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: about 7 years ago
1 dependent package
161 downloads last month

Papers Mentioning PHENIX 2,287

10.1371/journal.pone.0097015
Structural Studies of an Anti-Inflammatory Lectin from Canavalia boliviana Seeds in Complex with Dimannosides
Cited by: 22
Author(s): G.A. Bezerra, Roland Viertlmayr, Tales Rocha de Moura, P. Delatorre, B.A.M. Rocha, Kyria S. Nascimento, Jozi Godoy Figueiredo, Ingrid Gonçalves Bezerra, C.S. Teixeira, Rafael Conceição Simões, Celso Shiniti Nagano, Nylane Maria Nunes de Alencar, Karl Gruber, Benildo S. Cavada
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pone.0215555
Heavy-atom labeling of RNA by PLOR for de novo crystallographic phasing
Cited by: 6
Author(s): Jason R. Stagno, Ping Yü, Marcin Dyba, Yun‐Xing Wang, Yu Liu
Software Mentions: 2
Published: about 5 years ago
10.1107/S0907444913011438
Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement
Cited by: 7
Author(s): Debora L. Makino, Elena Conti
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0018413
Co-Crystal Structures of PKG Iβ (92–227) with cGMP and cAMP Reveal the Molecular Details of Cyclic-Nucleotide Binding
Cited by: 51
Author(s): Jeong Joo Kim, Darren E. Casteel, Gary B. Huang, Tai Hun Kwon, Ronnie Kuo Ren, Peter H. Zwart, Jeffrey J. Headd, Nicholas G. Brown, Dar Chone Chow, Timothy Palzkill, Choel Kim
Software Mentions: 2
Published: about 13 years ago
10.1107/S2059798318008793
The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order
Cited by: 8
Author(s): D.H. Juers, Christopher Farley, Chris Saxby, R.A. Cotter, John W. Cahn, Kaitlin Harrison, Zhenguo Wu
Software Mentions: 2
Published: almost 6 years ago
10.3390/biom11010043
On the Mechanism of Bioinspired Formation of Inorganic Oxides: Structural Evidence of the Electrostatic Nature of the Interaction between a Mononuclear Inorganic Precursor and Lysozyme
Cited by: 3
Author(s): Lucia Gigli, Enrico Ravera, V. Calderone, Claudio Luchinat
Software Mentions: 2
Published: over 3 years ago
10.3390/biom10010090
Structural and Biophysical Analyses of Human N-Myc Downstream-Regulated Gene 3 (NDRG3) Protein
Cited by: 6
Author(s): Kyung Rok Kim, Kyung A. Kim, Joon Sung Park, Jun Young Jang, Yuri Choi, Hyung Ho Lee, Dong Chul Lee, Kyung Chan Park, Young Il Yeom, Hyun-Jung Kim, Byung Woo Han
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0224753
Streptococcal phosphotransferase system imports unsaturated hyaluronan disaccharide derived from host extracellular matrices
Cited by: 8
Author(s): Shigetoshi Oiki, Yusuke Nakamichi, Yukie Maruyama, Bunzo Mikami, Kousaku Murata, Wataru Hashimoto
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0024227
Get Phases from Arsenic Anomalous Scattering: de novo SAD Phasing of Two Protein Structures Crystallized in Cacodylate Buffer
Cited by: 22
Author(s): Xiang Liu, Heng Zhang, Wang Xiao-jun, Lanfen Li, Xiao‐Dong Su
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0052066
Structural and Functional Insights into (S)-Ureidoglycolate Dehydrogenase, a Metabolic Branch Point Enzyme in Nitrogen Utilization
Cited by: 4
Author(s): Myungil Kim, Inchul Shin, Suhee Cho, Jee Hyun Lee, Sangkee Rhee
Software Mentions: 2
Published: over 11 years ago
10.1016/j.cell.2021.06.020
Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum
Cited by: 571
Author(s): C Liu, H. Ginn, Wanwisa Dejnirattisai, Piyada Supasa, Beibei Wang, Aekkachai Tuekprakhon, Rungtiwa Nutalai, Daming Zhou, Alexander J. Mentzer, Yuguang Zhao, Duyvesteyn Hme., César López-Camacho, J Slon-Campos, T S Walter, Donal Skelly, Síle A. Johnson, Thomas G. Ritter, Chris Mason, Sue Ann Costa Clemens, Felipe Gomes Naveca, Valdinete Alves do Nascimento, Fernanda Nascimento, Cristiano Fernandes da Costa, Paola Cristina Resende, Alex Pauvolid‐Corrêa, Marilda Mendonça Siqueira, Christina Dold, Nigel Temperton, Tao Dong, Andrew J. Pollard, Julian C. Knight, Derrick W. Crook, Teresa Lambe, Elizabeth A. Clutterbuck, Sagida Bibi, Amy Flaxman, Mustapha Bittaye, Sandra Belij‐Rammerstorfer, Sarah C. Gilbert, Tariq Malik, Miles W. Carroll, Paul Klenerman, Eleanor Barnes, Susanna Dunachie, Vicky L. Baillie, Natali Serafin, Zanele Ditse, K Da Silva, Neil G. Paterson, Mark A. Williams, David R. Hall, Shabir A. Madhi, Marta C Nunes, Philip Goulder, Elizabeth E. Fry, Juthathip Mongkolsapaya, Jingshan Ren, D.I. Stuart, Gavin Screaton
