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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 301–400 of 1,025

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The impact of genetic diversity on gene essentiality within the Escherichia coli species
François Rousset, Jose Cabezas-Caballero, Florence Piastra-Facon, Jesús Fernández-Rodríguez, Olivier Clermont, Érick Denamur, Eduardo P. C. Rocha, David Bikard · 2021 · Nature Microbiology
The genetic landscape of the human solute carrier (SLC) transporter superfamily
Lena Schaller, Volker Martin Lauschke · 2019 · Human Genetics
Bacteriophage Adherence to Mucus Mediates Preventive Protection against Pathogenic Bacteria
Gabriel Magno de Freitas Almeida, Elina Laanto, Roghaieh Ashrafi, Lotta‐Riina Sundberg · 2019 · mBio
A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat
Markus C. Kolodziej, Jyoti Singla, Javier Sánchez‐Martín, Helen Zbinden, Hana Šimková, Miroslava Karafiátová, Jaroslav Doležel, Julien Gronnier, Manuel Poretti, Gaétan Glauser et al. · 2021 · Nature Communications
Insights into the smooth‐to‐rough transitioning in Mycobacterium bolletii unravels a functional Tyr residue conserved in all mycobacterial MmpL family members
Audrey Bernut, Albertus J. Viljoen, Christian Dupont, Guillaume Sapriel, Mickaël Blaise, Christiane Bouchier, Roland Brosch, Chantal de Chastellier, Jean‐Louis Herrmann, Laurent Kremer · 2015 · Molecular Microbiology
Cryo-EM structures of the human volume-regulated anion channel LRRC8
Go Kasuya, Takanori Nakane, Takeshi Yokoyama, Yanyan Jia, Masato Inoue, Kengo Watanabe, Ryoki Nakamura, Tomohiro Nishizawa, Tsukasa Kusakizako, Akihisa Tsutsumi et al. · 2018 · Nature Structural & Molecular Biology
Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche
Paul‐Adrian Bulzu, Adrian‐Ștefan Andrei, Michaela M. Salcher, Maliheh Mehrshad, Keiichi Inoue, Hideki Kandori, Oded Béjà, Rohit Ghai, Horia Leonard Banciu · 2019 · Nature Microbiology
Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat ( Triticum aestivum )
Wenqiang J. Jiang, Lei Yang, Yiqin H. He, Haotian Zhang, Wei Li, Huaigu Chen, Dongfang M. Ma, Junliang Yin · 2019 · PeerJ
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Anna K Stavrinides, Evangelos C. Tatsis, Lorenzo Caputi, Emilien Foureau, Clare E. M. Stevenson, David M. Lawson, Vincent Courdavault, Sarah Ellen O'Connor · 2016 · Nature Communications
A Novel Role for Progesterone Receptor Membrane Component 1 (PGRMC1): A Partner and Regulator of Ferrochelatase
Robert B. Piel, Mesafint T. Shiferaw, Ajay Amar Vashisht, Jason R. Marcero, Jeremy L. Praissman, John D. Phillips, James Akira Wohlschlegel, Amy E. Medlock · 2016 · Biochemistry
DYNC1H1 mutations associated with neurological diseases compromise processivity of dynein–dynactin–cargo adaptor complexes
Ha Thi Hoang, Max A. Schlager, Andrew P. Carter, Simon L. Bullock · 2017 · Proceedings of the National Academy of Sciences
Immunoinformatics: In Silico Approaches and Computational Design of a Multi-epitope, Immunogenic Protein
Armina Alagheband Bahrami, Zahra Payandeh, Saeed Khalili, Alireza Zakeri, Mojgan Bandehpour · 2019 · International Reviews of Immunology
Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B
Ting-Hai Xu, Minmin Liu, X. Edward Zhou, Gangning Liang, Gongpu Zhao, H. Eric Xu, Karsten Melcher, Peter A. Jones · 2020 · Nature
A strategy for dissecting the architectures of native macromolecular assemblies
Yi Shi, Riccardo Pellarin, Peter C. Fridy, Javier Fernández-Martı́nez, Mary K Thompson, Yinyin Li, Qing Jun Wang, Andrej Šali, Michael P. Rout, Brian T. Chait · 2015 · Nature Methods
