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

Papers Mentioning PHENIX 2,287

10.3389/fmicb.2018.01468
Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase From Shigella flexneri
Cited by: 15
Author(s): Xiaopan Gao, Zhixia Mu, Xia Yu, Bo Qin, Justyna Aleksandra Wojdyla, Meitian Wang, Sheng Cui
Software Mentions: 2
Published: over 6 years ago
10.3390/molecules25102404
Structural Basis for Broad Substrate Selectivity of Alcohol Dehydrogenase YjgB from Escherichia coli
Cited by: 2
Author(s): Giang T. Nguyen, Yeon-Gil Kim, Joo‐Myung Ahn, Jeong Ho Chang
Software Mentions: 2
Published: over 4 years ago
10.1016/j.cell.2021.03.055
Antibody evasion by the P.1 strain of SARS-CoV-2
Cited by: 480
Author(s): Wanwisa Dejnirattisai, Daming Zhou, Piyada Supasa, C Liu, Alexander J. Mentzer, H. Ginn, Yuguang Zhao, Duyvesteyn Hme., Aekkachai Tuekprakhon, Rungtiwa Nutalai, Beibei Wang, César López-Camacho, J Slon-Campos, Thomas S. Walter, Donal Skelly, Sue Ann Costa Clemens, Felipe Gomes Naveca, Valdinete Alves do Nascimento, Felipe Franco Nascimento, Cristiano Fernandes da Costa, Paola Cristina Resende, Alex Pauvolid‐Corrêa, Marilda Mendonça Siqueira, Christina Dold, Robert H. Levin, 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, Miles W. Carroll, Paul Klenerman, Eleanor Barnes, Susanna Dunachie, Neil G. Paterson, Mark A. Williams, ' Hall, Ruben J.G. Hulswit, Thomas A. Bowden, Elizabeth E. Fry, Juthathip Mongkolsapaya, Jingshan Ren, D.I. Stuart, Gavin Screaton
Software Mentions: 2
Published: over 3 years ago
10.1016/j.cell.2018.10.037
Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design
Cited by: 52
Author(s): Yin Dong, Hua Wang, A.C.W. Pike, Stephen A. Cochrane, Sadra Hamedzadeh, Filip J. Wyszyński, S.R. Bushell, Sylvain Royer, David A. Widdick, Andaleeb Sajid, Helena I. Boshoff, Yumi Park, Ricardo Dantas de Lucas, Weimin Liu, Seung Seo Lee, Takuya Machida, Leanne Minall, Shahid Mehmood, Katsiaryna Belaya, Weiwei Liu, Amy Chu, L. Shrestha, Shubhashish M.M. Mukhopadhyay, Claire Strain-Damerell, R. Chalk, N. Burgess-Brown, Mervyn J. Bibb, Clifton E. Barry, Carol V. Robinson, David Beeson, Benjamin G. Davis, E.P. Carpenter
Software Mentions: 2
Published: about 6 years ago
10.3389/fmolb.2017.00068
Structure and Interactions of the TPR Domain of Sgt2 with Yeast Chaperones and Ybr137wp
Cited by: 18
Author(s): E. Krysztofinska, N.J. Evans, Arjun Thapaliya, James W. Murray, Rhodri M. L. Morgan, Santiago Martínez-Lumbreras, Rivka L. Isaacson
Software Mentions: 2
Published: about 7 years ago
10.3389/fphar.2019.00474
Crystal Structure of the Monomeric Extracellular Domain of α9 Nicotinic Receptor Subunit in Complex With α-Conotoxin RgIA: Molecular Dynamics Insights Into RgIA Binding to α9α10 Nicotinic Receptors
Cited by: 38
Author(s): Marios Zouridakis, Athanasios Papakyriakou, Igor A. Ivanov, Igor E. Kasheverov, Victor I. Tsetlin, Socrates J. Tzartos, Petros Giastas
Software Mentions: 2
Published: over 5 years ago
10.1107/S2059798316016910
Strategies for carbohydrate model building, refinement and validation
Cited by: 45
Author(s): Jon Agirre
Software Mentions: 2
Published: almost 8 years ago
10.3389/fphys.2013.00320
The N-terminal cytoplasmic region of NCBE displays features of an intrinsic disordered structure and represents a novel target for specific drug screening
Cited by: 3
Author(s): Kaare Bjerregaard-Andersen, Harmonie Perdreau‐Dahl, Hanne Guldsten, Jeppe Prætorius, Jan K. Jensen, J. Preben Morth
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0034918