Software Mentions: 2
Published: almost 3 years ago
10.1002/2211-5463.12644
Structural insights into interactions between viral suppressor of <scp>RNA</scp> silencing protein p19 mutants and small <scp>RNA</scp>s
Cited by: 5
Author(s): Dana V. Foss, N.T. Schirle, Ian J. MacRae, John Paul Pezacki
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0044124
Complex Structure of Engineered Modular Domains Defining Molecular Interaction between ICAM-1 and Integrin LFA-1
Cited by: 3
Author(s): Sungkwon Kang, Chae Un Kim, Xiaoling Gu, Róisı́n M. Owens, Sarah J. van Rijn, Vanissra Boonyaleepun, Yuxin Mao, Timothy A. Springer, Moonsoo M. Jin
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0015535
Quantitative High-Throughput Screening Identifies 8-Hydroxyquinolines as Cell-Active Histone Demethylase Inhibitors
Cited by: 195
Author(s): Oliver N. King, Xuan Shirley Li, Masaaki Sakurai, Akane Kawamura, Nathan R. Rose, Stanley S. Ng, Amy Quinn, Ganesha Rai, Bryan T. Mott, Paul J. Beswick, Robert J. Klose, U. Oppermann, Ajit Jadhav, Tom D. Heightman, David J. Maloney, Christopher J. Schofield, Anton Simeonov
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0081526
Structural Insights into the Mechanism for Recognizing Substrate of the Cytochrome P450 Enzyme TxtE
Cited by: 18
Author(s): Feng Yu, Minjun Li, Chunyan Xu, Zhijun Wang, Huan Zhou, Min Yang, Yaxing Chen, Lin Tang, Jianhua He
Software Mentions: 2
Published: over 10 years ago
10.1107/S2059798318012081
Status of the neutron time-of-flight single-crystal diffraction data-processing software <i>STARGazer</i>
Cited by: 12
Author(s): Naomine Yano, Taro Yamada, Takamitsu Hosoya, Takashi Ohhara, Ichiro Tanaka, Nobuo Nakabayashi, Katsuhiro Kusaka
Software Mentions: 2
Published: over 5 years ago
10.1107/S2059798316001212
Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from<i>Klebsiella pneumoniae</i>and comparison with a related<i>Streptococcus pneumoniae</i>complex
Cited by: 25
Author(s): D. A. Veselkov, Ivan Laponogov, Xiao-Su Pan, Jogitha Selvarajah, Galyna B. Skamrova, Arthur Branstrom, Jana Narasimhan, J. V. N. Vara Prasad, L. Mark Fisher, Mark Sanderson
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0107289
Structure of the N-Terminal Gyrase B Fragment in Complex with ADP⋅Pi Reveals Rigid-Body Motion Induced by ATP Hydrolysis
Cited by: 44
Author(s): Frédéric V. Stanger, Christoph Dehio, Tilman Schirmer
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0086050
Tracking Molecular Recognition at the Atomic Level with a New Protein Scaffold Based on the OB-Fold
Cited by: 18
Author(s): John D. Steemson, Matthias Baake, Jasna Rakonjac, Vickery L. Arcus, Mark T. Liddament
Software Mentions: 2
Published: over 10 years ago
10.1107/S2059798317015236
The crystal structure of the<i>Yersinia pestis</i>iron chaperone YiuA reveals a basic triad binding motif for the chelated metal
Cited by: 5
Author(s): C.D. Radka, Dongquan Chen, Lawrence J. DeLucas, Stephen G. Aller
Software Mentions: 2
Published: over 6 years ago
10.1107/S2059798316015540
Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C
Cited by: 15
Author(s): Francesco Manzoni, K. Saraboji, J. Sprenger, Rohit Kumar, Ann Louise Noresson, Ulf J. Nilsson, Hakon Leffler, S.Z. Fisher, Tobias E. Schrader, Andreas Ostermann, Leighton Coates, Matthew P. Blakeley, Esko Oksanen, D.T. Logan
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0121494
Crystal Structures of the Kinase Domain of the Sulfate-Activating Complex in Mycobacterium tuberculosis
Cited by: 9
Author(s): Ömer Poyraz, Katharina Brunner, Bernhard Lohkamp, Hanna Axelsson, Lars G.J. Hammarström, R. Schnell, Günter Schneider
