The Phyre2 web portal for protein modeling, prediction and analysis

Kelley, Lawrence A, Mezulis, Stefans, Yates, Christopher M, Wass, Mark N, Sternberg, Michael J E·2015·Nature Protocols

DOI 10.1038/nprot.2015.053

Cited by (1,025)

Items 201–300 of 1,025

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Structure of the processive human Pol δ holoenzyme
Claudia Lancey, Muhammad Tehseen, Vlad‐Stefan Raducanu, Fahad Rashid, Nekane Merino, Timothy J. Ragan, Christos G. Savva, Manal S. Zaher, Afnan Shirbini, Francisco J. Blanco et al. · 2020 · Nature Communications
Ubiquitin-dependent chloroplast-associated protein degradation in plants
Qihua Ling, William J. Broad, Raphael Trösch, Mats Töpel, Tijen Demiral, Panagiotis Lymperopoulos, Amy J. Baldwin, Paul Jarvis · 2019 · Science
Cryo-EM structures of herpes simplex virus type 1 portal vertex and packaged genome
Yun-Tao Liu, Jonathan Jih, Xinghong Dai, Guo‐Qiang Bi, Z. Hong Zhou · 2019 · Nature
The Proline Cycle As a Potential Cancer Therapy Target
John J. Tanner, Sarah‐Maria Fendt, Donald Becker · 2018 · Biochemistry
Lipid Droplet-Derived Monounsaturated Fatty Acids Traffic via PLIN5 to Allosterically Activate SIRT1
Charles P. Najt, Salmaan Ahmed Khan, Timothy D. Heden, Bruce A. Witthuhn, Minervo Perez, Jason L. Heier, Linnea E. Mead, Mallory P. Franklin, Kenneth K. Karanja, Mark J. Graham et al. · 2019 · Molecular Cell
LSD1 activation promotes inducible EMT programs and modulates the tumour microenvironment in breast cancer
Tara Boulding, Robert McCuaig, A. Tan, Kristine Hardy, Fan Wu, J. Dunn, Murugan Kalimutho, Christopher R. Sutton, Jade Kenneth Forwood, Andrew G. Bert et al. · 2018 · Scientific Reports
SPOCD1 is an essential executor of piRNA-directed de novo DNA methylation
A. Zoch, T. Auchynnikava, Rebecca V Berrens, Y. Kabayama, Theresa Schöpp, M. Heep, L. Vasiliauskaitė, Yuvia A. Pérez-Rico, A. Cook, A. Shkumatava et al. · 2020 · Nature
Engineered toxin–intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations
Rocío López‐Igual, Joaquín Bernal-Bayard, Alfonso Rodríguez‐Patón, Jean‐Marc Ghigo, Didier Mazel · 2019 · Nature Biotechnology
A global analysis of function and conservation of catalytic residues in enzymes
António J. M. Ribeiro, Jonathan D. Tyzack, Neera Borkakoti, Gemma L. Holliday, Janet M. Thornton · 2019 · Journal of Biological Chemistry
The complete structure of the chloroplast 70S ribosome in complex with translation factor pY
P. Bieri, Marc Leibundgut, Martin Saurer, Daniel Boehringer, Nenad Ban · 2016 · The EMBO Journal
SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome
Natalie D. Shaw, Harrison Brand, Zachary A Kupchinsky, Hemant Bengani, Lacey Plummer, Takako Iida Jones, Serkan Erdin, Kathleen A. Williamson, Joe Rainger, Alexei Stortchevoi et al. · 2017 · Nature Genetics
Architecture of eukaryotic mRNA 3′-end processing machinery
Ana Casañal, Ananthanarayanan Kumar, Chris H. Hill, Ashley Easter, Paul Emsley, Gianluca Degliesposti, Yuliya Gordiyenko, Balaji Santhanam, Jana Wolf, Katrin Wiederhold et al. · 2017 · Science
Arabidopsis WRKY50 and TGA Transcription Factors Synergistically Activate Expression of PR1
Rana M. F. Hussain, Arsheed Hussain Sheikh, Imran Haider, Mussa Quareshy, Huub J. M. Linthorst · 2018 · Frontiers in Plant Science
TMEM41B acts as an ER scramblase required for lipoprotein biogenesis and lipid homeostasis
