cran: PHENIX | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0115082

Ethenoguanines Undergo Glycosylation by Nucleoside 2′-Deoxyribosyltransferases at Non-Natural Sites
Cited by: 10
Author(s): Wenjie Ye, Debajyoti Paul, Lina Gao, Jolita Šečkutė, R. Sangaiah, K. Jayaraj, Zhenfa Zhang, P.A. Kaminski, S.E. Ealick, Avram Gold, Louise M. Ball
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.ppat.1008394

Structural and functional insights into a novel two-component endolysin encoded by a single gene in Enterococcus faecalis phage
Cited by: 21
Author(s): Biao Zhou, Xiangkai Zhen, Huan Zhou, Feiyang Zhao, Chao Fan, Vanja Perčulija, Yigang Tong, Zhiqiang Mi, Songying Ouyang
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pbio.1001669

An RNA-Binding Complex Involved in Ribosome Biogenesis Contains a Protein with Homology to tRNA CCA-Adding Enzyme
Cited by: 32
Author(s): Jinzhong Lin, Jing Lü, Yingang Feng, Mengyi Sun, Keqiong Ye
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0022767

X-Ray Structure Reveals a New Class and Provides Insight into Evolution of Alkaline Phosphatases
Cited by: 18
Author(s): Subhash C. Bihani, Amit Kumar Das, Kayzad Nilgiriwala, Vishal Prashar, Michel Pirocchi, Shree Kumar Apte, Jean‐Luc Ferrer, M.V. Hosur
Software Mentions: 3
Published: over 13 years ago

10.1111/febs.15514

Structure‐based design of peptides that trigger Streptococcus pneumoniae cell death
Cited by: 11
Author(s): Sung-Min Kang, Chun Jin, Do-Hee Kim, Sung Jean Park, Sang-Woo Han, Bong-Jin Lee
Software Mentions: 3
Published: about 4 years ago

10.3389/fmolb.2021.652530

Cryo-EM Map–Based Model Validation Using the False Discovery Rate Approach
Cited by: 4
Author(s): Mateusz Olek, Agnel Praveen Joseph
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.03583

Structure and transport mechanism of the sodium/proton antiporter MjNhaP1
Cited by: 65
Author(s): Cristina Paulino, David Wöhlert, Ekaterina Kapotova, Özkan Yıldız, Werner Kühlbrandt
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0241513

Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX
Cited by: 12
Author(s): Linda Yingqi Lin, Sawyer McCarthy, Barrett M. Powell, Yanti Manurung, Irene M. Xiang, William L. Dean, Brad Chaires, Liliya A. Yatsunyk
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0156344

A Novel Phenanthridionone Based Scaffold As a Potential Inhibitor of the BRD2 Bromodomain: Crystal Structure of the Complex
Cited by: 11
Author(s): Shailesh Tripathi, Shruti Mathur, Prashant Deshmukh, R Manjula, Balasundaram Padmanabhan
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.46417

Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
Cited by: 58
Author(s): Gregory M. Martin, Min Woo Sung, Zhongying Yang, Laura Innes, Krishnaswamy Balamurugan, Larry L. David, Craig Yoshioka, Show Ling Shyng
Software Mentions: 3
Published: over 5 years ago

10.1038/s41421-019-0103-0

Molecular basis for hierarchical histone de-β-hydroxybutyrylation by SIRT3
Cited by: 64
Author(s): Xingrun Zhang, Ruili Cao, Jinrong Niu, Sen Yang, Huida Ma, Shuai Zhao, Haitao Li
Software Mentions: 3
Published: over 5 years ago

10.1038/cddis.2017.487

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2
Cited by: 20
Author(s): M. Merski, Cátia Moreira, Rui M.V. Abreu, María J. Ramos, Pedro A. Fernandes, L. Miguel Martins, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro
Software Mentions: 3
Published: about 7 years ago

10.1016/j.cell.2021.02.045

Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling
Cited by: 18
Author(s): R.A. Robinson, Samuel C. Griffiths, Lieke L van de Haar, Tomas Malinauskas, Eljo Y. van Battum, Pavol Zelina, Rebekka A. Schwab, Dimple Karia, L. Malinauskaite, Sara Brignani, Marleen H. van den Munkhof, O. Dudukcu, A.A. De Ruiter, Dianne M.A. van den Heuvel, B. Bishop, J. Elegheert, A. Radu Aricescu, R. Jeroen Pasterkamp, Christian Siebold
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.27829