Insights into the Mechanism of Bovine CD38/NAD+Glycohydrolase from the X-Ray Structures of Its Michaelis Complex and Covalently-Trapped Intermediates
Cited by: 20
Author(s): Pascal F. Egea, Hélène Muller-Steffner, Isabelle Kuhn, Céline Cakir-Kiefer, Norman J. Oppenheimer, Robert M. Stroud, Esther Kellenberger, Francis Schuber
Software Mentions: 2
Published: over 12 years ago
10.3389/fpls.2018.01737
Expanding the Plant GSTome Through Directed Evolution: DNA Shuffling for the Generation of New Synthetic Enzymes With Engineered Catalytic and Binding Properties
Cited by: 10
Author(s): Evangelia Chronopoulou, Anastassios C. Papageorgiou, Farid S. Ataya, Irini Nianiou-Obeidat, Panagiotis Madesis, Nikolaos E. Labrou
Software Mentions: 2
Published: almost 6 years ago
10.3390/molecules23071538
Crystal Structure of LSD1 in Complex with 4-[5-(Piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile
Cited by: 18
Author(s): Hideaki Niwa, Shin Sato, Tomoko Hashimoto, Kenji Matsuno, Takashi Umehara
Software Mentions: 2
Published: over 6 years ago
10.1107/S1399004715009438
High-resolution crystal structures of the solubilized domain of porcine cytochrome<i>b</i><sub>5</sub>
Cited by: 3
Author(s): Yu Hirano, Shigenobu Kimura, Taro Tamada
Software Mentions: 2
Published: over 9 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: about 5 years ago
10.1107/S2059798319008933
Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data
Cited by: 0
Author(s): Laurel Jones, Michael Tynes, Paul Smith
Software Mentions: 2
Published: over 5 years ago
10.1155/2012/721869
Crystal Structure of a 9-Subunit Archaeal Exosome in Pre-Catalytic States of the Phosphorolytic Reaction
Cited by: 19
Author(s): Esben Lorentzen, Elena Conti
Software Mentions: 2
Published: almost 13 years ago
10.1007/s00253-014-6015-x
Biochemical and structural characterization of a thermostable β-glucosidase from Halothermothrix orenii for galacto-oligosaccharide synthesis
Cited by: 57
Author(s): Noor Hassan, Thu Hà Nguyễn, Montira Intanon, Lokesh D. Kori, Bharat K. C. Patel, Dietmar Haltrich, Christina Divne, T.C. Tan
Software Mentions: 2
Published: about 10 years ago
10.1107/S0907444911047834
Use of knowledge-based restraints in <i>phenix.refine</i> to improve macromolecular refinement at low resolution
Cited by: 213
Author(s): Jeffrey J. Headd, Nathaniel Echols, Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Vincent B. Chen, Nigel W. Moriarty, David C. Richardson, Jane S. Richardson, Paul D. Adams
Software Mentions: 2
Published: over 12 years ago
10.3390/cancers12061412
A H-REV107 Peptide Inhibits Tumor Growth and Interacts Directly with Oncogenic KRAS Mutants
Cited by: 10
Author(s): Chang Woo Han, Mi Suk Jeong, Soonhoi Ha, Se Bok Jang
Software Mentions: 2
Published: over 4 years ago
10.1107/S2059798318006356
Crystal structure of the spliceosomal DEAH-box ATPase Prp2
Cited by: 21
Author(s): Andreas Schmitt, Florian Hamann, Piotr Neumann, Ralf Ficner
Software Mentions: 2
Published: over 6 years ago
10.1128/AEM.01692-19
Crystal Structure of the Catalytic and Cytochrome <i>b</i> Domains in a Eukaryotic Pyrroloquinoline Quinone-Dependent Dehydrogenase
Cited by: 15
Author(s): Kouta Takeda, Takuya Ishida, Makoto Yoshida, Masahiro Samejima, Hiroyuki Ohno, Kiyohiko Igarashi, Nobuhumi Nakamura
Software Mentions: 2
Published: almost 5 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: over 11 years ago
10.1111/mmi.12656
The structure, function and properties of sirohaem decarboxylase - an enzyme with structural homology to a transcription factor family that is part of the alternative haem biosynthesis pathway
Cited by: 14