Dong Huang, Bolin Xu, Lu Liu, Lingzhi Wu, Yuangang Zhu, Alireza Ghanbarpour, Yawei Wang, Feng‐Jung Chen, Jia Lyu, Yating Hu et al. · 2021 · Cell Metabolism
Molecular basis for the recognition of the human AAUAAA polyadenylation signal
Yadong Sun, Yixiao Zhang, Keith Hamilton, James L. Manley, Yongsheng Shi, Thomas Walz, Liang Tong · 2017 · Proceedings of the National Academy of Sciences
Structure of the complex I-like molecule NDH of oxygenic photosynthesis
Thomas G. Laughlin, Andrew N. Bayne, Jean‐François Trempe, David F. Savage, Karen M. Davies · 2019 · Nature
Cryo-EM structure of the exocyst complex
Mei, Kunrong, Li, Yan, Wang, Shaoxiao, Shao, Guangcan, Wang, Jia, Ding, Yuehe, Luo, Guangzuo, Yue, Peng, Liu, Jun-Jie, Wang, Xinquan et al. · 2018 · Nature Structural & Molecular Biology
The tethered peptide activation mechanism of adhesion GPCRs
Ximena Barros-Álvarez, Robert M. Nwokonko, Alexander Vizurraga, Donna Matzov, Feng He, Makaía M. Papasergi-Scott, Michael J. Robertson, Ouliana Panova, Eliane Hadas Yardeni, Alpay Burak Seven et al. · 2022 · Nature
Phyre2.2: A Community Resource for Template-based Protein Structure Prediction
Harold R. Powell, Suhail A. Islam, Alessia David, Michael J.E. Sternberg · 2025 · Journal of Molecular Biology
Genetic and Structural Analyses of RRNPP Intercellular Peptide Signaling of Gram-Positive Bacteria
Matthew B. Neiditch, Glenn C. Capodagli, Gerd Prehna, Michael J. Federle · 2017 · Annual Review of Genetics
INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers
Sandipan Brahma, Maheshi Udugama, Jongseong Kim, Arjan Hada, Saurabh K. Bhardwaj, Solomon G. Hailu, Tae-Hee Lee, Blaine Bartholomew · 2017 · Nature Communications
Structure of a green algal photosystem I in complex with a large number of light-harvesting complex I subunits
Xiaochun Qin, Xiong Pi, Wenda Wang, Guangye Han, Lixia Zhu, Mingmei Liu, Linpeng Cheng, Jian‐Ren Shen, Tingyun Kuang, Sen‐Fang Sui · 2019 · Nature Plants
Metals and Methanotrophy
Jeremy D. Semrau, Alan A. DiSpirito, Wenyu Gu, Sukhwan Yoon · 2018 · Applied and Environmental Microbiology
Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements
Rafael Pinilla‐Redondo, Saadlee Shehreen, Nicole D. Marino, Robert D. Fagerlund, Chris M. Brown, Søren Johannes Sørensen, Peter C. Fineran, Joseph Bondy‐Denomy · 2020 · Nature Communications
Two nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming
Seongbeom Kim, Chi-Yeol Kim, Sook-Young Park, Ki‐Tae Kim, Jongbum Jeon, Hyunjung Chung, Gobong Choi, Seomun Kwon, Jaeyoung Choi, Junhyun Jeon et al. · 2020 · Nature Communications
GNA14 Somatic Mutation Causes Congenital and Sporadic Vascular Tumors by MAPK Activation
Young Hee Lim, Antonella Bacchiocchi, Jingyao Qiu, Robert Straub, Anna L. Bruckner, Lionel G Bercovitch, Deepak Narayan, Jennifer Madison McNiff, Christine J. Ko, Leslie Robinson‐Bostom et al. · 2016 · The American Journal of Human Genetics
Pathogenesis related protein-1 (PR-1) genes in tomato (Solanum lycopersicum L.): Bioinformatics analyses and expression profiles in response to drought stress
M. Aydın Akbudak, Sukran Yildiz, Ertuğrul Filiz · 2020 · Genomics
Glacier ice archives nearly 15,000-year-old microbes and phages
Zhi-Ping Zhong, Funing Tian, Simon Roux, María Consuelo Gazitúa, Natalie Solonenko, Yueh-Fen Li, M. E. Davis, James L. Van Etten, Ellen Mosley‐Thompson, Virginia I. Rich et al. · 2021 · Microbiome
Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae
Milena Jaskólska, David William Adams, Melanie Blokesch · 2022 · Nature