Structure-based analysis of CysZ-mediated cellular uptake of sulfate
Cited by: 9
Author(s): Zahra Assur Sanghai, Qun Liu, Oliver B Clarke, Meagan Belcher Dufrisne, Pattama Wiriyasermkul, Maria Giese, Edgar Leal-Pinto, Brian Kloss, Shantelle Tabuso, J. Love, Marco Punta, Surajit Banerjee, Kanagalaghatta R. Rajashankar, Burkhard Rost, Diomedes E. Logothetis, Matthias Quick, Wayne A. Hendrickson, Filippo Mancia
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.41741

Crystal structure of a natural light-gated anion channelrhodopsin
Cited by: 30
Author(s): Hai Li, Chia‐Ying Huang, Elena G. Govorunova, Christopher T. Schafer, Oleg A. Sineshchekov, Meitian Wang, Lei Zheng, John L. Spudich
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2019.02084

YtrASa, a GntR-Family Transcription Factor, Represses Two Genetic Loci Encoding Membrane Proteins in Sulfolobus acidocaldarius
Cited by: 9
Author(s): Liesbeth Lemmens, Laurentijn Tilleman, Ezra De Koning, K. Valegård, Ann-Christin Lindås, Filip Van Nieuwerburgh, Dominique Maes, Eveline Peeters
Software Mentions: 3
Published: about 5 years ago

10.1016/j.str.2021.04.004

Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein
Cited by: 8
Author(s): Patryk Ludzia, E.D. Lowe, Gabriele Marcianò, Shabaz Mohammed, Christina Redfield, Bungo Akiyoshi
Software Mentions: 3
Published: about 3 years ago

10.1107/S205225251900246X

Subatomic resolution X-ray structures of green fluorescent protein
Cited by: 24
Author(s): Kiyotsugu Takaba, Yang Tai, Haruhiko Eki, Hoang Anh Dao, Yuya Hanazono, Kazuya Hasegawa, Kunio Miki, Kazuki Takeda
Software Mentions: 3
Published: over 5 years ago

10.1016/j.str.2020.04.010

CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions
Cited by: 16
Author(s): Takashi Ochi, Valentina Quarantotti, Huawen Lin, Jérôme Jullien, Ivan Rosa e Silva, Francesco Boselli, Deepak D. Barnabas, Christopher M. Johnson, Stephen H. McLaughlin, Stefan Freund, Andrew N. Blackford, Yuu Kimata, Raymond E. Goldstein, Stephen Jackson, Tom L. Blundell, Susan K. Dutcher, Fanni Gergely, M. van Breugel
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.56889

An ER translocon for multi-pass membrane protein biogenesis
Cited by: 68
Author(s): Philip T. McGilvray, S. Anghel, Arunkumar Sundaram, Frank Zhong, Michael J. Trnka, James R. Fuller, Hong Yu Hu, Alma L. Burlingame, Robert J. Keenan
Software Mentions: 3
Published: over 4 years ago

10.1128/mBio.01569-16

The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment
Cited by: 24
Author(s): Leo Hanke, Kevin E. Knockenhauer, R. Camille Brewer, Eline van Diest, Florian I. Schmidt, Thomas Schwartz, Hidde L. Ploegh
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.65339

Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein
Cited by: 12
Author(s): Xiangrong Chen, Yusuf Ali, Charlotte E L Fisher, Raquel Arribas-Bosacoma, Mohan B. Rajasekaran, Gareth Williams, Sarah Walker, Jessica R Booth, Jessica J. R. Hudson, S. Mark Roe, Laurence H. Pearl, Simon E. Ward, Frances M. G. Pearl, Antony W. Oliver
Software Mentions: 3
Published: over 3 years ago

10.1038/celldisc.2016.51

Structural mechanism for the arginine sensing and regulation of CASTOR1 in the mTORC1 signaling pathway
Cited by: 33
Author(s): Zhongchao Gai, Qian Wang, Can Yang, Lei Wang, Wei Deng, Geng Wu
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pntd.0008091

Trypanosomatid selenophosphate synthetase structure, function and interaction with selenocysteine lyase
Cited by: 4
Author(s): Marco Túlio Alves da Silva, Ivan Rosa e Silva, Lívia Maria Faim, Natália Karla Bellini, Murilo Leão Pereira, Ana Laura Lima, Teresa Cristina Leandro de Jesus, Fernanda Cristina Costa, Tatiana F. Watanabe, H.M. Pereira, Sandro Roberto Valentini, Cleslei Fernando Zanelli, Júlio César Borges, Márcio Vinícius Bertacini Dias, Júlia Pinheiro Chagas da Cunha, Bidyottam Mittra, Norma W. Andrews, Otávio Henrique Thiemann
Software Mentions: 3
Published: about 4 years ago

10.1007/s00792-013-0542-8

The role of disulfide bond in hyperthermophilic endocellulase
Cited by: 13
Author(s): Han-Woo Kim, Kazuhiko Ishikawa
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-018-21667-5