Author(s): David J. Palmer, Susanne Schroeder, Andrew D. Lawrence, Evelyne Deery, Susana A.L. Lobo, Lı́gia M. Saraiva, Kirsty J. McLean, Andrew W. Munro, Stuart J. Ferguson, Richard W. Pickersgill, David G. Brown, Martin J. Warren
Software Mentions: 2
Published: over 10 years ago
10.1107/S2059798319010866
Structures of the substrate-binding protein YfeA in apo and zinc-reconstituted holo forms
Cited by: 8
Author(s): C.D. Radka, Shaunivan Labiuk, Lawrence J. DeLucas, Stephen G. Aller
Software Mentions: 2
Published: over 5 years ago
10.1107/S1399004715002308
Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array
Cited by: 67
Author(s): A.Y. Lyubimov, Thomas D. Murray, Antoine Koehl, Ismail Emre Araci, Monarin Uervirojnangkoorn, Oliver B. Zeldin, Aina E. Cohen, S. Michael Soltis, E.L. Baxter, Aaron S. Brewster, Nicholas K. Sauter, Axel T. Brunger, James M. Berger
Software Mentions: 2
Published: over 9 years ago
10.1186/1743-422X-7-359
Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives
Cited by: 40
Author(s): Timothy C. Mueser, Jennifer M. Hinerman, Juliette M. Devos, Ryan A Boyer, Kandace J. Williams
Software Mentions: 2
Published: almost 14 years ago
10.1107/S2053230X14003355
A range of C∊3–C∊4 interdomain angles in IgE Fc accommodate binding to its receptor CD23
Cited by: 13
Author(s): B. Dhaliwal, M.O.Y. Pang, Daopeng Yuan, Andrew J. Beavil, Brian J. Sutton
Software Mentions: 2
Published: almost 11 years ago
10.1107/S0907444911007888
Structure of HLA-A*0301 in complex with a peptide of proteolipid protein: insights into the role of HLA-A alleles in susceptibility to multiple sclerosis
Cited by: 27
Author(s): Róisín M. McMahon, Lone Smidstrup Friis, Christian Siebold, Manuel A. Friese, Lars Fugger, E Y Jones
Software Mentions: 2
Published: over 13 years ago
10.1074/jbc.M115.685065
Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity
Cited by: 13
Author(s): Min‐Feng Hsu, Hsu Yuan Fu, Chun-Jie Cai, Hsiu-Pin Yi, Chii‐Shen Yang, Andrew H.-J. Wang
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pone.0074788
The Structural Basis of Erwinia rhapontici Isomaltulose Synthase
Cited by: 17
Author(s): Zheng Xu, Sha Li, Jie Li, Yan Li, Xiaohai Feng, Renxiao Wang, Hong Xu, Jiahai Zhou
Software Mentions: 2
Published: about 11 years ago
10.3390/cancers13020356
A Selective Competitive Inhibitor of Aldehyde Dehydrogenase 1A3 Hinders Cancer Cell Growth, Invasiveness and Stemness In Vitro
Cited by: 16
Author(s): Edoardo Luigi Maria Gelardi, Giorgia Colombo, Francesca Picarazzi, Davide M. Ferraris, Andrea Mangione, Giovanni Petrarolo, Eleonora Aronica, Menico Rizzi, Mattia Mori, Concettina La Motta, Silvia Garavaglia
Software Mentions: 2
Published: almost 4 years ago
10.1016/j.cell.2016.08.025
Structure of the Bacterial Sex F Pilus Reveals an Assembly of a Stoichiometric Protein-Phospholipid Complex
Cited by: 100
Author(s): Tiago Costa, Aravindan Ilangovan, Marta Ukleja, Adam Redzej, Joanne M. Santini, Terry Smith, Edward H. Egelman, Gabriel Waksman
Software Mentions: 2
Published: about 8 years ago
10.3390/v9110321
Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction
Cited by: 6
Author(s): Nikéa Pittman, Adam Misseldine, Lorena Geilen, Sujata Halder, J. W. G. Smith, Justin Kurian, Paul R. Chipman, Mandy E.W. Janssen, Robert McKenna, Timothy S. Baker, Anthony D’Abramo, Susan F. Cotmore, Peter Tattersall, Mavis Agbandje‐McKenna
Software Mentions: 2
Published: about 7 years ago
10.1107/S2053230X17006021
Crystal structures of human Fabs targeting the Bexsero meningococcal vaccine antigen NHBA
Cited by: 4
