei Heptokinase WcbL: From Structure to Drug DiscoveryCited by: 7
Author(s): Mirella Vivoli, Michail N. Isupov, Rebecca Nicholas, Andrew M. Hill, Andrew E. Scott, Paul Kosma, Joann L. Prior, Nicholas J. Harmer
Software Mentions: 1
Published: over 8 years ago
10.1016/j.jbc.2021.100262
Conserved binding site in the N-lobe of prokaryotic MATE transporters suggests a role for Na+ in ion-coupled drug effluxCited by: 5
Author(s): Steven Castellano, Derek Claxton, Emel Ficici, Tsukasa Kusakizako, Robyn Stix, Wenchang Zhou, Osamu Nureki, Hassane S. Mchaourab, José D. Faráldo-Gómez
Software Mentions: 1
Published: over 3 years ago
10.1016/j.jbc.2021.100368
Structural analysis of carbohydrate binding by the macrophage mannose receptor CD206Cited by: 44
Author(s): H. Feinberg, Sabine A. F. Jégouzo, Yi Lasanajak, David F. Smith, Kurt Drickamer, William I. Weis, Maureen E. Taylor
Software Mentions: 1
Published: over 3 years ago
10.1016/j.jbc.2021.100351
NAD(H) phosphates mediate tetramer assembly of human C-terminal binding protein (CtBP)Cited by: 4
Author(s): Jeffry C. Nichols, Celia A. Schiffer, William E. Royer
Software Mentions: 1
Published: over 3 years ago
10.1016/j.jinorgbio.2016.07.013
Use of ferrous iron by metallo-β-lactamasesCited by: 20
Author(s): Samuel T. Cahill, Hanna Tarhonskaya, Anna M. Rydzik, Emily Flashman, M.A. McDonough, Christopher J. Schofield, Jürgen Brem
Software Mentions: 1
Published: over 7 years ago
10.1016/j.jbc.2021.100474
A conserved arginine residue is critical for stabilizing the N2 FeS cluster in mitochondrial complex ICited by: 7
Author(s): Mikhail A. Hameedi, Daniel N. Grba, Katherine H. Richardson, Andrew J. Y. Jones, Wei Song, Maxie M. Roessler, John J. Wright, Judy Hirst
Software Mentions: 1
Published: over 3 years ago
10.1016/j.jinorgbio.2018.08.002
Structural and catalytic properties of the peroxygenase P450 enzyme CYP152K6 from Bacillus methanolicusCited by: 14
Author(s): Hazel M. Girvan, Harshwardhan Poddar, Kirsty J. McLean, David R. Nelson, Katherine A. Hollywood, Colin Levy, D. Leys, Andrew W. Munro
Software Mentions: 1
Published: over 5 years ago
10.1016/j.jlr.2021.100054
Molecular basis for the interaction of cellular retinol binding protein 2 (CRBP2) with nonretinoid ligandsCited by: 6
Author(s): J.A. Silvaroli, Jacqueline Plau, Charlie H. Adams, Surajit Banerjee, Made Airanthi K. Widjaja‐Adhi, William S. Blaner, Marcin Golczak
Software Mentions: 1
Published: over 3 years ago
10.1016/j.jbc.2021.100692
Structural and biochemical analysis of human ADP-ribosyl-acceptor hydrolase 3 reveals the basis of metal selectivity and different roles for the two magnesium ionsCited by: 1
Author(s): Yasin Pourfarjam, Zhijun Ma, Igor Kurinov, Joel Moss, In‐Kwon Kim
Software Mentions: 1
Published: over 3 years ago
10.1016/j.jbc.2021.100685
Molecular basis for Ras suppressor-1 binding to PINCH-1 in focal adhesion assemblyCited by: 4
Author(s): Koichi Fukuda, Fan Lü, Jun Qin
Software Mentions: 1
Published: over 3 years ago
10.1021/acs.jmedchem.0c00373
Shedding X-ray Light on the Role of Magnesium in the Activity of <i>Mycobacterium tuberculosis</i> Salicylate Synthase (MbtI) for Drug DesignCited by: 18
Author(s): Matteo Mori, Giovanni Stelitano, Arianna Gelain, Elena Pini, Laurent R. Chiarelli, Josè Camilla Sammartino, Giulio Poli, Tiziano Tuccinardi, Giangiacomo Beretta, Alessio Porta, M. Bellinzoni, Stefania Villa, Fiorella Meneghetti
Software Mentions: 1
Published: almost 4 years ago
10.1038/s42003-021-02122-0
Mechanosensitive channel YnaI has lipid-bound extended sensor paddlesCited by: 5
Author(s): Wenxin Hu, Zhiming Wang, Hongjin Zheng
Software Mentions: 1
Published: about 3 years ago
10.1016/j.jbc.2021.100698
Lectins engineered to favor a glycan-binding conformation have enhanced antiviral activityCited by: 5