Structure based function-annotation of hypothetical protein MGG_01005 from Magnaporthe oryzae reveals it is the dynein light chain orthologue of dynlt1/3
Cited by: 2
Author(s): Guorui Li, Jinguang Huang, Jun Yang, Dan He, Chao Wang, Xiaoxuan Qi, Ian A. Taylor, Junfeng Liu, You-Liang Peng
Software Mentions: 3
Published: over 6 years ago

10.3389/fbioe.2020.00707

An (R)-Selective Transaminase From Thermomyces stellatus: Stabilizing the Tetrameric Form
Cited by: 18
Author(s): Christian M. Heckmann, L.J. Gourlay, Beatriz Domı́nguez, Francesca Paradisi
Software Mentions: 3
Published: over 4 years ago

10.1016/j.febslet.2015.11.030

Crystal structure of the Z-ring associated cell division protein ZapC from Escherichia coli
Cited by: 13
Author(s): Cristina Ortiz, Danguole Kureisaite-Ciziene, Florian Schmitz, Stephen H. McLaughlin, Miguel Vicente, Jan Löwe
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep38564

Structure and dynamics of a constitutively active neurotensin receptor
Cited by: 55
Author(s): Brian E. Krumm, Sangbae Lee, Supriyo Bhattacharya, Istvan Botos, Courtney F. White, Haijuan Du, Nagarajan Vaidehi, Reinhard Grisshammer
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-017-10085-8

Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq
Cited by: 14
Author(s): Eike C. Schulz, Markus Seiler, Cecilia Zuliani, Franka Voigt, Vladimir Rybin, Vivian Pogenberg, Norbert Mücke, Matthias Wilmanns, Toby J. Gibson, O. Barábas
Software Mentions: 3
Published: about 7 years ago

10.1016/j.str.2017.01.002

Crystal Structure of the Heterotrimeric Integrin-Binding Region of Laminin-111
Cited by: 28
Author(s): David Pulido, Sadaf-Ahmahni Hussain, Erhard Hohenester
Software Mentions: 3
Published: over 7 years ago

10.1126/sciadv.abh0250

X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis
Cited by: 19
Author(s): Patrick Rabe, Jos J. A. G. Kamps, Kyle D. Sutherlin, J. Linyard, Pierre Aller, Cindy C. Pham, Hiroki Makita, I.J. Clifton, M.A. McDonough, T.M. Leissing, Denis Shutin, Pauline A. Lang, A. Butryn, Jürgen Brem, Sheraz Gul, Franklin D. Fuller, In-Sik Kim, Mun Hon Cheah, Thomas Fransson, Asmit Bhowmick, I.D. Young, Lee J. O’Riordan, Aaron S. Brewster, Ilaria Pettinati, Margaret Doyle, Yasumasa Joti, Shigeki Owada, Kensuke Tono, A. Batyuk, Mark S. Hunter, Roberto Alonso-Mori, Uwe Bergmann, R.L. Owen, Nicholas K. Sauter, Timothy D. W. Claridge, Carol V. Robinson, Vittal K. Yachandra, Junko Yano, Jan Kern, Allen M. Orville, Christopher J. Schofield
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.48907

Two new polymorphic structures of human full-length alpha-synuclein fibrils solved by cryo-electron microscopy
Cited by: 191
Author(s): Ricardo C. Guerrero-Ferreira, Nicholas M. I. Taylor, Ana-Andreea Arteni, Pratibha Kumari, Daniel Mona, Philippe Ringler, Markus Britschgi, Matthias E. Lauer, Ali Makky, Joeri Verasdonck, Roland Riek, Ronald Melki, Beat H. Meier, Anja Böckmann, Luc Bousset, Henning Stahlberg
Software Mentions: 3
Published: almost 5 years ago

10.1002/pro.3804

Structural and biochemical analysis of the metallo‐β‐lactamase L1 from emerging pathogen Stenotrophomonas maltophilia revealed the subtle but distinct di‐metal scaffold for catalytic activity
Cited by: 19
Author(s): Young Chang Kim, N. Maltseva, Mateusz Wilamowski, C. Tesar, M. Endres, A. Joachimiak
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pcbi.1003478

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor
Cited by: 69
Author(s): Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, Brian M. Baker
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.ppat.1009775

Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses
Cited by: 10
Author(s): Sofia Banchenko, Ferdinand Krupp, Christine Gotthold, Jörg Bürger, Andrea Graziadei, Francis J. O’Reilly, Ludwig Sinn, Olga Ruda, Juri Rappsilber, C.M.T. Spahn, Thorsten Mielke, Ian A. Taylor, David Schwefel
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1008736