Author(s): Martina Maritan, Roberta Cozzi, Paola Lo Surdo, Daniele Veggi, Matthew J. Bottomley, E. Malito
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0231513
Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121
Cited by: 8
Author(s): Keita Saito, Alexander Holm Viborg, Shiho Sakamoto, T. Arakawa, Chihaya Yamada, Kiyotaka Fujita, Shinya Fushinobu
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0062021
Structure of the Non-Catalytic Domain of the Protein Disulfide Isomerase-Related Protein (PDIR) Reveals Function in Protein Binding
Cited by: 20
Author(s): R. Vinaik, Guennadi Kozlov, Kalle Gehring
Software Mentions: 2
Published: over 11 years ago
10.1107/S0907444912017453
Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with<i>PrimeX</i>
Cited by: 19
Author(s): Jeffrey A. Bell, Kenneth L. Ho, Ramy Farid
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.ppat.1006714
A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase
Cited by: 15
Author(s): Isabelle Jupin, Maya Ayach, Lucile Jomat, Sonia Fieulaine, Stéphane Bressanelli
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.ppat.1006935
Structural basis for recognition of the central conserved region of RSV G by neutralizing human antibodies
Cited by: 45
Author(s): Harrison G. Jones, Tina Ritschel, Gabriel Pascual, Just P. J. Brakenhoff, Elissa Keogh, Polina Furmanova-Hollenstein, Ellen Lanckacker, Jehangir S. Wadia, M.S.A. Gilman, R. Anthony Williamson, Dirk Roymans, Angélique B. van ’t Wout, Johannes P. M. Langedijk, Jason S. McLellan
Software Mentions: 2
Published: over 6 years ago
10.3390/antiox7120171
Crystal Structure of Chloroplastic Thioredoxin f2 from Chlamydomonas reinhardtii Reveals Distinct Surface Properties
Cited by: 16
Author(s): Stéphane D. Lemaire, Daniele Tedesco, Pierre Crozet, Laure Michelet, Simona Fermani, Mirko Zaffagnini, Julien Henri
Software Mentions: 2
Published: about 6 years ago
10.1107/S1399004714019725
Structural characterization of the virulence factor nuclease A from<i>Streptococcus agalactiae</i>
Cited by: 7
Author(s): A.F. Moon, Philippe Gaudu, Lars C. Pedersen
Software Mentions: 2
Published: about 10 years ago
10.3390/v12121346
Structural Basis of Zika Virus Specific Neutralization in Subsequent Flavivirus Infections
Cited by: 7
Author(s): Madhumati Sevvana, Thomas F. Rogers, Andrew Miller, Feng Long, Thomas Klose, Nathan Beutler, Yu-Cheng Lai, Mara Parren, Laura M. Walker, Geeta Buda, Dennis R. Burton, Michael G. Rossmann, Richard Kühn
Software Mentions: 2
Published: almost 4 years ago
10.1107/S2053230X19006472
Structure of the Prx6-subfamily 1-Cys peroxiredoxin from <i>Sulfolobus islandicus</i>
Cited by: 5
Author(s): Sander Stroobants, Inge Van Molle, Queen Saidi, Karl Jonckheere, Dominique Maes, Eveline Peeters
Software Mentions: 2
Published: over 5 years ago
10.1107/S2059798315024110
Data-collection strategy for challenging native SAD phasing
Cited by: 40
Author(s): V. Oliéric, T. Weinert, Aaron D. Finke, Carolin Anders, Dianfan Li, Natacha Olieric, Camelia N. Borca, Michel O. Steinmetz, Martin Caffrey, Martin Jinek, Meitian Wang
Software Mentions: 2
Published: over 8 years ago
10.1107/S0907444913001479
Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data
Cited by: 79
Author(s): Qun Li, Qinglian Liu, Wayne A. Hendrickson
Software Mentions: 2
Published: over 11 years ago
10.3390/v13071374
Structural Investigation of Orf Virus Bcl-2 Homolog ORFV125 Interactions with BH3-Motifs from BH3-Only Proteins Puma and Hrk
Cited by: 3
Author(s): Chathura D. Suraweera, Mark G. Hinds, Marc Kvansakul
Software Mentions: 2
Published: over 3 years ago
