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
Cited by (1,025)
Items 701–800 of 1,025
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- Antitumor activity of an engineered decoy receptor targeting CLCF1–CNTFR signaling in lung adenocarcinomaJun W. Kim, César P. Márquez, Kaja Kostyrko, Amanda L. Koehne, Kieren D. Marini, David R. Simpson, Alex Gia Lee, Stanley G. Leung, Leanne C. Sayles, Joseph B. Shrager et al. · 2019 · Nature Medicine
- Biosynthesis of the Stress-Protectant and Chemical Chaperon Ectoine: Biochemistry of the Transaminase EctBA.A. Richter, Christopher-Nils Mais, Laura Czech, Kyra Geyer, A. Hoeppner, Sander H. J. Smits, Tobias J. Erb, Gert Bange, Erhard Bremer · 2019 · Frontiers in Microbiology
- Vaccine Design from the Ensemble of Surface Glycoprotein Epitopes of SARS-CoV-2: An Immunoinformatics ApproachNoor Rahman, Fawad Ali, Zarrin Basharat, Muhammad Shehroz, Muhammad Kazim Khan, Philippe Jeandet, Eugenie Nepovimová, Kamil Kuča, Haroon Zaman Khan · 2020 · Vaccines
- Engineering AraC to make it responsive to light instead of arabinoseEdoardo Romano, Armin Baumschlager, Emir Bora Akmeriç, Navaneethan Palanisamy, Moustafa Houmani, Gregor W. Schmidt, Mehmet Ali Öztürk, Leonard Ernst, Mustafa Khammash, Barbara Di Ventura · 2021 · Nature Chemical Biology
- Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt StressZahra Musavizadeh, Hamid Najafi-Zarrini, Seyed Kamal Kazemitabar, Seyyed Hamidreza Hashemipetroudi, Sahar Faraji, Gianni Barcaccia, Parviz Heidari · 2021 · Genes
- Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein2022
- The archaeal Ced system imports DNAMarleen van Wolferen, Alexander Wagner, Chris van der Does, Sonja‐Verena Albers · 2016 · Proceedings of the National Academy of Sciences
- The Group B Streptococcal surface antigen I/II protein, BspC, interacts with host vimentin to promote adherence to brain endothelium and inflammation during the pathogenesis of meningitis.Deng, Liwen, Spencer, Brady L., Holmes, Joshua A., Mu, Rong, Rego, Sara, Weston, Thomas A., Hu, Yoonsung, Sanches, Glenda F., Yoon, Sunghyun, Park, Nogi et al. · 2019 · PLOS Pathogens
- YidC Insertase of Escherichia coli: Water Accessibility and Membrane ShapingYuanyuan Chen, Sara Capponi, Lu Zhu, Patrick Gellenbeck, J. Alfredo Freites, Stephen H. White, Ross Dalbey · 2017 · Structure
- The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization MechanismNadine M. Shaban, Ke Shi, Kate V. Lauer, Michael A. Carpenter, Christopher M. Richards, Daniel J. Salamango, Jiayi Wang, Michael W. Lopresti, Surajit Banerjee, Rena Levin-Klein et al. · 2017 · Molecular Cell
- MultitaskProtDB-II: an update of a database of multitasking/moonlighting proteinsLuís Franco-Serrano, Sergio Hernández, Alejandra Calvo, María Angélica Severi, Gabriela Ferragut, Josep Antoni Perez-Pons, Jaume Piñol, Òscar Q. Pich, Ángel Mozo-Villarias, Isaac Amela et al. · 2017 · Nucleic Acids Research
- Proofreading-Deficient Coronaviruses Adapt for Increased Fitness over Long-Term Passage without Reversion of Exoribonuclease-Inactivating MutationsKevin W. Graepel, Xiaotao Lu, James Brett Case, Nicole R. Sexton, Everett Clinton Smith, Mark R. Denison · 2017 · mBio
- Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial virusesYan‐Jiun Lee, Nan Dai, Shannon E. Walsh, Stephanie I. Müller, Morgan E. Fraser, Kathryn M. Kauffman, Chudi Guan, Ivan Reis Correa Junior, Peter Weigele · 2018 · Proceedings of the National Academy of Sciences
- The Dynamic Structures of the Type IV PilusMatthew McCallum, Lori L. Burrows, P. Lynne Howell · 2019 · Microbiology Spectrum
- Recognition and Activation of the Plant AKT1 Potassium Channel by the Kinase CIPK23María José Sánchez-Barrena, Antonio Chaves-Sanjuán, Natalia Raddatz, Imelda Mendoza, Álvaro Cortés, Federico Gago, Juana María González-Rubio, Juan Luis Benavente, Francisco Javier Quintero, José M. Pardo et al. · 2020 · PLANT PHYSIOLOGY
- A phytobacterial TIR domain effector manipulates NAD + to promote virulenceSamuel Eastman, Thomas G. Smith, Mark A. Zaydman, Panya Kim, Samuel Martinez, Neha Damaraju, Aaron DiAntonio, Jeffrey Milbrandt, Thomas E. Clemente, James R. Alfano et al. · 2021 · New Phytologist
- Understanding the Role of Prevotella Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep SequencingDao Trong Khoa, Thi Huyen, Ngoc Giang Le, Hong-Duong Nguyen, Thi-Quy Nguyen, Thi-Thu-Hong Le, Nam-Hai Truong · 2021 · Animals
- Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosumQurat-ul ain-Ali, Nida Mushtaq, Rabia Amir, Alvina Gul, Muhammad Nouman Tahir, Faiza Munir · 2021 · PLoS ONE
- Enzymatic polyethylene biorecycling: Confronting challenges and shaping the futureJin Jin, Jane Arciszewski, Karine Auclair, Zongchao Jia · 2023 · Journal of Hazardous Materials
- Cryo-EM structure of a metazoan separase–securin complex at near-atomic resolutionAndreas Boland, Thomas G Martin, Ziguo Zhang, Jing Yang, Xiao‐chen Bai, Leifu Chang, Sjors H. W. Scheres, David Barford · 2017 · Nature Structural & Molecular Biology
- Cyclic-di-GMP regulates lipopolysaccharide modification and contributes to Pseudomonas aeruginosa immune evasionRonan R. McCarthy, María J. Mazón, Joana A. Moscoso, Youai Hao, Joseph S. Lam, Christophe Bordi, Serge Mostowy, Alain Filloux · 2017 · Nature Microbiology
- Conserved cytoplasmic domains promote Hrd1 ubiquitin ligase complex formation for ER-associated degradation (ERAD)Schulz, Jasmin, Avci, Dönem, Queisser, Markus A., Gutschmidt, Aljona, Dreher, Lena-Sophie, Fenech, Emma J., Volkmar, Norbert, Hayashi, Yuki, Hoppe, Thorsten, Christianson, John C. · 2017 · Journal of Cell Science
- Chitinase Chi1 from Myceliophthora thermophila C1, a Thermostable Enzyme for Chitin and Chitosan DepolymerizationMalgorzata Krolicka, Sandra W. A. Hinz, Martijn J. Koetsier, Rob Joosten, Gerrit Eggink, L.A.M. van den Broek, Carmen Gabriela Boeriu · 2018 · Journal of Agricultural and Food Chemistry
- ICE1 promotes the link between splicing and nonsense-mediated mRNA decayThomas D Baird, Ken Chih-Chien Cheng, Yu‐Chi Chen, Eugen C. Buehler, Scott E. Martin, James Inglese, J. Robert Hogg · 2018 · eLife