Augmentor α and β (FAM150) are ligands of the receptor tyrosine kinases ALK and LTK: Hierarchy and specificity of ligand–receptor interactions
Andrey V. Reshetnyak, Phillip B. Murray, Xiarong Shi, Elizabeth S. Mo, Jyotidarsini Mohanty, Francisco Tomé, Hanwen Bai, Murat Günel, Irit Lax, Joseph Schlessinger · 2015 · Proceedings of the National Academy of Sciences
Modeling the Architecture of Depolymerase-Containing Receptor Binding Proteins in Klebsiella Phages
Agnieszka Łątka, P.G. Leiman, Zuzanna Drulis‐Kawa, Yves Briers · 2019 · Frontiers in Microbiology
Designing a multi-epitope peptide based vaccine against SARS-CoV-2
Abhishek Singh, Mukesh Kumar Thakur, Lalit Kumar Sharma, Kailash Chandra · 2020 · Scientific Reports
X-linked primary ciliary dyskinesia due to mutations in the cytoplasmic axonemal dynein assembly factor PIH1D3
Chiara Olcese, Mitali Patel, Amelia Shoemark, Santeri Kiviluoto, Marie Legendre, Hywel J. Williams, Cara K. Vaughan, Jane D. Hayward, Alice Goldenberg, Richard David Emes et al. · 2017 · Nature Communications
Modular assembly of the nucleolar pre-60S ribosomal subunit
Zahra Assur Sanghai, Linamarie Miller, Kelly R. Molloy, Jonas Barandun, Mirjam Hunziker, Malik Chaker-Margot, Junjie Wang, Brian T. Chait, Sebastian Klinge · 2018 · Nature
Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2
Tânia F. Custódio, Hrishikesh Das, Daniel J. Sheward, Leo Hanke, Samuel Pažický, Joanna Pieprzyk, Michèle Sorgenfrei, Martin A. Schroer, Andrey Yu. Gruzinov, Cy Michael Jeffries et al. · 2020 · Nature Communications
Molecular docking in organic, inorganic, and hybrid systems: a tutorial review
Madhuchhanda Mohanty, Priti S. Mohanty · 2023 · Monatshefte für Chemie - Chemical Monthly
Effect of linker length and residues on the structure and stability of a fusion protein with malaria vaccine application
Shabnam Shamriz, Hamideh Ofoghi, Nasrin Moazami · 2016 · Computers in Biology and Medicine
The Electron Bifurcating FixABCX Protein Complex from Azotobacter vinelandii: Generation of Low-Potential Reducing Equivalents for Nitrogenase Catalysis
Rhesa N. Ledbetter, Amaya M. Garcia Costas, Carolyn E. Lubner, David W. Mulder, Monika Tokmina‐Lukaszewska, Jacob H. Artz, Angela Patterson, Timothy S. Magnuson, Zackary J. Jay, H. Diessel Duan et al. · 2017 · Biochemistry
Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex
Arnaud Vanden Broeck, Christophe Lotz, Julio O. Ortiz, Valérie Lamour · 2019 · Nature Communications
The Pseudomonas aeruginosa T6SS-VgrG1b spike is topped by a PAAR protein eliciting DNA damage to bacterial competitors
Panayiota Pissaridou, Luke P. Allsopp, Sarah Wettstadt, Sophie A. Howard, Despoina A. I. Mavridou, Alain Filloux · 2018 · Proceedings of the National Academy of Sciences
Genomic basis of European ash tree resistance to ash dieback fungus
Jonathan Stocks, Carey L. Metheringham, William J. Plumb, Steve J. Lee, Laura J. Kelly, Richard A. Nichols, Richard J. A. Buggs · 2019 · Nature Ecology & Evolution
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters
María Consuelo Gazitúa, Dean R. Vik, Simon Roux, Ann Gregory, Benjamin Bolduc, Brittany Widner, Margaret R. Mulholland, Steven Hallam, Osvaldo Ulloa, Matthew B. Sullivan · 2020 · The ISME Journal
Surface chemistry-mediated modulation of adsorbed albumin folding state specifies nanocarrier clearance by distinct macrophage subsets