Recognition of a highly conserved glycoprotein B epitope by a bivalent antibody neutralizing HCMV at a post-attachment step
Cited by: 14
Author(s): Xiaohua Ye, Hang Su, Daniel Wrapp, Daniel C. Freed, Fengsheng Li, Zihao Yuan, Aimin Tang, Leike Li, Zhiqiang Ku, Wei Xiong, Dabbu Kumar Jaijyan, Hua Zhu, Dai Wang, Jason S. McLellan, Ningyan Zhang, Tong-Ming Fu, Zhiqiang An
Software Mentions: 3
Published: over 4 years ago

10.1073/pnas.1911776116

Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection
Cited by: 14
Author(s): Fiona Whelan, Aleix Lafita, Samuel C. Griffiths, R.E.M. Cooper, J.L. Whittingham, J.P. Turkenburg, Iain W. Manfield, Alexander N. St John, Emanuele Paci, Alex Bateman, Jennifer R. Potts
Software Mentions: 3
Published: almost 5 years ago

10.1038/srep33553

Crystal structures of the bifunctional tRNA methyltransferase Trm5a
Cited by: 7
Author(s): Caiyan Wang, Qian Jia, Ran Chen, Yuming Wei, Juntao Li, Jie Ma, Wei Xie
Software Mentions: 3
Published: about 8 years ago

10.1128/mBio.02858-18

Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket
Cited by: 13
Author(s): Pierrick Craveur, A.T. Gres, Karen A. Kirby, Dandan Liu, John A. Hammond, Yisong Deng, Stefano Forli, David S. Goodsell, James R. Williamson, Stefan G. Sarafianos, Arthur J. Olson
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2017.02034

Molecular Insight into the Acryloyl-CoA Hydration by AcuH for Acrylate Detoxification in Dimethylsulfoniopropionate-Catabolizing Bacteria
Cited by: 10
Author(s): Hai‐Yan Cao, Peng Wang, Fei Xu, Ping‐Yi Li, Bin-Bin Xie, Qi‐Long Qin, Yuzhong Zhang, Chunyang Li, Xiu-Lan Chen
Software Mentions: 3
Published: about 7 years ago

10.1016/j.str.2017.12.005

Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa
Cited by: 27
Author(s): Osman Salih, Shaoda He, Sara Planamente, Lasse Stach, James T. MacDonald, Eleni Manoli, S.H.W. Scheres, Alain Filloux, Paul S. Freemont
Software Mentions: 3
Published: almost 7 years ago

10.1107/S0907444911035943

High-resolution structure of a retroviral protease folded as a monomer
Cited by: 22
Author(s): Mirosław Gilski, Maciej Kazmierczyk, Szymon Krzywda, Helena Zábranská, Seth Cooper, Zoran Popović, Firas Khatib, Frank DiMaio, James Thompson, David Baker, Iva Pichová, Mariusz Jaskólski
Software Mentions: 3
Published: about 13 years ago

10.15252/embj.2021107985

Neutralization of SARS‐CoV‐2 by highly potent, hyperthermostable, and mutation‐tolerant nanobodies
Cited by: 56
Author(s): Thomas Güttler, Metin Aksu, Antje Dickmanns, Kim M. Stegmann, Kathrin Gregor, Renate Rees, Waltraud Taxer, Oleh Rymarenko, Jürgen Schünemann, Christian Dienemann, Philip Gunkel, Bianka Mußil, Jens Krull, Ulrike Teichmann, Uwe Groß, Volker C. Cordes, Matthias Dobbelstein, Dirk Görlich
Software Mentions: 3
Published: over 3 years ago

10.1107/S2059798317007707

DNA conformational transitions inferred from re-evaluation ofm|Fo| −D|Fc| electron-density maps
Cited by: 3
Author(s): Tomoko Sunami, Toshiyuki Chatake, Hidetoshi Kono
Software Mentions: 3
Published: over 7 years ago

10.1107/S2059798319003991

Structural analysis of a replication protein encoded by a plasmid isolated from a multiple sclerosis patient
Cited by: 5
Author(s): Turgay Kilic, A. Popov, Amelie Burk-Körner, A.D. Koromyslova, Harald zur Hausen, Timo Bund, Grant S. Hansman
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-26601-3

Molecular recognition of wood polyphenols by phase II detoxification enzymes of the white rot Trametes versicolor
Cited by: 36
Author(s): Mathieu Schwartz, Thomas Perrot, Emmanuel Aubert, Stéphane Dumarçay, F. Favier, Philippe Gérardin, Mélanie Morel‐Rouhier, Guillermo Mulliert, Fanny Saiag, Claude Didierjean, Éric Gelhaye
Software Mentions: 3
Published: over 6 years ago