Author(s): Yasuyuki Matoba, Yoji Sato, Kosuke Oda, Yoshinori Hatori, Kanehisa Morimoto
Software Mentions: 1
Published: over 3 years ago
10.1016/j.jbc.2021.100777
Reduced virulence of the MARTX toxin increases the persistence of outbreak-associated Vibrio vulnificus in host reservoirsCited by: 1
Author(s): Sunghee Choi, Byoung Sik Kim, Jun Hyun Hwang, Myung Hee Kim
Software Mentions: 1
Published: over 3 years ago
10.1038/s42003-019-0365-y
Arsinothricin, an arsenic-containing non-proteinogenic amino acid analog of glutamate, is a broad-spectrum antibioticCited by: 28
Author(s): Venkadesh Sarkarai Nadar, Jian Chen, Dharmendra S. Dheeman, Adriana E Galván, Kunie Yoshinaga-Sakurai, P. Kandavelu, Banumathi Sankaran, Masato Kuramata, Shinya Ishikawa, Barry P. Rosen, Masafumi Yoshinaga
Software Mentions: 1
Published: about 5 years ago
10.7554/eLife.11297
Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alphaCited by: 34
Author(s): Janine Weber, Han Bao, Christoph Hartlmüller, Zhiqin Wang, Almut Windhager, Robert Janowski, Tobias Madl, Peng Jin, Dierk Niessing
Software Mentions: 1
Published: over 8 years ago
10.1038/s41422-018-0131-6
Structural insights into a high fidelity variant of SpCas9Cited by: 36
Author(s): Muchun Guo, Kewei Ren, Yuwei Zhu, Zhonglin Tang, Yuhang Wang, Bailing Zhang, Zhiwei Huang
Software Mentions: 1
Published: over 5 years ago
10.1038/s42003-020-01286-5
Caffeine inhibits Notum activity by binding at the catalytic pocketCited by: 10
Author(s): Yuguang Zhao, Jingshan Ren, James Hillier, Wenjing Lu, E.Y. Jones
Software Mentions: 1
Published: over 3 years ago
10.7554/eLife.35828
Functional and structural characterization of an ECF-type ABC transporter for vitamin B12Cited by: 33
Author(s): Joana A Santos, S. Rempel, S. Mous, Cristiane Tambascia Pereira, Josy ter Beek, Jan‐Willem de Gier, Albert Guskov, Dirk Jan Slotboom
Software Mentions: 1
Published: almost 6 years ago
10.1016/j.jbc.2021.100975
Interactions between AMOT PPxY motifs and NEDD4L WW domains function in HIV-1 releaseCited by: 7
Author(s): Lara Rheinemann, Tuscan Thompson, Gaëlle Mercenne, Elliott L. Paine, Francis C. Peterson, Brian F. Volkman, Steven L. Alam, Akram Alian, Wesley I. Sundquist
Software Mentions: 1
Published: almost 3 years ago
10.1016/j.jmb.2010.11.039
Structural Basis for Langerin Recognition of Diverse Pathogen and Mammalian Glycans through a Single Binding SiteCited by: 101
Author(s): H. Feinberg, Maureen E. Taylor, Nahid Razi, Ryan McBride, Yuriy A. Knirel, Sarah A. Graham, Kurt Drickamer, William I. Weis
Software Mentions: 1
Published: over 13 years ago
10.1038/s42003-021-01815-w
Entropy-driven binding of gut bacterial β-glucuronidase inhibitors ameliorates irinotecan-induced toxicityCited by: 13
Author(s): Hong-Shiang Lin, Chia-Yu Chen, Ting-Chien Lin, Lun-Fu Yeh, Wei‐Che Hsieh, Shijay Gao, Pierre-Alain Burnouf, Bing‐Mae Chen, T.J. Hsieh, P. Dashnyam, Yen-Hsi Kuo, Zhijay Tu, Steve R. Roffler, Chun‐Hung Lin
Software Mentions: 1
Published: about 3 years ago
10.7554/eLife.59991
Structures reveal gatekeeping of the mitochondrial Ca2+ uniporter by MICU1-MICU2Cited by: 40
Author(s): Chongyuan Wang, Agata Jacewicz, Bryce D Delgado, Rozbeh Baradaran, Stephen B. Long
Software Mentions: 1
Published: almost 4 years ago
10.1016/j.jbc.2021.101046
Actinobacillus utilizes a binding protein–dependent ABC transporter to acquire the active form of vitamin B6Cited by: 5
Author(s): Chuxi Pan, A. Zimmer, Megha Shah, Minh Sang Huynh, Christine Chieh-Lin Lai, Brandon Sit, Yogesh Hooda, David M. Curran, Trevor F. Moraes
Software Mentions: 1
Published: over 2 years ago
10.1016/j.jbc.2021.101143