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A type VI secretion system effector delivery mechanism dependent on PAAR and a chaperone–co-chaperone complex
Brianne J. Burkinshaw, Xiaoye Liang, Megan J. Q. Wong, Alexander N. H. Le, Linh Lam, Tao Dong · 2018 · Nature Microbiology
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Genome-Wide Variation in Potyviruses
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M. Shaminur Rahman, M. Rafiul Islam, A. S. M. Rubayet Ul Alam, Israt Islam, M. Nazmul Hoque, Salma Akter, Md. Mizanur Rahaman, Munawar Sultana, M. Anwar Hossain · 2020 · Journal of Medical Virology
Homology modeling in the time of collective and artificial intelligence
Tareq Hameduh, Yazan Haddad, Vojtěch Adam, Zbyněk Heger · 2020 · Computational and Structural Biotechnology Journal
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Kathryn M. Kauffman, William K. Chang, Julia M. Brown, Fatima A. Hussain, Joy Yang, Martin F. Polz, Libusha Kelly · 2022 · Nature Communications
A Phytophthora sojae effector suppresses endoplasmic reticulum stress-mediated immunity by stabilizing plant Binding immunoglobulin Proteins
Maofeng Jing, Baodian Guo, Haiyang Li, Bo Yang, Haonan Wang, Guanghui Kong, Yao Zhao, Huawei Xu, Yan Wang, Wenwu Ye et al. · 2016 · Nature Communications
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Peng Liu, Erik Župa, Annett Neuner, Anna Böhler, J. Loerke, Dirk Flemming, Thomas Ruppert, Till Rudack, Christoph Peter, Christian M. T. Spahn et al. · 2019 · Nature
Structure–Function Analysis of SMAX1 Reveals Domains That Mediate Its Karrikin-Induced Proteolysis and Interaction with the Receptor KAI2
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Chimeric adaptor proteins translocate diverse type VI secretion system effectors in Vibrio cholerae
Daniel Unterweger, Benjamin Kostiuk, Rina Ötjengerdes, Ashley Wilton, Laura Diaz‐Satizabal, Stefan U. Pukatzki · 2015 · The EMBO Journal
TIFA Signaling in Gastric Epithelial Cells Initiates the cag Type 4 Secretion System-Dependent Innate Immune Response to Helicobacter pylori Infection
Alevtina Gall, Ryan G. Gaudet, Scott D. Gray‐Owen, Nina R. Salama · 2017 · mBio
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Nathan M. Good, Huong N. Vu, Carly J. Suriano, Gabriel A. Subuyuj, Elizabeth Skovran, Norma Cecilia Martinez-Gomez · 2016 · Journal of Bacteriology
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Mejhert, Niklas, Kuruvilla, Leena, Gabriel, Katlyn R., Elliott, Shane D., Guie, Marie-Aude, Wang, Huajin, Lai, Zon Weng, Lane, Elizabeth A., Christiano, Romain, Danial, Nika N. et al. · 2020 · Molecular Cell
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Sampriti Mukherjee, Dina A. Moustafa, Vasiliki Stergioula, Chari D. Smith, Joanna B. Goldberg, Bonnie L. Bassler · 2018 · Proceedings of the National Academy of Sciences
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Kaige Yan, Jing Yang, Ziguo Zhang, Stephen H. McLaughlin, Leifu Chang, Domenico Fasci, Ann E. Ehrenhofer‐Murray, Albert J. R. Heck, David Barford · 2019 · Nature
Asymmetric Molecular Architecture of the Human γ-Tubulin Ring Complex
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Jérôme Clatot, Malcolm Hoshi, Xiaoping Wan, Haiyan Liu, Ankur Jain, Krekwit Shinlapawittayatorn, Céline Marionneau, Eckhard K. Ficker, Taekjip Ha, Isabelle Deschênes · 2017 · Nature Communications