10.1107/S2059798317017235

DIALS: implementation and evaluation of a new integration package
Cited by: 750
Author(s): Graeme Winter, David Waterman, James M. Parkhurst, Aaron S. Brewster, Richard J. Gildea, Markus Gerstel, Luis Fuentes-Montero, M. Vollmar, Tara Michels-Clark, I.D. Young, Nicholas K. Sauter, Gwyndaf Evans
Software Mentions: 3
Published: almost 7 years ago

10.1016/j.jbc.2021.100927

Beyond PKA: Evolutionary and structural insights that define a docking and dimerization domain superfamily
Cited by: 3
Author(s): Heather R. Dahlin, Ning Zheng, John D. Scott
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-39641-0

Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H
Cited by: 13
Author(s): Chang Woo Lee, Sun Ha Park, Chang-Sung Jeong, Sun Mi Shin, Hyun Park, Jun Hyuck Lee
Software Mentions: 3
Published: over 5 years ago

10.1186/s13045-020-00979-y

Discovery of a dual inhibitor of NQO1 and GSTP1 for treating glioblastoma
Cited by: 28
Author(s): Kecheng Lei, Xiaoxia Gu, Alvaro G. Alvarado, Yuhong Du, Shilin Luo, Eun Hee Ahn, Seong Su Kang, Bing Ji, Xia Liu, Hui Mao, Haian Fu, Harley I. Kornblum, Lingjing Jin, Li Hua, Keqiang Ye
Software Mentions: 3
Published: about 4 years ago

10.1186/s13104-015-1760-1

Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation
Cited by: 6
Author(s): Noriko Inoguchi, Kittichai Chaiseeda, Mamoru Yamanishi, Moon Ki Kim, Yunho Jang, M. Bajaj, Catherine P. Chia, Donald F. Becker, Hideaki Moriyama
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-018-37522-6

MITF has a central role in regulating starvation-induced autophagy in melanoma
Cited by: 60
Author(s): Katrín Möller, Sara Sigurbjörnsdóttir, Asgeir Ö. Arnthórsson, Vivian Pogenberg, Ramile Dilshat, Valerie Fock, Sólveig Hlín Brynjólfsdóttir, Christian Bindesbøll, M. Bessadóttir, Helga M. Ögmundsdóttir, Anne Simonsen, Lionel Larue, Matthias Wilmanns, Vésteinn Thórsson, Eiríkur Steingrimsson, Margrét H. Ögmundsdóttir
Software Mentions: 3
Published: almost 6 years ago

10.1074/jbc.RA119.007709

Structure and interactions of the archaeal motility repression module ArnA–ArnB that modulates archaellum gene expression in Sulfolobus acidocaldarius
Cited by: 15
Author(s): Lena Hoffmann, Katrin Anders, Lisa Franziska Bischof, Xing Ye, Julia Reimann, Sunia Khadouma, Trong Khoa Pham, Chris van der Does, Phillip C. Wright, Lars‐Oliver Essen, Sonja‐Verena Albers
Software Mentions: 3
Published: over 5 years ago

10.1107/S1399004715004241

Using support vector machines to improve elemental ion identification in macromolecular crystal structures
Cited by: 4
Author(s): Nader Morshed, Nathaniel Echols, Paul D. Adams
Software Mentions: 3
Published: over 9 years ago

10.1107/S0907444910029690

Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from Bacillus anthracis
Cited by: 19
Author(s): Ekaterina Morgunova, Boris Illarionov, Sabine Saller, Aleksander Popov, Thota Sambaiah, Adelbert Bacher, Mary Cushman, Markus Fischer, Rudolf Ladenstein
Software Mentions: 3
Published: over 14 years ago

10.1107/S1399004714025875

Data Exploration Toolkitfor serial diffraction experiments
Cited by: 27
Author(s): Oliver B. Zeldin, Aaron S. Brewster, Johan Hattne, Monarin Uervirojnangkoorn, A.Y. Lyubimov, Qiuhong Zhou, Minglei Zhao, William I. Weis, Nicholas K. Sauter, Axel T. Brunger
Software Mentions: 3
Published: almost 10 years ago

10.1107/S0907444912001308

Towards automated crystallographic structure refinement with phenix.refine
Cited by: 4,334
Author(s): Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Nathaniel Echols, Jeffrey J. Headd, Nigel W. Moriarty, Marat Mustyakimov, Thomas C. Terwilliger, Alexandre Urzhumtsev, Peter H. Zwart, Paul D. Adams
Software Mentions: 3
Published: over 12 years ago

10.1107/S2053230X15018336

Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I
Cited by: 8
Author(s): Mathias Enderle, A.A. McCarthy, Karthik S. Paithankar, Martin Grininger
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-018-30154-w