- Cryo-EM structure of the homohexameric T3SS ATPase-central stalk complex reveals rotary ATPase-like asymmetryD.D. Majewski, L.J. Worrall, Chuan Hong, Claire E. Atkinson, Marija Vuckovic, Nobuhiko Watanabe, Zhiheng Yu, Natalie C. J. Strynadka · 2019 · Nature Communications
- Viroid-like colonists of human microbiomesZheludev, Ivan N., Edgar, Robert C., Lopez-Galiano, Maria Jose, de la Peña, Marcos, Babaian, Artem, Bhatt, Ami S., Fire, Andrew Z. · 2024 · Cell
- Combating tigecycline resistant Acinetobacter baumannii: A leap forward towards multi-epitope based vaccine discoverySajjad Ahmad, Kara E. Ranaghan, Syed Sikander Azam · 2019 · European Journal of Pharmaceutical Sciences
- Origin of Gibberellin-Dependent Transcriptional Regulation by Molecular Exploitation of a Transactivation Domain in DELLA ProteinsJorge Hernández‐García, Asier Briones‐Moreno, Renaud Dumas, Miguel Angel Blázquez · 2019 · Molecular Biology and Evolution
- Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic AlphaproteobacteriumBarbara Bayer, Claus Pelikan, Meriel Bittner, Thomas Reinthaler, Martin Könneke, Gerhard J. Herndl, Pierre Offre · 2019 · mSystems
- Crystal structure of Drosophila PiwiSonomi Yamaguchi, Akira Oe, Kazumichi M. Nishida, Keitaro Yamashita, Asako Kajiya, Seiichi Hirano, Naoki Matsumoto, Naoshi Dohmae, Ryuichiro Ishitani, Kuniaki Saito et al. · 2020 · Nature Communications
- Commensal Oral Rothia mucilaginosa Produces Enterobactin, a Metal-Chelating SiderophoreCarla Uranga, Pablo Arroyo, Brendan M. Duggan, William H. Gerwick, Anna Edlund · 2020 · mSystems
- Insights into the κ/ι-carrageenan metabolism pathway of some marine Pseudoalteromonas speciesAndrew G. Hettle, Joanne K. Hobbs, Benjamin Pluvinage, Chelsea J. Vickers, Kento T. Abe, Orly Salama-Alber, Bailey E. McGuire, Jan‐Hendrik Hehemann, Joseph P. M. Hui, Fabrice Berrué et al. · 2019 · Communications Biology
- Integrated Molecular Modeling and Machine Learning for Drug DesignSong Xia, Eric Chen, Yingkai Zhang · 2023 · Journal of Chemical Theory and Computation
- The mysterious nature of bacterial surface (gliding) motility: A focal adhesion-based mechanism in Myxococcus xanthusSalim T. Islam, Tâm Mignot · 2015 · Seminars in Cell and Developmental Biology
- Bacteriophage LM33_P1, a fast-acting weapon against the pandemic ST131-O25b:H4Escherichia coliclonal complexNicolas Dufour, Olivier Clermont, Béatrice La Combe, Jonathan Messika, Sara Dion, Varun Khanna, Érick Denamur, Jean-Damien Ricard, Laurent Debarbieux · 2016 · Journal of Antimicrobial Chemotherapy
- Identification and Characterization of Dpo42, a Novel Depolymerase Derived from the Escherichia coli Phage vB_EcoM_ECOO78Zhimin Guo, Jing Huang, Guangmou Yan, Liancheng Lei, Shuang Wang, Ling Yu, Liang Zhou, Anchong Gao, Xin Feng, Wenyu Han et al. · 2017 · Frontiers in Microbiology
- Isolation of state-dependent monoclonal antibodies against the 12-transmembrane domain glucose transporter 4 using virus-like particlesDavid F. Tucker, Jonathan T. Sullivan, Kimberly-Anne Mattia, Christine R. Fisher, Trevor Barnes, Manu N. Mabila, Rona Wilf, Chidananda Sulli, Meghan Pitts, Riley J. Payne et al. · 2018 · Proceedings of the National Academy of Sciences
- Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNAErnesto Arias‐Palomo, Neha Puri, Valerie L. O’Shea, Qianyun Yan, James M. Berger · 2019 · Molecular Cell
- OsCIPK7 point‐mutation leads to conformation and kinase‐activity change for sensing cold responseDajian Zhang, Xiaoyu Guo, Yunyuan Xu, Hao Li, Liang Ma, Xuefeng Yao, Yuxiang Weng, Yan Guo, Chunming Liu, Kang Chong · 2019 · Journal of Integrative Plant Biology
- SopF, a phosphoinositide binding effector, promotes the stability of the nascent Salmonella-containing vacuoleNicole Lau, Amanda L. Haeberle, Brittany J. O’Keeffe, Eleanor A. Latomanski, Jean Celli, Hayley J. Newton, Leigh A. Knodler · 2019 · PLoS Pathogens
- SARS-CoV-2 and SARS-CoV differ in their cell tropism and drug sensitivity profilesDenisa Bojková, Jake E McGreig, Katie-May McLaughlin, Stuart G. Masterson, Marek Widera, Verena Krähling, Sandra Ciesek, Mark N. Wass, Martin Michaelis, Jindrich Jr. Cinatl · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Viroid-like colonists of human microbiomesZheludev, Ivan N., Edgar, Robert C., Lopez-Galiano, Maria Jose, de la Peña, Marcos, Babaian, Artem, Bhatt, Ami S., Fire, Andrew Z. · 2024
- Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA.Ma, Rui, Lian, Tengfei, Huang, Rick, Renn, Jonathan P., Petersen, Jennifer D., Zimmerberg, Joshua, Duffy, Patrick E., Tolia, Niraj H. · 2021 · Nature Microbiology
- The Landscape of Recombination Events That Create Nonribosomal Peptide DiversityBaunach, Martin, Chowdhury, Somak, Stallforth, Pierre, Dittmann, Elke · 2021 · Molecular Biology and Evolution
- Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machineryMartin Saurer, David J. F. Ramrath, Moritz Niemann, Salvatore Calderaro, Céline Jasmin Prange, Simone Mattei, Alain Scaiola, Alexander Leitner, P. Bieri, Elke K. Horn et al. · 2019 · Science
- Overexpression of Saussurea involucrata dehydrin gene SiDHN promotes cold and drought tolerance in transgenic tomato plantsXinyong Guo, Li Zhang, Xiaozhen Wang, Minhuan Zhang, Yuxin Xi, Aiying Wang, Jianbo Zhu · 2019 · PLoS ONE
- Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunityTao Ni, Fang Jiao, Xiulian Yu, Saša Aden, Lucy Ginger, Sophie I. Williams, Fangfang Bai, Vojtěch Pražák, Dimple Karia, Phillip James Stansfeld et al. · 2020 · Science Advances
- Isotype Switching Converts Anti-CD40 Antagonism to Agonism to Elicit Potent Antitumor ActivityXiaojie Yu, H.T. Claude Chan, Hayden Fisher, Christine A. Penfold, Jinny Kim, Tatyana Inzhelevskaya, Christopher Ian Mockridge, Ruth R. French, Patrick J. Duriez, Leon R. Douglas et al. · 2020 · Cancer Cell
- The genetic factors of bilaterian evolutionPeter Heger, Wen Li Zheng, Anna Rottmann, Kristen A. Panfilio, Thomas Wiehe · 2020 · eLife
- Efficient removal of various textile dyes from wastewater by novel thermo-halotolerant laccaseElaheh Motamedi, Kaveh Kavousi, Seyedeh Fatemeh Sadeghian Motahar, Mohammad Reza Ghaffari, Atefeh Sheykh Abdollahzadeh Mamaghani, Ghasem Hosseini Salekdeh, Shohreh Ariaeenejad · 2021 · Bioresource Technology