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.pone.0043019
Structures of Human DPP7 Reveal the Molecular Basis of Specific Inhibition and the Architectural Diversity of Proline-Specific Peptidases
Cited by: 23
Author(s): G.A. Bezerra, E. Dobrovetsky, Aiping Dong, Almagul Seitova, Lissete Crombett, Lisa M. Shewchuk, Annie M. Hassell, Sharon Sweitzer, Thomas D. Sweitzer, Patrick McDevitt, Kyung Johanson, Karen M. Kennedy-Wilson, D. Cossar, A. Bochkarev, Karl Gruber, Sirano Dhe‐Paganon
Software Mentions: 2
Published: almost 12 years ago
10.1107/S0907444912039042
Structure of the catalytic domain of the<i>Salmonella</i>virulence factor SseI
Cited by: 16
Author(s): Shyam S. Bhaskaran, C. Erec Stebbins
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0160694
Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA
Cited by: 15
Author(s): Yinglu Zhang, Katarzyna Rataj, Gordon G. Simpson, Liang Tong
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0242686
Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ
Cited by: 12
Author(s): William C. Scott, Brian Lowrance, Alexander C Anderson, Joel T. Weadge
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0123195
An Unexpected Mode Of Binding Defines BMS948 as A Full Retinoic Acid Receptor β (RARβ, NR1B2) Selective Agonist
Cited by: 12
Author(s): Nadendla EswarKumar, Catherine Teyssier, V. Delfosse, Valérie Vivat, Krishnasamy Gunasekaran, Hinrich Gronemeyer, William Bourguet, Pierre Germain
Software Mentions: 2
Published: about 9 years ago
10.1016/j.bbapap.2017.08.005
Thermal sensitivity and flexibility of the Cε3 domains in immunoglobulin E
Cited by: 9
Author(s): K.A. Dore, Anna M. Davies, N. Drinkwater, Andrew J. Beavil, James M. McDonnell, Brian J. Sutton
Software Mentions: 2
Published: over 6 years ago
10.1107/S2059798315021683
<i>In meso in situ</i>serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures
Cited by: 89
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Nicole Howe, Lutz Vogeley, Xiangyu Liu, Rangana Warshamanage, T. Weinert, Ezequiel Panepucci, Brian K. Kobilka, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 2
Published: over 8 years ago
10.1016/j.bbabio.2018.03.014
Structure of the NDH-2 – HQNO inhibited complex provides molecular insight into quinone-binding site inhibitors
Cited by: 19
Author(s): J. Petri, Yosuke Shimaki, Wanting Jiao, Hannah R. Bridges, Euan R. Russell, E.J. Parker, D. Aragão, Gregory M. Cook, Yoshio Nakatani
Software Mentions: 2
Published: almost 6 years ago
10.1016/j.bbabio.2015.07.002
Calcium-induced conformational changes in the regulatory domain of the human mitochondrial ATP-Mg/Pi carrier
Cited by: 34
Author(s): Steven P. D. Harborne, Jonathan J. Ruprecht, Edmund R. S. Kunji
Software Mentions: 2
Published: over 8 years ago
10.1021/acs.biochem.1c00258
Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag
Cited by: 62
Author(s): Jonas Wilhelm, Stefanie F. Kühn, Mirosław Tarnawski, Guillaume Gotthard, Jana Tünnermann, Timo Tänzer, Iuliia A. Karpenko, Nicole Mertes, Lin Xue, Ulrike Uhrig, Jochen Reinstein, Julien Hiblot, Kai Johnsson
Software Mentions: 2
Published: almost 3 years ago
10.1107/S1399004715017927
<i>MeshAndCollect</i>: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines
Cited by: 104
Author(s): U. Zander, Gleb Bourenkov, А. Н. Попов, Daniele de Sanctis, Olof Svensson, A.A. McCarthy, Ekaterina Round, Valentin Gordeliy, Christoph Mueller-Dieckmann, Gordon A. Leonard
Software Mentions: 2
Published: over 8 years ago
10.1042/BCJ20160791
Structure and lipid-binding properties of the kindlin-3 pleckstrin homology domain
Cited by: 39
Author(s): Ni Tien, Antreas C. Kalli, Fiona B. Naughton, Luke A. Yates, Omar Naneh, Mirijam Kozorog, Gregor Anderluh, Mark S. P. Sansom, Robert J.C. Gilbert
Software Mentions: 2
Published: over 7 years ago
10.1242/bio.037663
Development and validation of RdRp Screen, a crystallization screen for viral RNA-dependent RNA polymerases