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Wei Hui Zheng, Chengxin Zhang, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang · 2019 · Nucleic Acids Research
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Anna-Maria T. Baumann, Mark J. G. Bakkers, Falk F. R. Buettner, Maike Hartmann, Melanie Grove, Martijn A. Langereis, Raoul J. de Groot, Martina Mühlenhoff · 2015 · Nature Communications
Hyperexpansion of RNA Bacteriophage Diversity
Siddharth R. Krishnamurthy, Andrew B. Janowski, Guoyan Zhao, Dan H. Barouch, David Wang · 2016 · PLoS Biology
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Jan Janouškovec, D. Tikhonenkov, F. Burki, Alexis T. Howe, F. Rohwer, A. P. Mylnikov, P. Keeling · 2017 · Current Biology
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Arwa A. Abbas, Louis J. Taylor, Marisol I. Dothard, Jacob S. Leiby, Ayannah S. Fitzgerald, Layla A. Khatib, Ronald G. Collman, Frederic D. Bushman · 2019 · Cell Host & Microbe
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Kevin Macé, Abhinav Koyamangalath Vadakkepat, Adam Redzej, Natalya Lukoyanova, Clasien J. Oomen, Nathalie Braun, Marta Ukleja, Fang Lu, Tiago R. D. Costa, Elena V. Orlova et al. · 2022 · Nature
Copper homeostasis networks in the bacterium Pseudomonas aeruginosa
Julia Quintana, Lorena Novoa‐Aponte, JOSÉ M. ARGÜELLO · 2017 · Journal of Biological Chemistry
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Nana Liu, Yun Sun, Yakun Pei, Xueyan Zhang, Ping Wang, Xiancai Li, Fuguang Li, Yuxia Hou · 2018 · PLANT PHYSIOLOGY
Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases
John R. Horton, Amanda Engstrom, Elizabeth L. Zoeller, Xu Liu, John R. Shanks, Xing Zhang, Margaret A. Johns, Paula M. Vertino, Haian Fu, Xiaodong Cheng · 2015 · Journal of Biological Chemistry
De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome and abrogate nasal development
Christopher T. Gordon, Shifeng Xue, Gökhan Yigit, Hicham Filali, Kelan Chen, Nadine Rosin, Koh-ichiro Yoshiura, Myriam Oufadem, Tamara J Beck, Ruth McGowan et al. · 2017 · Nature Genetics
Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei
Domenico Fasci, Hugo van Ingen, Richard A. Scheltema, Albert J. R. Heck · 2018 · Molecular & Cellular Proteomics
Properties and Biotechnological Applications of Acyl‐CoA:diacylglycerol Acyltransferase and Phospholipid:diacylglycerol Acyltransferase from Terrestrial Plants and Microalgae
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Adekunle W. Adesanya, Mark D. Lavine, Timothy W. Moural, Laura Corley Lavine, Fang Zhu, Douglas B. Walsh · 2021 · Journal of Pest Science
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Hanpeng Liao, Chen Liu, Chaofan Ai, Tian Gao, Qiue Yang, Zhen Yu, Shao‐Ming Gao, Shungui Zhou, Ville‐Petri Friman · 2023 · The ISME Journal
The complete structure of the small-subunit processome
Jonas Barandun, Malik Chaker-Margot, Mirjam Hunziker, Kelly R. Molloy, Brian T. Chait, Sebastian Klinge · 2017 · Nature Structural & Molecular Biology
The cryo-EM structure of African swine fever virus unravels a unique architecture comprising two icosahedral protein capsids and two lipoprotein membranes
Germán Andrés, Diego Charro, Tania Matamoros, Rebecca S. Dillard, Nicola G. A. Abrescia · 2019 · Journal of Biological Chemistry
Neural versus alternative integrative systems: molecular insights into origins of neurotransmitters
Moroz, Leonid L., Romanova, Daria Y., Kohn, Andrea B. · 2021 · Philosophical Transactions of the Royal Society B