- Different Shades of Listeria monocytogenes: Strain, Serotype, and Lineage-Based Variability in Virulence and Stress Tolerance ProfilesFrancis Muchaamba, Athmanya Konegadde Eshwar, Marc J. A. Stevens, Roger Stephan, Taurai Tasara · 2022 · Frontiers in Microbiology
- Identification of a phage-derived depolymerase specific for KL47 capsule of Klebsiella pneumoniae and its therapeutic potential in miceMin Li, Hui Wang, Long Chen, Genglin Guo, Pei Li, Jiale Ma, Rong Chen, Hong Du, Yuqing Liu, Wei Zhang · 2022 · Virologica Sinica
- Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansionsMonica Hongrø Solbakken, Ole K. Tørresen, Alexander J. Nederbragt, Marit Seppola, Tone Fredsvik Gregers, Kjetill S. Jakobsen, Sissel Jentoft · 2016 · Scientific Reports
- Pseudomonas aeruginosa Pore-Forming Exolysin and Type IV Pili Cooperate To Induce Host Cell LysisPauline Basso, Michel Ragno, Sylvie Elsen, Emeline Reboud, Guillaume R. Golovkine, Stéphanie Bouillot, Philippe Huber, Stephen J. Lory, Éric Faudry, Ina Attrée · 2017 · mBio
- Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative PhosphorylationPaul Sunnucks, Hernán E. Morales, Annika Mae Lamb, Alexandra Pavlova, Chris Greening · 2017 · Frontiers in Genetics
- Transient receptor potential vanilloid 4 (TRPV4) activation by arachidonic acid requires protein kinase A–mediated phosphorylationSheng Cao, Andriy Anishkin, Natalya S. Zinkevich, Yoshinori Nishijima, Ankush Korishettar, Zhihao Wang, Juan Fang, David A. Wilcox, David X. Zhang · 2018 · Journal of Biological Chemistry
- Arabidopsis O‐GlcNAc transferase SEC activates histone methyltransferase ATX1 to regulate floweringLijing Xing, Yan Liu, Shujuan Xu, Jun Ying Xiao, Bo Wang, Hanwen Deng, Zhuang Lu, Yunyuan Xu, Kang Chong · 2018 · The EMBO Journal
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- Site-specific phosphorylation of TRANSPARENT TESTA GLABRA1 mediates carbon partitioning in Arabidopsis seedsChengxiang Li, Bin Zhang, Bin Chen, Lianghui Ji, Hao Qiang Yu · 2018 · Nature Communications
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- Infectious spleen and kidney necrosis disease (ISKND) outbreaks in farmed barramundi (Lates calcarifer) in VietnamHa Thanh Dong, Sarocha Jitrakorn, Pattanapon Kayansamruaj, Nopadon Pirarat, Channarong Rodkhum, Triwit Rattanarojpong, Saengchan Senapin, Vanvimon Saksmerprome · 2017 · Fish & Shellfish Immunology
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- Structures of telomerase at several steps of telomere repeat synthesisYao He, Yaqiang Wang, Baocheng Liu, Christina Helmling, Lukas Sušac, Ryan Cheng, Z. Hong Zhou, Juli F. Feigon · 2021 · Nature
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- Structure and function of multidrug and toxin extrusion proteins (MATEs) and their relevance to drug therapy and personalized medicineAnne T. Nies, Katja Damme, Stephan Kruck, Elke Schaeffeler, Matthias Georg Schwab · 2016 · Archives of Toxicology
- Loss of CpSRP54 function leads to a truncated light-harvesting antenna size in Chlamydomonas reinhardtiiJooyeon Jeong, Kwangryul Baek, Henning Kirst, Anastasios Melis, EonSeon Jin · 2016 · Biochimica et Biophysica Acta (BBA) - Bioenergetics