Structure and substrate specificity determinants of NfnB, a dinitroaniline herbicide–catabolizing nitroreductase from Sphingopyxis sp. strain HMHCited by: 6
Author(s): Sang-Hoon Kim, Sangyun Park, Eun‐Young Park, Jeong‐Han Kim, Sunil Ghatge, Hor‐Gil Hur, Sangkee Rhee
Software Mentions: 1
Published: over 2 years ago
10.1038/s42003-020-0951-z
Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeationCited by: 33
Author(s): Ryoki Nakamura, Tomohiro Numata, Go Kasuya, Takeshi Yokoyama, Takashi Nishizawa, Tsukasa Kusakizako, Tosio Kato, Tatsuya Hagino, Naoshi Dohmae, Miyako Inoue, K. Watanabe, Hidenori Ichijo, Masahide Kikkawa, Mikako Shirouzu, Thomas J. Jentsch, Ryuichiro Ishitani, Yasunobu Okada, Osamu Nureki
Software Mentions: 1
Published: about 4 years ago
10.1002/cmdc.201500014
Selective Targeting of the TPX2 Site of Importin-α Using Fragment-Based Ligand DesignCited by: 11
Author(s): Rhian S. Holvey, Eugene Valkov, David Neal, Murray Stewart, Chris Abell
Software Mentions: 1
Published: about 9 years ago
10.7554/eLife.70427
Cryo-EM reveals new species-specific proteins and symmetry elements in the Legionella pneumophila Dot/Icm T4SSCited by: 17
Author(s): M.J. Sheedlo, C.L. Durie, Jeong Min Chung, Louise Chang, Jacquelyn Roberts, Michele S. Swanson, D. Borden Lacy, Melanie D. Ohi
Software Mentions: 1
Published: over 2 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 laserCited by: 6
Author(s): Jienv Ding, Monalisa Swain, Ping Yü, Jason R. Stagno, Yun‐Xing Wang
Software Mentions: 1
Published: over 4 years ago
10.1083/jcb.201709092
A Numb–Mdm2 fuzzy complex reveals an isoform-specific involvement of Numb in breast cancerCited 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: over 6 years ago
10.7554/eLife.30189
Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiaeCited by: 78
Author(s): André Heuer, Emma Thomson, Christian M. Schmidt, Otto Berninghausen, Thomas Becker, Ed Hurt, Roland Beckmann
Software Mentions: 1
Published: over 6 years ago
10.1038/s42003-019-0642-9
Identification of a monoclonal antibody that targets PD-1 in a manner requiring PD-1 Asn58 glycosylationCited by: 33
Author(s): Mingzhu Wang, Junchao Wang, Rongjuan Wang, Shasha Jiao, Shuang Wang, Jinchao Zhang, Min Zhang
Software Mentions: 1
Published: over 4 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: about 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 designCited by: 15
Author(s): O.Y. Borbulevych, Roger I. Martin, Lance M. Westerhoff
Software Mentions: 1
Published: over 3 years ago
10.1155/2016/6179635
Sulfatide Preserves Insulin Crystals Not by Being Integrated in the Lattice but by Stabilizing Their SurfaceCited 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: over 8 years ago
10.1016/j.jmb.2011.01.029
Structure of Rhomboid Protease in a Lipid EnvironmentCited by: 81
Author(s): Kutti R. Vinothkumar
Software Mentions: 1
Published: about 13 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 inhibitorCited 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: over 3 years ago
10.1038/s42003-020-01211-w
Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptorCited by: 17
Author(s): Linda J. Olson, Sandeep K. Misra, Mayumi Ishihara, Kevin P. Battaile, Oliver C. Grant, Amika Sood, Robert J. Woods, Jung‐Ja P. Kim, Michael Tiemeyer, Gang Ren, Joshua S. Sharp, Nancy M. Dahms
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.ppat.1000186
Prevention of Cytotoxic T Cell Escape Using a Heteroclitic Subdominant Viral T Cell DeterminantCited 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: over 15 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/p75Cited by: 141
Author(s): S. Hare, Ming-Chieh Shun, Saikat Das Gupta, Eugene Valkov, Alan Engelman, Peter Cherepanov
Software Mentions: 1
Published: over 15 years ago
10.1080/19336950.2018.1457898