10.3390/v13081495
Crystal Structure of a Retroviral Polyprotein: Prototype Foamy Virus Protease-Reverse Transcriptase (PR-RT)
Cited by: 3
Author(s): Jerry Joe Ebow Kingsley Harrison, Steve Tuske, Kalyan Kumar Das, Francesc Xavier Ruiz, J.D. Bauman, Paul L. Boyer, Jeffrey J. DeStefano, Stephen H. Hughes, Eddy Arnold
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0239702
SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique
Cited by: 7
Author(s): Timothy R. Stachowski, M. Elizabeth Snell, Edward H. Snell
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0090915
Crystal Structures of the Novel Cytosolic 5′-Nucleotidase IIIB Explain Its Preference for m7GMP
Cited by: 13
Author(s): Thomas Monecke, Juliane Buschmann, Piotr Neumann, Elmar Wahle, Ralf Ficner
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0178752
Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis
Cited by: 3
Author(s): Fabiola R. Calviño, Markus Kornprobst, Géza Schermann, Fabienne Birkle, Klemens Wild, Tamás Fischer, Ed Hurt, Yasar Luqman Ahmed, Irmgard Sinning
Software Mentions: 2
Published: over 7 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: almost 7 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: almost 12 years ago
10.1371/journal.pone.0175815
Biochemical and structural investigations on phosphoribosylpyrophosphate synthetase from Mycobacterium smegmatis
Cited by: 18
Author(s): Stefano Donini, Silvia Garavaglia, Davide M. Ferraris, Riccardo Miggiano, Shiro Mori, Keigo Shibayama, Menico Rizzi
Software Mentions: 2
Published: over 7 years ago
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: over 10 years ago
10.1073/pnas.1921245117
Ancient MAPK ERK7 is regulated by an unusual inhibitory scaffold required for <i>Toxoplasma</i> apical complex biogenesis
Cited by: 37
Author(s): Peter Back, William O’Shaughnessy, Andy S Moon, Pravin S Dewangan, Xiaoyu Hu, Jihui Sha, James A. Wohlschlegel, Peter J. Bradley, Michael L. Reese
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0122512
Crystal Structure of a Two-Subunit TrkA Octameric Gating Ring Assembly
Cited by: 2
Author(s): Marc C. Deller, Hope A. Johnson, Mitchell D. Miller, Glen Spraggon, Marc‐André Elsliger, Ian A. Wilson, Scott A. Lesley
Software Mentions: 2
Published: over 9 years ago
10.1073/pnas.2020486118
Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser
Cited by: 35
Author(s): Ji Hye Yun, Xuanxuan Li, Jianing Yue, Jae Hyun Park, Zeyu Jin, Chufeng Li, Hao Hu, Yingchen Shi, Suraj Pandey, Sergio Carbajo, Sébastien Boutet, Mark S. Hunter, Mao Liang, Raymond G. Sierra, Thomas J Lane, Liang Zhou, Uwe Weierstall, Nadia A. Zatsepin, Mio Ohki, J.R.H. Tame, Sam Yong Park, John C. H. Spence, Wenkai Zhang, Marius Schmidt, Weontae Lee, Haiguang Liu
Software Mentions: 2
Published: over 3 years ago
10.1107/S2053230X15003337
High-resolution crystal structure of a polyextreme GH43 glycosidase from<i>Halothermothrix orenii</i>with α-<scp>L</scp>-arabinofuranosidase activity
Cited by: 7
Author(s): Noor Hassan, Lokesh D. Kori, Rosaria Gandini, Bharat K. C. Patel, Christina Divne, T.C. Tan
Software Mentions: 2
Published: almost 10 years ago
10.1007/s11120-017-0450-3
Crystal structure of Psb27 from Arabidopsis thaliana determined at a resolution of 1.85 Å
Cited by: 7
Author(s): Xingxing Cheng, Jiuyang Liu, Huan Zhang, Fudong Li, Zhang Shuya, Min Xu, Ke Ruan, Yuhua Wang, Aigen Fu
Software Mentions: 2
Published: about 7 years ago
10.1107/S1399004714001850
A conformational landscape for alginate secretion across the outer membrane of<i>Pseudomonas aeruginosa</i>
Cited by: 44