- HqiA, a novel quorum-quenching enzyme which expands the AHL lactonase familyMarta Torres, Stéphane Uroz, Rafael Salto, Laure Fauchery, Emilia Quesada, Inmaculada Llamas · 2017 · Scientific Reports
- Outerwear through the ages: evolutionary cell biology of vesicle coatsJoel B. Dacks, Margaret S. Robinson · 2017 · Current Opinion in Cell Biology
- Direct induction of microtubule branching by microtubule nucleation factor SSNA1Nirakar Basnet, Hana Nedozrálová, Álvaro H. Crevenna, Satish Bodakuntla, Thomas Schlichthaerle, Michael John Taschner, Giovanni Cardone A, Carsten Janke, Ralf Jungmann, Maria M. Magiera et al. · 2018 · Nature Cell Biology
- A Novel d -Allulose 3-Epimerase Gene from the Metagenome of a Thermal Aquatic Habitat and d -Allulose Production by Bacillus subtilis Whole-Cell CatalysisSatya Narayan Patel, Girija Kaushal, Sudhir P. Singh · 2019 · Applied and Environmental Microbiology
- Homozygous loss-of-function mutations in SLC26A7 cause goitrous congenital hypothyroidismCangul, Hakan, Liao, Xiao-Hui, Schoenmakers, Erik, Kero, Jukka, Barone, Sharon, Srichomkwun, Panudda, Iwayama, Hideyuki, Serra, Eva G., Saglam, Halil, Eren, Erdal et al. · 2018 · JCI Insight
- Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteriaMeining Xing, Yifeng Wei, Yan Zhou, Jun Zhang, Lianyun Lin, Yiling Hu, Gaoqun Hua, Ankanahalli N. Nanjaraj Urs, Dazhi Liu, Feifei Wang et al. · 2019 · Nature Communications
- Cryo-EM structures of S-OPA1 reveal its interactions with membrane and changes upon nucleotide bindingDanyang Zhang, Yan Zhang, Jun Ma, Chunmei Zhu, Tongxin Niu, Wenbo Chen, Xiaoyun Pang, Yujia Zhai, Fei Sun · 2020 · eLife
- Yaravirus: A novel 80-nm virus infecting Acanthamoeba castellaniiPaulo Victor de Miranda Boratto, Graziele Pereira Oliveira, Talita Bastos Machado, Ana Cláudia S. P. Andrade, Jean‐Pierre Baudoin, Thomas Klose, Frederik Schulz, Saı̈d Azza, Philippe Decloquement, Éric Chabrière et al. · 2020 · Proceedings of the National Academy of Sciences
- Machine learning‐based prediction of enzyme substrate scope: Application to bacterial nitrilasesZhongyu Mou, Jason Eakes, Connor J. Cooper, Carmen M. Foster, Robert F. Standaert, Mircea Podar, Mitchel J. Doktycz, Jerry M. Parks · 2020 · Proteins Structure Function and Bioinformatics
- Biallelic inheritance of hypomorphic PKD1 variants is highly prevalent in very early onset polycystic kidney diseaseMiranda Durkie, Jiehan Chong, Manoj Kumar Valluru, Peter C. Harris, Albert C.M. Ong · 2020 · Genetics in Medicine
- Ca 2+ signals critical for egress and gametogenesis in malaria parasites depend on a multipass membrane protein that interacts with PKGAurélia C. Balestra, Konstantinos Koussis, Natacha Klages, Steven A. Howell, Helen R. Flynn, Marcus Bantscheff, Carla Pasquarello, Abigail J. Perrin, Lorenzo Brusini, Patrizia Arboit et al. · 2021 · Science Advances
- Structural, molecular, and functional insights into Schlafen proteinsUkhyun Jo, Yves G. Pommier · 2022 · Experimental & Molecular Medicine
- Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicumHajra Maqsood, Faiza Munir, Rabia Amir, Alvina Gul · 2022 · Frontiers in Plant Science