Genome-wide association study and genomic prediction using parental and breeding populations of Japanese pear (Pyrus pyrifolia Nakai)
Cited by: 44
Author(s): Mai F. Minamikawa, Norio Takada, Shingo Terakami, Toshihiro Saito, Akio Onogi, Hiromi Kajiya‐Kanegae, Takeshi Hayashi, Takatsugu Yamamoto, Hiroyoshi Iwata
Software Mentions: 3
Published: over 6 years ago

10.1107/S1399004715005210

In meso in situ serial X-ray crystallography of soluble and membrane proteins
Cited by: 98
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Ezequiel Panepucci, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 3
Published: over 9 years ago

10.1093/aobpla/plw042

Experimental assessment of factors mediating the naturalization of a globally invasive tree on sandy coastal plains: a case study from Brazil
Cited by: 10
Author(s): Thalita Gabriella Zimmermann, Antônio Carlos Silva de Andrade, David M. Richardson
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms21207683

Hydroxylation of Antitubercular Drug Candidate, SQ109, by Mycobacterial Cytochrome P450
Cited by: 12
Author(s): Sergey Bukhdruker, Tatsiana Varaksa, Irina Grabovec, Egor Marin, Polina Shabunya, Maria Kadukova, Sergei Grudinin, Anton Kavaleuski, Anastasiia Gusach, Andrei A. Gilep, Valentin Borshchevskiy, Natallia Strushkevich
Software Mentions: 3
Published: about 4 years ago

10.1107/S1399004715004514

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams
Cited by: 112
Author(s): Nicolas Coquelle, Aaron S. Brewster, U. Kapp, Anastasya Shilova, Britta Weinhausen, Manfred Burghammer, J.P. Colletier
Software Mentions: 3
Published: over 9 years ago

10.1128/JVI.01664-19

Structure of Merkel Cell Polyomavirus Capsid and Interaction with Its Glycosaminoglycan Attachment Receptor
Cited by: 12
Author(s): Niklas Johannes Bayer, Dovile Januliene, Georg Zocher, Thilo Stehle, Arne Moeller, Bärbel S. Blaum
Software Mentions: 3
Published: about 4 years ago

10.1107/S2053273316010731

Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm
Cited by: 9
Author(s): Hongxing He, Hengrui Fang, Mitchell D. Miller, George N. Phillips, W. P. Su
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0080947

Crystal Structures of the Human G3BP1 NTF2-Like Domain Visualize FxFG Nup Repeat Specificity
Cited by: 43
Author(s): T. Vognsen, Ingvar R. Möller, Ole Kristensen
Software Mentions: 3
Published: almost 11 years ago

10.3390/ijms22168631

The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales
Cited by: 5
Author(s): Marie-Caroline Müller, T. Wagner
Software Mentions: 3
Published: over 3 years ago

10.1107/S1744309113012931

Structure of PatF fromProchloron didemni
Cited by: 26
Author(s): Andrew F. Bent, Jesko Koehnke, Wael E. Houssen, Margaret Caroline MacHin Smith, Marcel Jaspars, James H. Naismith
Software Mentions: 3
Published: over 11 years ago

10.1098/rsob.160292

Structural, mechanistic and functional insight into gliotoxin bis -thiomethylation in Aspergillus fumigatus
Cited by: 32
Author(s): Stephen K. Dolan, Thomas Böck, Vanessa Hering, Rebecca A. Owens, Gary W. Jones, Wulf Blankenfeldt, Seán Doyle
Software Mentions: 3
Published: almost 8 years ago

10.1107/S0907444910052224

Recent advances in theCRANKsoftware suite for experimental phasing
Cited by: 79
Author(s): Navraj S. Pannu, Willem Jan Waterreus, Pavol Skubák, Irakli Sikharulidze, Jan Pieter Abrahams, R. A. G. de Graaff
Software Mentions: 3
Published: over 13 years ago

10.1016/j.str.2013.10.013

Structure and Self-Assembly of the Calcium Binding Matrix Protein of Human Metapneumovirus
Cited by: 45
Author(s): C. Leyrat, Max Renner, K. Harlos, Juha T. Huiskonen, Jonathan M. Grimes
Software Mentions: 3
Published: almost 11 years ago

10.1016/j.jmb.2015.10.027

A Substrate Mimic Allows High-Throughput Assay of the FabA Protein and Consequently the Identification of a Novel Inhibitor of Pseudomonas aeruginosa FabA
Cited by: 6
Author(s): L. Moynié, Anthony G. Hope, Kara Finzel, J.W. Schmidberger, Stuart M. Leckie, Günter Schneider, Michael D. Burkart, Andrew D. Smith, David W. Gray, James H. Naismith
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.jsb.2020.107545

Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER
Cited by: 72
Author(s): Kailash Ramlaul, Colin M. Palmer, Takanori Nakane, C.H.S. Aylett
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-40432-w