PpEst is a novel PBAT degrading polyesterase identified by proteomic screening of Pseudomonas pseudoalcaligenes
Paal William Wallace, Karolina Haernvall, Doris Ribitsch, Sabine Zitzenbacher, Matthias Schittmayer, Georg Steinkellner, Karl F. Gruber, Georg M. Guebitz, Ruth Birner‐Gruenberger · 2016 · Applied Microbiology and Biotechnology
Design principles of a minimal auxin response system
Hirotaka Kato, Sumanth Kumar Mutte, Hidemasa Suzuki, Isidro Crespo, Shubhajit Das, Tatyana Radoeva, Mattia Fontana, Yoshihiro Yoshitake, Emi Hainiwa, W. van den Berg et al. · 2020 · Nature Plants
Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution
Nina Dombrowski, Tom A. Williams, Jiarui Sun, Ben J. Woodcroft, Jun-Hoe Lee, Bùi Quang Minh, Christian Rinke, Anja Spang · 2020 · Nature Communications
Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to animals: an updated review
Sina Salajegheh Tazerji, Phelipe Magalhães Duarte, Parastoo Rahimi, Fatemeh Shahabinejad, Santosh Dhakal, Yashpal Singh Malik, Awad Ali Shehata, Juan Lama, Jörn Klein, Muhammad Safdar et al. · 2020 · Journal of Translational Medicine
Defining molecular glues with a dual-nanobody cannabidiol sensor
Cao, Shiyun, Kang, Shoukai, Mao, Haibin, Yao, Jiayu, Gu, Liangcai, Zheng, Ning · 2022 · Nature Communications
Exploring the Use of Molecular Docking to Identify Bioaccumulative Perfluorinated Alkyl Acids (PFAAs)
Carla A. Ng, Konrad Hungerbühler · 2015 · Environmental Science & Technology
DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis
Amr Nassrallah, Martin Rougée, Clara Bourbousse, Stéphanie Drevensek, Sandra Fonseca, Elisa Iniesto, Ouardia Aït-Mohamed, Anne-Flore Deton-Cabanillas, Gérald Zabulon, Ikhlak Ahmed et al. · 2018 · eLife
Lactoferrin: A Glycoprotein Involved in Immunomodulation, Anticancer, and Antimicrobial Processes
Quintín Rascón-Cruz, Edward Alexander Espinoza-Sánchez, Tania Siqueiros-Cendón, Sayuri I. Nakamura-Bencomo, Sigifredo Arévalo‐Gallegos, Blanca Flor Iglesias-Figueroa · 2021 · Molecules
Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case study involving the use of G-protein-coupled receptors
Chien Lee, Bo‐Han Su, Yufeng Jane Tseng · 2022 · Briefings in Bioinformatics
Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.)
Recep Vatansever, İbrahim Koç, İbrahim İlker Özyiğit, Uğur Şen, Mehmet Emin Uras, Naser A. Anjum, Eduarda Pereira, Ertuğrul Filiz · 2016 · Planta
Mechanistic Insights into Interactions between Bacterial Class I P450 Enzymes and Redox Partners
Wei Zhang, Lei Du, Fengwei Li, Xingwang Zhang, Zepeng Qu, Lei Han, Zhong Li, Jingran Sun, Fengxia Qi, Qiuping Yao et al. · 2018 · ACS Catalysis
Exploring the out of sight antigens of SARS-CoV-2 to design a candidate multi-epitope vaccine by utilizing immunoinformatics approaches
Ashkan Safavi, Amirhosein Kefayat, Elham Mahdevar, Ardavan Abiri, Fatemeh Haji Ghahremani · 2020 · Vaccine
Genetic characterization of a new candidate hemagglutinin subtype of influenza A viruses
Sasan R Fereidouni, Elke Starick, Kobey Karamendin, Cecilia Di Genova, Simon D. Scott, Yelizaveta Khan, Timm Harder, Aidyn I. Kydyrmanov · 2023 · Emerging Microbes & Infections
Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes
Clara C. Posthuma, Aartjan J.W. te Velthuis, Eric J. Snijder · 2017 · Virus Research
SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm
Fang Lu, Zhaoyuan Wei, Yong-Jiang Luo, Hailong Guo, Guoqing Zhang, Q. Xia, Yi Wang · 2019 · Nucleic Acids Res.