Cited by: 8
Author(s): Federica Riccio, Sandeep K. Talapatra, Sally Oxenford, Richard Angell, Michela Mazzon, Frank Kozielski
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0200387
Discovery of fragments that target key interactions in the signal recognition particle (SRP) as potential leads for a new class of antibiotics
Cited by: 8
Author(s): Camilla Faoro, Lorna Wilkinson-White, Ann H. Kwan, Sandro F. Ataide
Software Mentions: 2
Published: almost 6 years ago
10.1155/2019/6125068
Structural Basis for the Selective Inhibition of Cdc2-Like Kinases by CX-4945
Cited by: 17
Author(s): Joo Youn Lee, Ji-Sook Yun, Woo‐Keun Kim, Hang-Suk Chun, Hyeonseok Jin, Sungchan Cho, Jeong Ho Chang
Software Mentions: 2
Published: almost 5 years ago
10.3390/biom10040615
Insight into the RssB-Mediated Recognition and Delivery of σs to the AAA+ Protease, ClpXP
Cited by: 10
Author(s): Dimce Micevski, Kornelius Zeth, Terrence D. Mulhern, Verena J. Schuenemann, Jessica E. Zammit, Kaye N. Truscott, David A. Dougan
Software Mentions: 2
Published: about 4 years ago
10.3390/biom9060221
The Role of a Key Amino Acid Position in Species-Specific Proteinaceous dUTPase Inhibition
Cited by: 3
Author(s): András Benedek, Fanni Temesváry-Kis, Tamjidmaa Khatanbaatar, Ibolya Leveles, Éva Viola Surányi, J. Szabó, Lívius Wunderlich, Beáta G. Vértessy
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pone.0006820
The Crystal Structure of the Escherichia coli Autoinducer-2 Processing Protein LsrF
Cited by: 17
Author(s): Zamia Diaz, Karina B. Xavier, Stephen T. Miller
Software Mentions: 2
Published: almost 15 years ago
10.3390/biom10091239
N-Terminal Segment of TvCyP2 Cyclophilin from Trichomonas vaginalis Is Involved in Self-Association, Membrane Interaction, and Subcellular Localization
Cited by: 2
Author(s): Sarita Aryal, Heng-Ming Hsu, Yuan‐Chao Lou, Chien-Hsin Chu, Jung-Hsiang Tai, Chun‐Hua Hsu, Chinpan Chen
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0020420
VPS29 Is Not an Active Metallo-Phosphatase but Is a Rigid Scaffold Required for Retromer Interaction with Accessory Proteins
Cited by: 52
Author(s): James Swarbrick, Daniel Shaw, Sandeep Chhabra, Rajesh Ghai, Eugene Valkov, Suzanne J. Norwood, Matthew N. Seaman, Brett M. Collins
Software Mentions: 2
Published: about 13 years ago
10.1371/journal.pone.0165917
Crystal Structures of Group B Streptococcus Glyceraldehyde-3-Phosphate Dehydrogenase: Apo-Form, Binary and Ternary Complexes
Cited by: 14
Author(s): Norbert Schormann, Chapelle A. Ayres, Fry Alexandra, Todd Green, Surajit Banerjee, Glen C. Ulett, Debasish Chattopadhyay
Software Mentions: 2
Published: over 7 years ago
10.1107/S1399004714025188
Analysis of the HindIII-catalyzed reaction by time-resolved crystallography
Cited by: 2
Author(s): Takashi Kawamura, Tomoki Kobayashi, Nobuhisa Watanabe
Software Mentions: 2
Published: over 9 years ago
10.3390/biom11070996
Crystal Structure Reveals the Full Ras–Raf Interface and Advances Mechanistic Understanding of Raf Activation
Cited by: 28
Author(s): Trinity Cookis, Carla Mattos
Software Mentions: 2
Published: almost 3 years ago
10.3390/biom9030093
Structural Analysis of the 42 kDa Parvulin of Trypanosoma brucei
Cited by: 0
Author(s): Edisa Rehic, Dana Hoenig, Bianca Kamba, Anna Goehring, Eckhard Hofmann, Raphael Gasper, Anja Matena, Peter Bayer
Software Mentions: 2
Published: about 5 years ago
10.1042/BCJ20180867
Solution structures and biophysical analysis of full-length group A PAKs reveal they are monomeric and auto-inhibited in <i>cis</i>
Cited by: 10
Author(s): F.J. Sorrell, Lena Marie Kilian, J.M. Elkins
Software Mentions: 2
Published: about 5 years ago
10.1107/S2059798319009574
Biochemical and structural explorations of α-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction
Cited by: 4
Author(s): Hsien‐Wei Yeh, Kuan Hung Lin, S.Y. Lyu, Yi Shan Li, Chun Man Huang, Yung Lin Wang, Hao Wei Shih, N.S. Hsu, Chang Jer Wu, Tsung Lin Li
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pone.0221226
Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor
Cited by: 39
Author(s): John F. C. Steele, Richard K. Hughes, Mark J. Banfield
Software Mentions: 2
Published: almost 5 years ago
10.1107/S1399004715018519
Sent packing: protein engineering generates a new crystal form of<i>Pseudomonas aeruginosa</i>DsbA1 with increased catalytic surface accessibility
Cited by: 5
Author(s): Róisín M. McMahon, M. Coincon, Stephanie Tay, Begoña Heras, Craig J. Morton, M.J. Scanlon, Jennifer L. Martin
Software Mentions: 2
Published: over 8 years ago
10.1107/S2059798315021580
Using selenomethionyl derivatives to assign sequence in low-resolution structures of the AP2 clathrin adaptor
Cited by: 1
Author(s): Bernard T. Kelly, Stephen C. Graham, David J. Owen
Software Mentions: 2
Published: over 8 years ago
10.1016/j.bmc.2018.02.043
Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-β-lactamases
Cited by: 18
Author(s): D. Zhang, Marios S. Markoulides, Dmitrijs Stepanovs, Anna M. Rydzik, Ahmed El-Hussein, C. Bon, Jos J. A. G. Kamps, Klaus‐Daniel Umland, P. Collins, Samuel T. Cahill, D.Y. Wang, Frank von Delft, Jürgen Brem, McDonough, Christopher J. Schofield
Software Mentions: 2
Published: almost 6 years ago
10.1107/S205979831900175X
Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data
Cited by: 13
Author(s): Octav Caldararu, Francesco Manzoni, Esko Oksanen, D.T. Logan, Ulf Ryde
Software Mentions: 2
Published: about 5 years ago
10.1107/S205979831601723X
The N14 anti-afamin antibody Fab: a rare V<sub>L</sub>1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative<i>versus</i>enthusiastic modelling
Cited by: 10
Author(s): Andreas Naschberger, Barbara G. Fürnrohr, Tihana Lenac Roviš, Suzana Malić, Klaus Scheffzek, Hans Dieplinger, Bernhard Rupp
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0216979
Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis
Cited by: 2
Author(s): Ke Shi, Chong-Min Kyung, Kelly G. Aukema, Thomas Lee, Asim K. Bera, Jennifer L. Seffernick, Lawrence P. Wackett, Hideki Aihara
Software Mentions: 2
Published: almost 5 years ago
10.1107/S2059798318017047
The crystal structure of the<i>N</i>-acetylglucosamine 2-epimerase from<i>Nostoc</i>sp. KVJ10 reveals the true dimer
Cited by: 5
Author(s): Marie Josée Haglund Halsør, U. Rothweiler, Bjørn Altermark, Inger Lin Uttakleiv Ræder
Software Mentions: 2
Published: over 5 years ago
10.1042/BSR20170001
Crystal structure of thermostable alkylsulfatase SdsAP from <i>Pseudomonas sp. S9</i>
Cited by: 3
Author(s): Lifang Sun, Pu Chen, Su Y, Zhixiong Cai, Lingwei Ruan, Xun Xu, Yunkun Wu
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.pone.0032336
Myelin 2′,3′-Cyclic Nucleotide 3′-Phosphodiesterase: Active-Site Ligand Binding and Molecular Conformation
Cited by: 31
Author(s): Matti Myllykoski, Arne Raasakka, Huijong Han, Petri Kursula
Software Mentions: 2
Published: over 12 years ago
10.1107/S1399004714015788
Solving the RNA polymerase I structural puzzle
Cited by: 21
Author(s): María Moreno-Morcillo, Nicholas M. I. Taylor, Tim Gruene, Pierre Legrand, Umar Rashid, Federico M. Ruiz, Ulrich Steuerwald, Christoph W. Müller, Carlos Fernández‐Tornero
Software Mentions: 2
Published: over 9 years ago
10.1107/S2059798317018289
The deduced role of a chitinase containing two nonsynergistic catalytic domains
Cited by: 16
Author(s): Tian Liu, Weixing Zhu, Jing Wang, Yong Zhou, Yanwei Duan, Mingli Qu, Qing Yang
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0196642
Structure of frequency-interacting RNA helicase from Neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance
Cited by: 9
Author(s): Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean Johnson
Software Mentions: 2
Published: about 6 years ago
10.1042/BSR20150183
Epsilon glutathione transferases possess a unique class-conserved subunit interface motif that directly interacts with glutathione in the active site
Cited by: 10
Author(s): Jantana Wongsantichon, Robert Robinson, Albert J. Ketterman