Author(s): Jian Tan, Sarah L. Rouse, Dianfan Li, V.E. Pye, Lutz Vogeley, Alette Brinth, Toufic El Arnaout, John C. Whitney, P. Lynne Howell, Mark S. P. Sansom, Martin Caffrey
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0071835
Functional Mapping of Human Dynamin-1-Like GTPase Domain Based on X-ray Structure Analyses
Cited by: 60
Author(s): Julia Wenger, Eva Klinglmayr, Chris Fröhlich, Clarissa Eibl, Ana Gimeno, Manuel Hessenberger, Sandra Puehringer, Oliver Daumke, Peter Goettig
Software Mentions: 2
Published: over 11 years ago
10.1107/S2053230X15019986
Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking
Cited by: 28
Author(s): Tobias Rumpf, S. Gerhardt, Oliver Einsle, Manfred Jung
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.pbio.1000589
Structural Basis of Response Regulator Dephosphorylation by Rap Phosphatases
Cited by: 86
Author(s): Vijay Parashar, Nicolas Mirouze, David Dubnau, Matthew B. Neiditch
Software Mentions: 2
Published: almost 14 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: over 6 years ago
10.1107/S2053230X17008093
Crystal structure of a family 6 cellobiohydrolase from the basidiomycetePhanerochaete chrysosporium
Cited by: 8
Author(s): Mikako Tachioka, Akihiko Nakamura, Takuya Ishida, Kiyohiko Igarashi, Masahiro Samejima
Software Mentions: 2
Published: over 7 years ago
10.1107/S2053230X19009786
Crystal structure of the Schizosaccharomyces pombe U7BR E2-binding region in complex with Ubc7
Cited by: 1
Author(s): Z.S. Hann, Meredith B. Metzger, Allan M. Weissman, Christopher D. Lima
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pbio.1002480
The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation
Cited by: 39
Author(s): Sohail Khoshnevis, Isabel Askenasy, Matthew C. Johnson, Maria D. Dattolo, Crystal L. Young-Erdos, M. Elizabeth Stroupe, Katrin Karbstein
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0107000
Crystal Structure of the Mineralocorticoid Receptor DNA Binding Domain in Complex with DNA
Cited by: 39
Author(s): William Henry Hudson, Christine Youn, Eric A. Ortlund
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pone.0069833
An Activating Mutation Reveals a Second Binding Mode of the Integrin α2 I Domain to the GFOGER Motif in Collagens
Cited by: 29
Author(s): Federico Carafoli, Samir Hamaia, Dominique Bihan, Erhard Hohenester, Richard W. Farndale
Software Mentions: 2
Published: over 11 years ago
10.1107/S2059798318004357
On the application of the expected log-likelihood gain to decision making in molecular replacement
Cited by: 35
Author(s): Robert D. Oeffner, Pavel V. Afonine, Claudia Millán, Massimo Sammito, Isabel Usón, Randy J. Read, Airlie J. McCoy
Software Mentions: 2
Published: over 6 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: about 13 years ago
10.1371/journal.pone.0042473
Crystal Structures of the Network-Forming Short-Arm Tips of the Laminin β1 and γ1 Chains
Cited by: 51
Author(s): Federico Carafoli, Sadaf-Ahmahni Hussain, Erhard Hohenester
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0140984
Improving the pH-stability of Versatile Peroxidase by Comparative Structural Analysis with a Naturally-Stable Manganese Peroxidase
Cited by: 40
Author(s): Verónica Sáez-Jiménez, Elena Fernández‐Fueyo, F.J. Medrano, Antonio Romero, Ángel T. Martínez, Francisco J. Ruíz-Dueñas
Software Mentions: 2
Published: about 9 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: over 5 years ago
10.1371/journal.pone.0070518
Mcm10 Self-Association Is Mediated by an N-Terminal Coiled-Coil Domain
Cited by: 15