Reactive centre loop dynamics and serpin specificity
Cited by: 28
Author(s): Emilia M. Marijanovic, James Fodor, Blake T. Riley, Benjamin T. Porebski, Maurício G. S. Costa, Itamar Kass, David E. Hoke, Sheena McGowan, Ashley M. Buckle
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-29058-6

Structural determinants of specificity and regulation of activity in the allosteric loop network of human KLK8/neuropsin
Cited by: 7
Author(s): Mekdes Debela, Viktor Magdolen, Wolfgang Skala, Brigitta Elsässer, Eric L. Schneider, Charles S. Craik, Martin L. Biniossek, Oliver Schilling, Wolfram Bode, Hans Brandstetter, Peter Goettig
Software Mentions: 3
Published: over 6 years ago

10.1080/14756366.2021.1931862

Structure-based virtual screening of highly potent inhibitors of the nematode chitinase CeCht1
Cited by: 7
Author(s): Wei Chen, Qi Chen, Ashutosh Kumar, Xi Jiang, Kam Y. J. Zhang, Qing Yang
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.ppat.1003754

The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies
Cited by: 165
Author(s): Devin Sok, Uri Laserson, Jonathan Laserson, Yiping Liu, François Vigneault, Jean-Philippe Julien, Bryan Briney, Alejandra Ramos, Karen Saye, Khoa Le, Alison E. Mahan, Shenshen Wang, Mehran Kardar, Gur Yaari, Laura M. Walker, Birgitte B. Simen, Elizabeth St. John, Po-Ying Chan-Hui, Kristine M. Swiderek, Stephen H. Kleinstein, Galit Alter, Michael S. Seaman, Arup K. Chakraborty, Daphne Koller, Ian A. Wilson, George M. Church, Dennis R. Burton, Pascal Poignard
Software Mentions: 3
Published: about 11 years ago

10.1038/s41598-018-29664-4

Structural basis for selective inhibition of immunoglobulin E-receptor interactions by an anti-IgE antibody
Cited by: 20
Author(s): Jiun-Bo Chen, Faruk Ramadani, M.O.Y. Pang, Rebecca L. Beavil, Mary D. Holdom, A.N. Mitropoulou, Andrew J. Beavil, Hannah J. Gould, Tse Wen Chang, Brian J. Sutton, James M. McDonnell, Anna M. Davies
Software Mentions: 3
Published: over 6 years ago

10.1016/j.jbc.2021.101061

A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase
Cited by: 7
Author(s): Emily Chen, Krystle Reiss, Dilip Shah, R Manjula, Brandon Allen, Eva Murphy, James W. Murphy, Víctor S. Batista, Vineet Bhandari, Elias Lolis, George P. Lisi
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-018-33193-5

Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas
Cited by: 10
Author(s): Hong‐Hsiang Guan, Yin-Cheng Hsieh, Po‐Chun Lin, Yen‐Chieh Huang, Masato Yoshimura, Liying Chen, Shao-Kang Chen, Phimonphan Chuankhayan, Chien-Chih Lin, Nai-Chi Chen, Atsushi Nakagawa, Sunney I. Chan, Chun‐Jung Chen
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-39588-2

The IKK-binding domain of NEMO is an irregular coiled coil with a dynamic binding interface
Cited by: 18
Author(s): Adam H. Barczewski, Michael J. Ragusa, Dale F. Mierke, Maria Pellegrini
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-68419-y

Enzymatic reaction mechanism of cis-aconitate decarboxylase based on the crystal structure of IRG1 from Bacillus subtilis
Cited by: 8
Author(s): Hye Lin Chun, So Yeon Lee, Sung Hoon Lee, Chang Sup Lee, Hyun Ho Park
Software Mentions: 3
Published: over 4 years ago

10.1016/j.jmb.2013.10.039

Structural Determinants of Unique Properties of Human IgG4-Fc
Cited by: 95
Author(s): Anna M. Davies, Theo Rispens, Pleuni Ooijevaar-de Heer, Hannah J. Gould, Royston Jefferis, Rob C. Aalberse, Brian J. Sutton
Software Mentions: 3
Published: almost 11 years ago

10.1016/j.jmb.2015.08.023

Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain
Cited by: 9
Author(s): Nora Cronin, Jing Yang, Ziguo Zhang, Kiran Kulkarni, Leifu Chang, Hiroyuki Yamano, David Barford
Software Mentions: 3
Published: about 9 years ago

10.7554/eLife.59225

Ebola and Marburg virus matrix layers are locally ordered assemblies of VP40 dimers
Cited by: 33
Author(s): William Wan, Mairi Clarke, Michael Norris, Larissa Kolesnikova, Alexander Koehler, Zachary A. Bornholdt, Stephan Becker, Erica Ollmann Saphire, John Briggs
Software Mentions: 3
Published: about 4 years ago