Software Mentions: 2
Published: over 8 years ago
10.1107/S0907444910007493
Features and development of <i>Coot</i>
Cited by: 21,554
Author(s): Paul Emsley, Bernhard Lohkamp, William G. Scott, Kevin Cowtan
Software Mentions: 2
Published: about 14 years ago
10.1371/journal.pone.0154190
X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1) Reveals Features of Its Chitin Binding Domain
Cited by: 32
Author(s): Firas Fadel, Yuguang Zhao, A. Cousido-Siah, Francesc Xavier Ruiz, A. Mitschler, A. Podjarny
Software Mentions: 2
Published: about 8 years ago
10.1107/S0907444911014302
Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain
Cited by: 7
Author(s): Gretchen Meinke, Paul J. Phelan, Amélie Fradet-Turcotte, Jacques Archambault, Peter A. Bullock
Software Mentions: 2
Published: about 13 years ago
10.1107/S2059798315023116
Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects
Cited by: 11
Author(s): Christian Reichen, Chaithanya Madhurantakam, Simon Hansen, Markus G. Grütter, Andreas Plückthun, Peer R. E. Mittl
Software Mentions: 2
Published: over 8 years ago
10.1042/BSR20193360
The Trp triad within the V-domain of the receptor for advanced glycation end products modulates folding, stability and ligand binding
Cited by: 2
Author(s): Venkata S.K. Indurthi, Jaime L. Jensen, Estelle Leclerc, Sangita C. Sinha, Christopher L. Colbert, Stefan Vetter
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0191610
Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii
Cited by: 1
Author(s): Bhumika S. Shah, Heather E. Ashwood, S.J. Harrop, Daniel N. Farrugia, Ian T. Paulsen, Bridget C. Mabbutt
Software Mentions: 2
Published: over 6 years ago
10.1107/S2059798318009397
High-pressure protein crystal structure analysis of <i>Escherichia coli</i> dihydrofolate reductase complexed with folate and NADP<sup>+</sup>
Cited by: 16
Author(s): T. Nagae, Hiroyuki Yamada, Nobuhisa Watanabe
Software Mentions: 2
Published: almost 6 years ago
10.1186/s13068-019-1449-0
An actinobacteria lytic polysaccharide monooxygenase acts on both cellulose and xylan to boost biomass saccharification
Cited by: 30
Author(s): Thamy Lívia Ribeiro Corrêa, Atílio Tomazini Júnior, L. D. Wolf, Marcos Silveira Buckeridge, Leandro Vieira dos Santos, Mário Tyago Murakami
Software Mentions: 2
Published: about 5 years ago
10.1107/S2059798319010027
Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX
Cited by: 11
Author(s): Katarina Koruza, Bénédicte Lafumat, Maria Nyblom, Brian P. Mahon, Wolfgang Knecht, Robert McKenna, S.Z. Fisher
Software Mentions: 2
Published: almost 5 years ago
10.1107/S139900471400830X
Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site
Cited by: 35
Author(s): Thanuja Gangi Setty, Christine Cho, Sowmya Govindappa, Michael A. Apicella, S. Ramaswamy
Software Mentions: 2
Published: almost 10 years ago
10.1042/BCJ20200368
Antitoxin autoregulation of <i>M. tuberculosis</i> toxin-antitoxin expression through negative cooperativity arising from multiple inverted repeat sequences
Cited by: 8
Author(s): Izaak N Beck, B. F. Usher, Hannah G Hampton, Peter C. Fineran, Tim R. Blower
Software Mentions: 2
Published: almost 4 years ago
10.1042/BCJ20200128
Nek7 conformational flexibility and inhibitor binding probed through protein engineering of the R-spine
Cited by: 10
Author(s): Matthew J. Byrne, Nazia Nasir, Christine Basmadjian, Chitra Bhatia, Rory F. Cunnison, Katherine H. Carr, Corine Mas-Droux, Sharon Yeoh, Céline Cano, Richard Bayliss
Software Mentions: 2
Published: about 4 years ago
10.1186/s13068-017-1009-4
Determination of the native features of the exoglucanase Cel48S from Clostridium thermocellum
Cited by: 21
Author(s): Yajun Li, Shiyue Liu, Sheng Dong, Renmin Li, Yingang Feng, Qiu Cui
Software Mentions: 2
Published: over 6 years ago
10.1107/S2059798319011938
The flavin mononucleotide cofactor in α-hydroxyacid oxidases exerts its electrophilic/nucleophilic duality in control of the substrate-oxidation level
Cited by: 2