X-ray crystallography of TRP channelsCited by: 5
Author(s): Appu Kumar Singh, L.L. McGoldrick, Kei Saotome, Alexander I. Sobolevsky
Software Mentions: 1
Published: over 6 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 HostCited 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: over 14 years ago
10.7554/eLife.14158
Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replicationCited by: 14
Author(s): Iris V. Hood, James M. Berger
Software Mentions: 1
Published: almost 8 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 ProteinCited 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: about 13 years ago
10.1371/journal.ppat.1002034
Structural Insights into Viral Determinants of Nematode Mediated Grapevine fanleaf virus TransmissionCited 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: about 13 years ago
10.1016/j.jmb.2017.08.010
Structures of Leishmania Fructose-1,6-Bisphosphatase Reveal Species-Specific Differences in the Mechanism of Allosteric InhibitionCited by: 9
Author(s): Meng Yuan, Montserrat G. Vásquez-Valdivieso, I.W. McNae, Paul A.M. Michels, Linda A. Fothergill‐Gilmore, Malcolm D. Walkinshaw
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.ppat.1002162
Structural Basis of Chemokine Sequestration by CrmD, a Poxvirus-Encoded Tumor Necrosis Factor ReceptorCited 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: almost 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 ComplexCited 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: over 12 years ago
10.1371/journal.ppat.1002249
Structural and Functional Analysis of Laninamivir and its Octanoate Prodrug Reveals Group Specific Mechanisms for Influenza NA InhibitionCited 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: over 12 years ago
10.1371/journal.ppat.1002524
Specialized Peptidoglycan Hydrolases Sculpt the Intra-bacterial Niche of Predatory Bdellovibrio and Increase Population FitnessCited 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: over 12 years ago
10.1371/journal.ppat.1002531
Structural and Functional Insights into the Pilotin-Secretin Complex of the Type II Secretion SystemCited by: 44
Author(s): Shuang Gu, Saima Rehman, Xiaohui Wang, Vladimir E. Shevchik, Richard W. Pickersgill
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.ppat.1002550
The Ebola Virus Interferon Antagonist VP24 Directly Binds STAT1 and Has a Novel, Pyramidal FoldCited 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: about 12 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 StateCited 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: about 12 years ago
10.1371/journal.ppat.1002559
Differential Function of Lip Residues in the Mechanism and Biology of an Anthrax HemophoreCited 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: about 12 years ago
10.1016/j.tcsw.2018.06.002
The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerizationCited by: 6
Author(s): Avinash S. Punekar, Firdaus Samsudin, Adrian J. Lloyd, Christopher G. Dowson, David J. Scott, Syma Khalid, David I. Roper
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.ppat.1002633
Loss of Anti-Viral Immunity by Infection with a Virus Encoding a Cross-Reactive Pathogenic EpitopeCited 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: about 12 years ago
10.7554/eLife.58675
Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19Cited by: 15
Author(s): Dong Cheng, Reiko Nakagawa, Kyohei Oyama, Yusuke Yamamoto, Weilian Zhang, Aiping Dong, Yanjun Li, Yuriko Yoshimura, Hiroyuki Kamiya, Jun‐ichi Nakayama, Junji Ueda, Jinrong Min
Software Mentions: 1
Published: over 3 years ago
10.1016/j.jmb.2007.09.055
Predicting Protein Function from Structure—The Roles of Short-chain Dehydrogenase/Reductase Enzymes in Bordetella O-antigen BiosynthesisCited by: 19