Toward the solution of the protein structure prediction problem
Robin Pearce, Yang Zhang · 2021 · Journal of Biological Chemistry
The SMX DNA Repair Tri-nuclease
Haley D.M. Wyatt, Rob C. Laister, Stephen R. Martin, C.H. Arrowsmith, Stephen Craig West · 2017 · Molecular Cell
Rare RNF213 variants in the C-terminal region encompassing the RING-finger domain are associated with moyamoya angiopathy in Caucasians
Stéphanie Guey, Markus Kraemer, Dominique Hervé, Thomas E Ludwig, Manoëlle Kossorotoff, Françoise Bergametti, Jan Claudius Schwitalla, Simone Choi, Lucile Broséus, Isabelle Callebaut et al. · 2017 · European Journal of Human Genetics
Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation
Akbar Adjie Pratama, Benjamin Bolduc, Ahmed A. Zayed, Zhi-Ping Zhong, Jiarong Guo, Dean R. Vik, María Consuelo Gazitúa, James M. Wainaina, Simon Roux, Matthew B. Sullivan · 2021 · PeerJ
AI-Based Protein Structure Prediction in Drug Discovery: Impacts and Challenges
Schauperl, Michael, Denny, Rajiah Aldrin · 2022 · Journal of Chemical Information and Modeling
Engineering a Bacterial DyP-Type Peroxidase for Enhanced Oxidation of Lignin-Related Phenolics at Alkaline pH
Vânia Brissos, Diogo Tavares, Ana Catarina Sousa, M. Paula Robalo, Lı́gia O. Martins · 2017 · ACS Catalysis
Cryo-EM structure of a herpesvirus capsid at 3.1 Å
Shuai Yuan, Jialing Wang, Dongjie Zhu, Nan Wang, Qiang Gao, Wenyuan Chen, Hao Tang, Junzhi Wang, Xinzheng Zhang, Hongrong Liu et al. · 2018 · Science
Small is big in Arabidopsis mitochondrial ribosome
Florent Waltz, Tan-Trung Nguyen, Mathilde Arrivé, Anthony Bochler, Johana Chicher, Philippe Hammann, Lauriane Kühn, Martine Quadrado, Hakim Mireau, Yaser Hashem et al. · 2019 · Nature Plants
Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily
Jiwei Liu, Matteo Tassinari, Diorge Paulo de Souza, Souvik Naskar, Jeffrey K. Noel, Olga Bohuszewicz, Martin Buck, Tom A. Williams, Buzz Baum, Harry H. Low · 2021 · Cell
Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome
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Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize
Li, Yixuan, Wei, Kaifa · 2020 · BMC Plant Biology
Calpain-14 and its association with eosinophilic esophagitis
Vladislav A. Litosh, Mark Rochman, Jeffrey K. Rymer, Aleksey Porollo, Leah Claire Kottyan, Marc E. Rothenberg · 2017 · Journal of Allergy and Clinical Immunology
Widespread distribution of prophage-encoded virulence factors in marine Vibrio communities
Daniel Castillo, Kathryn M. Kauffman, Fatima A. Hussain, Panos G. Kalatzis, Nanna Rørbo, Martin F. Polz, Mathias Middelboe · 2018 · Scientific Reports
Endogenous hydrogen sulfide (H2S) is up-regulated during sweet pepper (Capsicum annuum L.) fruit ripening. In vitro analysis shows that NADP-dependent isocitrate dehydrogenase (ICDH) activity is inhibited by H2S and NO
María Ángeles Muñoz-Vargas, Salvador González‐Gordo, Amanda Cañas, Javier López-Jaramillo, José Manuel Palma, Francisco J. Corpas · 2018 · Nitric Oxide
Pejvakin-mediated pexophagy protects auditory hair cells against noise-induced damage