Author(s): S.Y. Lyu, Kuan Hung Lin, Hsien‐Wei Yeh, Yi Shan Li, Chun Man Huang, Yung Lin Wang, Hao Wei Shih, N.S. Hsu, Chang Jer Wu, Tsung Lin Li
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0064901
Conserved Inhibitory Mechanism and Competent ATP Binding Mode for Adenylyltransferases with Fic Fold
Cited by: 33
Author(s): A. Goepfert, Frédéric V. Stanger, Christoph Dehio, Tilman Schirmer
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pone.0206709
The three dimensional structure of Bovine Salivary Protein 30b (BSP30b) and its interaction with specific rumen bacteria
Cited by: 1
Author(s): Heng Zhang, Judith Burrows, G.L. Card, Graeme T. Attwood, Tom T. Wheeler, Vickery L. Arcus
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0224689
Structural analysis of the manganese transport regulator MntR from Bacillus halodurans in apo and manganese bound forms
Cited by: 2
Author(s): Myeong Yeon Lee, Jun Young Lee, Hyun Kyu Joo, Kang Hwa Jeong, Jae Young Lee
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0036526
Structural Analyses of the Slm1-PH Domain Demonstrate Ligand Binding in the Non-Canonical Site
Cited by: 21
Author(s): K. Anand, Kenji Maeda, Anne‐Claude Gavin
Software Mentions: 2
Published: about 12 years ago
10.1371/journal.pone.0010504
Designed Inhibitors of Insulin-Degrading Enzyme Regulate the Catabolism and Activity of Insulin
Cited by: 94
Author(s): Malcolm A. Leissring, E. Malito, Sabrine Hedouin, Lael Reinstatler, Tomoko Sahara, Samer O. Abdul-Hay, Shakeel Choudhry, Ghulam M. Maharvi, Abdul H. Fauq, Malwina Huzarska, Philip S. May, Sung‐Woon Choi, Todd Logan, Benjamin E. Turk, Lewis C. Cantley, Marika Manolopoulou, Wei-Jen Tang, Ross L. Stein, Gregory D. Cuny, Dennis J. Selkoe
Software Mentions: 2
Published: about 14 years ago
10.1042/BCJ20160806
<i>Neisseria meningitidis</i> factor H-binding protein bound to monoclonal antibody JAR5: implications for antibody synergy
Cited by: 18
Author(s): E. Malito, Paola Lo Surdo, Daniele Veggi, Laura Santini, Heather Stefek, Brunella Brunelli, Enrico Luzzi, Matthew J. Bottomley, Peter T. Beernink, María Scarselli
Software Mentions: 2
Published: over 7 years ago
10.1107/S139900471501857X
Native sulfur/chlorine SAD phasing for serial femtosecond crystallography
Cited by: 50
Author(s): Takanori Nakane, Changyong Song, Mamoru Suzuki, Eriko Nango, Jun Kobayashi, Tetsuya Masuda, Shiro Inoue, Eiichi Mizohata, Toru Nakatsu, Tomoyuki Tanaka, Rie Tanaka, Tatsuro Shimamura, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, So Iwata, Michihiro Sugahara
Software Mentions: 2
Published: over 8 years ago
10.1107/S2059798319006831
Structural and functional characterization of CMP-<i>N</i>-acetylneuraminate synthetase from<i>Vibrio cholerae</i>
Cited by: 1
Author(s): Sucharita Bose, Debayan Purkait, Deepthi Joseph, Vinod Nayak, Ramaswamy Subramanian
Software Mentions: 2
Published: about 5 years ago
10.26508/lsa.202000873
A conserved PI(4,5)P2–binding domain is critical for immune regulatory function of DOCK8
Cited by: 8
Author(s): Tetsuya Sakurai, Mutsuko Kukimoto-Niino, Kazufumi Kunimura, Nana Yamane, Daiji Sakata, Ryosuke Aihara, Tomoharu Yasuda, Shigeyuki Yokoyama, Mikako Shirouzu, Yoshihiro Fukui, Takehito Uruno
Software Mentions: 2
Published: over 3 years ago
10.26508/lsa.202000776
Structure of human Dispatched-1 provides insights into Hedgehog ligand biogenesis
Cited by: 22
Author(s): Hongwen Chen, Yang Liu, Xiaochun Li
Software Mentions: 2
Published: almost 4 years ago
10.1107/S2059798318013347
Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space
Cited by: 23
Author(s): Brendan Sullivan, Rick Archibald, Patricia S. Langan, Holger Dobbek, Martin Bommer, Robert L. McFeeters, Leighton Coates, Xiaoping Wang, Franz X. Gallmeier, J.M. Carpenter, V. E. Lynch, Paul Langan
Software Mentions: 2
Published: over 5 years ago
10.1107/S2059798319010878
X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein
Cited by: 17
Author(s): Hiromi Yoshida, Katsuhiro Kojima, Masaki Shiota, Keiichi Yoshimatsu, Tomohiko Yamazaki, Stefano Ferri, Wakako Tsugawa, Shigehiro Kamitori, Koji Sode