Author(s): Jerry D. King, Nicholas J. Harmer, Andrew Preston, Colin M. Palmer, Martin Rejzek, Robert A. Field, Tom L. Blundell, Duncan J. Maskell
Software Mentions: 1
Published: over 16 years ago
10.1371/journal.ppat.1002876
A Unique Bivalent Binding and Inhibition Mechanism by the Yatapoxvirus Interleukin 18 Binding ProteinCited by: 25
Author(s): Brian E. Krumm, Xiangzhi Meng, Zhixin Wang, Yan Xiang, Junpeng Deng
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.ppat.1002958
Molecular Basis for Genetic Resistance of Anopheles gambiae to Plasmodium: Structural Analysis of TEP1 Susceptible and Resistant AllelesCited by: 36
Author(s): Binh M. Le, Marni Williams, Shankar Logarajah, Richard H. G. Baxter
Software Mentions: 1
Published: over 11 years ago
10.7554/eLife.26111
A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteasesCited by: 23
Author(s): Niels Bradshaw, V.M. Levdikov, Christina M. Zimanyi, Rachelle Gaudet, Anthony J. Wilkinson, Richard Losick
Software Mentions: 1
Published: about 7 years ago
10.1038/s42003-019-0482-7
Crystal structure of human endothelin ETB receptor in complex with peptide inverse agonist IRL2500Cited by: 27
Author(s): Chisae Nagiri, Wataru Shihoya, Asuka Inoue, Francois Marie Ngako Kadji, Junken Aoki, Osamu Nureki
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.ppat.1003121
A Pathogen Type III Effector with a Novel E3 Ubiquitin Ligase ArchitectureCited 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: over 11 years ago
10.1016/j.jmb.2017.08.007
Studies on the Interaction of the Histone Demethylase KDM5B with Tricarboxylic Acid Cycle IntermediatesCited by: 26
Author(s): Hanna Tarhonskaya, Radosław P. Nowak, C. Johansson, A. Szykowska, Anthony Tumber, Rebecca L. Hancock, Pauline A. Lang, Emily Flashman, U. Oppermann, Christopher J. Schofield, Akane Kawamura
Software Mentions: 1
Published: over 6 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 AssemblyCited 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: about 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 GlycansCited 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: about 11 years ago
10.1016/j.jmb.2008.09.085
Repetitive Architecture of the Haemophilus influenzae Hia Trimeric AutotransporterCited by: 52
Author(s): Guoyu Meng, Joseph W. St. Geme, Gabriel Waksman
Software Mentions: 1
Published: over 15 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 SpecificityCited by: 27
Author(s): K. McCarthy, Aaron Schmidt, Andrea Kirmaier, Allison L. Wyand, Ruchi M. Newman, Welkin E. Johnson
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.ppat.1003390
Structural and Functional Basis for Inhibition of Erythrocyte Invasion by Antibodies that Target Plasmodium falciparum EBA-175Cited by: 54
Author(s): Edwin Chen, May M. Paing, Nichole D. Salinas, B. Kim Lee Sim, Niraj H. Tolia
Software Mentions: 1
Published: almost 11 years ago
10.7554/eLife.06935
A high affinity RIM-binding protein/Aplip1 interaction prevents the formation of ectopic axonal active zonesCited by: 27
Author(s): Matthias Siebert, Mathias A. Böhme, J.H. Driller, Husam Babikir, Malou M. Mampell, Ulises Rey, Niraja Ramesh, Tanja Matkovic, Nicole Holton, Suneel Reddy-Alla, Fabian Göttfert, Dirk Kamin, Christine Quentin, Susan Klinedinst, Till F. M. Andlauer, Stefan W. Hell, Catherine A. Collins, Markus C. Wahl, Bernhard Loll, Stephan J. Sigrist
Software Mentions: 1
Published: almost 9 years ago
10.7554/eLife.49375
E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformationCited by: 48
Author(s): James Chen, Saumya Gopalkrishnan, Courtney Chiu, Albert Y. Chen, Elizabeth A. Campbell, Richard L. Gourse, Wilma Ross, Seth A. Darst
Software Mentions: 1
Published: over 4 years ago