10.1107/S1399004714027011

Three-dimensional structures ofPlasmodium falciparumspermidine synthase with bound inhibitors suggest new strategies for drug design
Cited by: 12
Author(s): J. Sprenger, Bo Svensson, J.C. Halander, Jannette Carey, Lo Persson, Salam Al-Karadaghi
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.60552

Cryo-EM analysis of PIP2 regulation in mammalian GIRK channels
Cited by: 43
Author(s): Yiming Niu, Xiao Tao, Kouki K Touhara, Roderick MacKinnon
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.21646

Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis
Cited by: 57
Author(s): Ashutosh Pudasaini, Jae Sung Shim, Young Hun Song, Hua Shi, Takatoshi Kiba, David E. Somers, Takato Imaizumi, Brian D. Zoltowski
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms22083812

Crystal Structure of the Epo1-Bem3 Complex for Bud Growth
Cited by: 0
Author(s): Jin Wang, Lei Li, Zhenhua Ming, Lijie Wu, Liming Yan
Software Mentions: 3
Published: over 3 years ago

10.1016/j.jbc.2021.100700

ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis
Cited by: 8
Author(s): Jitender Mehla, George W. Liechti, Randy M. Morgenstein, J. Harry Caufield, Ali Hosseinnia, Alla Gagarinova, Sadhna Phanse, Norman Goodacre, Mary R. Brockett, Neha Sakhawalkar, Mohan Babu, Rong Xiao, Gaetano T. Montelione, S.M. Vorobiev, T. den Blaauwen, J.F. Hunt, Peter Uetz
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.jbc.2021.100743

From integrative structural biology to cell biology
Cited by: 38
Author(s): Andrej Šali
Software Mentions: 3
Published: almost 4 years ago

10.1074/jbc.RA119.010697

Structural basis of cell-surface signaling by a conserved sigma regulator in Gram-negative bacteria
Cited by: 3
Author(s): Jaime L. Jensen, Beau D. Jernberg, Sangita C. Sinha, Christopher L. Colbert
Software Mentions: 3
Published: over 4 years ago

10.1107/S2059798320000418

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction
Cited by: 13
Author(s): Nicholas K. Sauter, Jan Kern, Junko Yano, James M. Holton
Software Mentions: 3
Published: almost 5 years ago

10.1074/jbc.RA118.006045

Structural insights into non-covalent ubiquitin activation of the cIAP1-UbcH5B∼ubiquitin complex
Cited by: 12
Author(s): Amrita Patel, Gary Sibbet, Danny T. Huang
Software Mentions: 3
Published: almost 6 years ago

10.1074/jbc.RA120.012788

Small molecule AX-024 reduces T cell proliferation independently of CD3ϵ/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain
Cited by: 10
Author(s): Kirsten Richter, Arne C. Rufer, Magali Muller, Dominique Burger, Fabio Casagrande, Tabea Grossenbacher, Sylwia Huber, Melanie N. Hug, Philipp Koldewey, Andrea D’Osualdo, Daniel Schlatter, Theodor Stoll, M.G. Rudolph
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-52825-y

A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser
Cited by: 2
Author(s): Si Hoon Park, Jaehyun Park, Sang Jae Lee, Woo Seok Yang, Sehan Park, Kyungdo Kim, Zee Yong Park, Hyun Kyu Song
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.17903

A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading
Cited by: 32
Author(s): Chun-Min Shan, Jiyong Wang, Ke Xu, Huijie Chen, Jia-Xing Yue, Stuart Andrews, James J. Moresco, John R. Yates, Péter L. Nagy, Liang Tong, Songtao Jia
Software Mentions: 3
Published: about 8 years ago

10.1016/j.yjsbx.2020.100031

In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors
Cited by: 1
Author(s): Jingxu Guo, A. Douangamath, Weixiao Song, Alun R. Coker, A. W. Edith Chan, Steve Wood, J.B. Cooper, E. Resnick, Nir London, F. von Delft
Software Mentions: 3
Published: almost 5 years ago

10.1074/jbc.M115.705863

Inhibition of PRL-2·CNNM3 Protein Complex Formation Decreases Breast Cancer Proliferation and Tumor Growth
Cited by: 38
Author(s): Elie Kostantin, Serge Hardy, William C. Valinsky, Andreas Kompatscher, Jeroen H. F. de Baaij, Yevgen Zolotarov, Mélissa Landry, Noriko Uetani, Luis Alfonso Martínez-Cruz, Joost G. J. Hoenderop, Alvin Shrier, Michel L. Tremblay
Software Mentions: 3
Published: over 8 years ago

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