Software Mentions: 2
Published: almost 5 years ago
10.1016/j.matbio.2017.02.002
Structural and functional analysis of two small leucine-rich repeat proteoglycans, fibromodulin and chondroadherin
Cited by: 31
Author(s): Patricia Paracuellos, Sebastian Kalamajski, Arkadiusz Bonna, Dominique Bihan, Richard W. Farndale, Erhard Hohenester
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0048742
New Insights into the Hendra Virus Attachment and Entry Process from Structures of the Virus G Glycoprotein and Its Complex with Ephrin-B2
Cited by: 30
Author(s): Kai Xu, Yee-Peng Chan, Kanagalaghatta R. Rajashankar, Dimple Khetawat, Lianying Yan, Momchil V. Kolev, Christopher C. Broder, Dimitar B. Nikolov
Software Mentions: 2
Published: over 11 years ago
10.1107/S205979831801519X
Iron–sulfur clusters have no right angles
Cited by: 15
Author(s): Nigel W. Moriarty, Paul D. Adams
Software Mentions: 2
Published: over 5 years ago
10.1186/1472-6807-13-30
Crystal structure of the γ-hydroxymuconic semialdehyde dehydrogenase from Pseudomonas sp. strainWBC-3, a key enzyme involved in para-Nitrophenol degradation
Cited by: 3
Author(s): Jing Su, Cong Zhang, Junjie Zhang, Tian‐Ran Wei, Deyu Zhu, Ning‐Yi Zhou, Lin Gu
Software Mentions: 2
Published: over 10 years ago
10.1186/s12934-019-1190-1
Structural and functional characterization of a novel cold-active S-formylglutathione hydrolase (SfSFGH) homolog from Shewanella frigidimarina, a psychrophilic bacterium
Cited by: 11
Author(s): Chang Woo Lee, Woo-Kyoung Yoo, Sunha Park, Ly Le, Chang-Sung Jeong, Bum Han Ryu, Seung Chul Shin, Han-Woo Kim, Hyun Park, Kyeong Kyu Kim, T. Doohun Kim, Jun Hyuck Lee
Software Mentions: 2
Published: almost 5 years ago
10.1107/S2059798318005764
From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation
Cited by: 6
Author(s): Pavel V. Afonine, Paul D. Adams, Alexandre Urzhumtsev
Software Mentions: 2
Published: almost 6 years ago
10.1016/j.cell.2019.12.006
In Situ Structure of an Intact Lipopolysaccharide-Bound Bacterial Surface Layer
Cited by: 73
Author(s): Andriko von Kügelgen, Haiping Tang, Gail G. Hardy, Danguole Kureisaite-Ciziene, Yves V. Brun, Phillip J. Stansfeld, Carol V. Robinson, Tanmay A. M. Bharat
Software Mentions: 2
Published: over 4 years ago
10.1107/S2059798317006349
Crystal structure of<i>Yersinia pestis</i>virulence factor YfeA reveals two polyspecific metal-binding sites
Cited by: 14
Author(s): C.D. Radka, Lawrence J. DeLucas, Landon Wilson, Matthew B. Lawrenz, Robert D. Perry, Stephen G. Aller
Software Mentions: 2
Published: almost 7 years ago
10.1107/S1399004714018732
Structural basis for the recognition of muramyltripeptide by<i>Helicobacter pylori</i>Csd4, a<scp>D</scp>,<scp>L</scp>-carboxypeptidase controlling the helical cell shape
Cited by: 19
Author(s): Hyoun Sook Kim, Jieun Kim, Ha Na Im, Doo Ri An, Mijoon Lee, Dušan Hesek, Shahriar Mobashery, Jin Young Kim, Kun Cho, Hye Jin Yoon, Byung Woo Han, Byung Il Lee, Se Won Suh
Software Mentions: 2
Published: over 9 years ago
10.1107/S1399004715001443
Structure of the N-terminal domain of the protein Expansion: an `Expansion' to the Smad MH2 fold
Cited by: 8
Author(s): Mads Beich-Frandsen, Eric Aragón, Marta Llimargas, J. Benach, Antoni Riéra, Joan Pous, María J. Macias
Software Mentions: 2
Published: about 9 years ago
10.1186/1472-6807-12-7
Crystal structure of a new benzoic acid inhibitor of influenza neuraminidase bound with a new tilt induced by overpacking subsite C6
Cited by: 10
Author(s): Lalitha Venkatramani, Eric S. Johnson, Gundurao Kolavi, Gillian M. Air, Wayne J. Brouillette, Blaine H. M. Mooers
Software Mentions: 2
Published: about 12 years ago
10.1107/S1399004714006439
Structural and functional analysis of the human spliceosomal DEAD-box helicase Prp28
Cited by: 17
Author(s): Sina Möhlmann, Rebecca Mathew, Piotr Neumann, Andreas Schmitt, Reinhard Lührmann, Ralf Ficner
Software Mentions: 2
Published: about 10 years ago