Jean Defourny, Alain Aghaie, Isabelle Perfettini, Paul Avan, Sedigheh Delmaghani, Christine Petit · 2019 · Proceedings of the National Academy of Sciences
Characterization of Fully Recombinant Human 20S and 20S-PA200 Proteasome Complexes
Ana Toste Rêgo, Paula C. A. da Fonseca · 2019 · Molecular Cell
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Sipin Zhu, Mei Liu, Samuel Bennett, Ziyi Wang, Kevin D. G. Pfleger, Jiake Xu · 2021 · Journal of Cellular Physiology
Dynamics of Human Mitochondrial Complex I Assembly: Implications for Neurodegenerative Diseases
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Dicer uses distinct modules for recognizing dsRNA termini
Niladri K. Sinha, Janet Iwasa, Peter S Shen, Brenda Bass · 2017 · Science
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D. Quentin, Shehryar Ahmad, Premy Shanthamoorthy, J. D. Mougous, J. C. Whitney, S. Raunser · 2018 · Nature Microbiology
The complete structure of the human TFIIH core complex
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VarSite: Disease variants and protein structure
Roman Aleksander Laskowski, James D. Stephenson, Ian Sillitoe, Christine Anne Orengo, Janet M. Thornton · 2019 · Protein Science
Cryo-EM structure of the respiratory syncytial virus RNA polymerase
Dongdong Cao, Yunrong Gao, Claire Roesler, Samantha Rice, Paul D’Cunha, Lisa Zhuang, Julia Slack, Mason Domke, Anna Antonova, Sarah Romanelli et al. · 2020 · Nature Communications
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Alastair Robert Plant, Antoine Larrieu, Barry E. Causier · 2021 · New Phytologist
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Anna Winger, Thomas Caspari · 2021 · Viruses
Structural basis of microRNA processing by Dicer-like 1
Xiaobin Wei, Huanhuan Ke, Aijia Wen, Bo Gao, Jing Shi, Yu Feng · 2021 · Nature Plants
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Long-term genomic coevolution of host-parasite interaction in the natural environment
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Wei-Chao Hao, Meijuan Dian, Ying Zhou, QiuLing Zhong, WenQian Pang, Zijian Li, YaYan Zhao, Jiacheng Ma, Xiaolin Lin, Renru Luo et al. · 2022 · Nature Communications
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Soung‐Hun Roh, Nicholas J. Stam, Corey F. Hryc, Sergio Couoh‐Cardel, Grigore D Pintilie, Wah Chiu, Stephan Wilkens · 2018 · Molecular Cell
Fungal G-protein-coupled receptors: mediators of pathogenesis and targets for disease control
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Anke Treuner‐Lange, Yi‐Wei Chang, Timo Glatter, Marco Herfurth, Steffi Lindow, Georges Chreifi, Grant J. Jensen, Lotte Søgaard‐Andersen · 2020 · Nature Communications
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David G. Christensen, Jesse G. Meyer, Jackson T. Baumgartner, Alexandria K. D’Souza, William C. Nelson, Samuel Payne, Misty L. Kuhn, Birgit Schilling, Alan J. Wolfe · 2018 · mBio
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Lim, Ci Ji, Barbour, Alexandra T., Zaug, Arthur J., Goodrich, Karen J., McKay, Allison E., Wuttke, Deborah S., Cech, Thomas R. · 2020 · Science
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Min Xu, Fei Zhang, Zhuo Cheng, Ghader Bashiri, Jing Wang, Jiali Hong, Yemin Wang, Lijun Xu, Xuefei Chen, Sheng‐Xiong Huang et al. · 2020 · Angewandte Chemie International Edition
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Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract
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Self-resistance guided genome mining uncovers new topoisomerase inhibitors from myxobacteria
Fabian Panter, Daniel Krug, Sascha Baumann, Rolf Müller · 2018 · Chemical Science
An enzymatic pathway in the human gut microbiome that converts A to universal O type blood
Peter Rahfeld, Lyann Sim, Haisle Moon, Iren Constantinescu, Connor Morgan‐Lang, Steven Hallam, Jayachandran N. Kizhakkedathu, Stephen G. Withers · 2019 · Nature Microbiology
One-Pot Biocatalytic Transformation of Adipic Acid to 6-Aminocaproic Acid and 1,6-Hexamethylenediamine Using Carboxylic Acid Reductases and Transaminases
Tatiana P. Fedorchuk, Anna N. Khusnutdinova, E. Evdokimova, Robert Flick, Rosa Di Leo, P.J. Stogios, Alexei V. Savchenko, Alexander F. Yakunin · 2019 · Journal of the American Chemical Society
Integration of innate immune signalling by caspase-8 cleavage of N4BP1
Alexander D. Gitlin, Klaus Heger, Alexander F. Schubert, Rohit Reja, Donghong Yan, Victoria C. Pham, Eric Suto, Juan Zhang, Youngsu C. Kwon, Emily C. Freund et al. · 2020 · Nature
Application of the immobilized enzyme on magnetic graphene oxide nano-carrier as a versatile bi-functional tool for efficient removal of dye from water
Shohreh Ariaeenejad, Elaheh Motamedi, Ghasem Hosseini Salekdeh · 2020 · Bioresource Technology
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Konan Ishida, Ryusuke Yokoyama · 2022 · Journal of plant research
Seipin forms a flexible cage at lipid droplet formation sites
Arlt, Henning, Sui, Xuewu, Folger, Brayden, Adams, Carson, Chen, Xiao, Remme, Roman, Hamprecht, Fred A., DiMaio, Frank, Liao, Maofu, Goodman, Joel M. et al. · 2022 · Nature Structural & Molecular Biology
Mechanism of N2 Reduction Catalyzed by Fe-Nitrogenase Involves Reductive Elimination of H2
Derek F. Harris, Dmitriy A. Lukoyanov, Sudipta Shaw, Philip Daniel Compton, Monika Tokmina‐Lukaszewska, Brian B. Bothner, Neil L. Kelleher, Dennis R. Dean, Brian M. Hoffman, Lance C. Seefeldt · 2017 · Biochemistry
CryoEM structure of the human SLC4A4 sodium-coupled acid-base transporter NBCe1
Kevin W. Huynh, Jiansen Jiang, Natalia K. Abuladze, Kirill Tsirulnikov, Liyo Kao, Xuesi Max Shao, Debra Newman, Rustam Azimov, Alexander Pushkin, Zhenqi Zhou et al. · 2018 · Nature Communications
Decrypting bacterial polyphenol metabolism in an anoxic wetland soil
Bridget B. McGivern, Malak Tfaily, Mikayla Borton, Suzanne M. Kosina, Rebecca A. Daly, Carrie Nicora, Samuel Owen Purvine, Allison R. Wong, Mary S. Weir Lipton, David W Hoyt et al. · 2021 · Nature Communications
The Staphylococcus aureus ArlRS two‐component system regulates virulence factor expression through MgrA
Heidi A. Crosby, Nitija Tiwari, Jakub M. Kwiecinski, Zhen Xu, Allison Dykstra, Christian Jenul, Ernesto J. Fuentes, Alexander R. Horswill · 2019 · Molecular Microbiology