Author(s): Wenyue Du, Ajeetha Josephrajan, Suraj Adhikary, Timothy M. Bowles, Anja‐Katrin Bielinsky, Brandt F. Eichman
Software Mentions: 2
Published: over 11 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: over 5 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: 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: almost 11 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: over 14 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: over 13 years ago
10.1371/journal.pone.0064426
Crystal Structure of Crataeva tapia Bark Protein (CrataBL) and Its Effect in Human Prostate Cancer Cell Lines
Cited by: 19
Author(s): Rodrigo S. Ferreira, Dongwen Zhou, Joana Gasperazzo Ferreira, Mariana Cristina Cabral Silva, Rosemeire A. Silva-Lucca, Reinhard Mentele, Edgar Julian Paredes‐Gamero, Thiago Carlos Bertolin, Maria Tereza dos Santos Correia, Patrícia Maria Guedes Paiva, Alla Gustchina, Alexander Wlodawer, Maria Luíza Vilela Oliva
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0020950
Conformational Changes of rBTI from Buckwheat upon Binding to Trypsin: Implications for the Role of the P8′ Residue in the Potato Inhibitor I Family
Cited by: 13
Author(s): Long Wang, Fei Zhao, Mei Li, Hongmei Zhang, Yu Gao, Peng Cao, Xiaowei Pan, Zhuanhua Wang, Wenrui Chang
Software Mentions: 2
Published: over 13 years ago
10.1016/j.cell.2021.02.032
The antigenic anatomy of SARS-CoV-2 receptor binding domain
Cited by: 294
Author(s): Wanwisa Dejnirattisai, Daming Zhou, H. Ginn, Duyvesteyn Hme., Piyada Supasa, William James, Yuguang Zhao, Thomas S. Walter, Alexander J. Mentzer, Chang Liu, Beibei Wang, Guido C. Paesen, J Slon-Campos, César López-Camacho, Natasha M. Kafai, Adam L. Bailey, Rita E. Chen, Ying Bai, Craig Thompson, Jai S Bolton, Alex Fyfe, Sunetra Gupta, Tiong Kit Tan, Javier Gilbert‐Jaramillo, Michael Knight, Miles W. Carroll, Donal Skelly, Christina Dold, Yanchun Peng, Robert H. Levin, Tao Dong, Andrew J. Pollard, Julian C. Knight, Paul Klenerman, Nigel Temperton, David R. Hall, Mark A. Williams, Neil G. Paterson, Felicity K.R. Bertram, C. Alistair Siebert, Daniel K. Clare, Andrew Howe, Julika Radecke, Yun Song, Alain Townsend, Kuan Ying A. Huang, Elizabeth E. Fry, Juthathip Mongkolsapaya, Michael S. Diamond, Jingshan Ren, D.I. Stuart, Gavin Screaton
Software Mentions: 2
Published: over 3 years ago
10.1107/S1399004713030149
Identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex
Cited by: 29
Author(s): Jacob Lauwring Andersen, Tenna Juul Schrøder, Søren Christensen, Dorthe Strandbygård, Lone Tjener Pallesen, María García-Alai, Samsa Lindberg, Morten Langgård, Jørgen Eskildsen, Laurent David, Lena Tagmose, Klaus B. Simonsen, Philip Maltas, Lars Christian B. Rønn, Inge E.M. de Jong, Ibrahim Malik, Jan Egebjerg, Jens-Jacob Karlsson, U. Srinivas, Durga Rao Sakumudi, Pradheep Eradi, Steven P. Watson, Søren Thirup
Software Mentions: 2
Published: almost 11 years ago
10.1007/s00401-021-02336-w
Structure of Tau filaments in Prion protein amyloidoses
Cited by: 41
Author(s): Grace I. Hallinan, Md Rejaul Hoq, Manali Ghosh, Frank S. Vago, Anllely Fernández, Holly J. Garringer, Rubén Vidal, Wen Jiang, Bernardino Ghetti
Software Mentions: 2
Published: over 3 years ago
10.1107/S2059798316007907
Structural basis for acyl-group discrimination by human Gcn5L2
Cited by: 44
Author(s): Alison E. Ringel, Cynthia Wolberger
Software Mentions: 2
Published: over 8 years ago
10.1107/S1744309111019312
Conservation of a crystallographic interface suggests a role for β-sheet augmentation in influenza virus NS1 multifunctionality
Cited by: 9
Author(s): Philip S. Kerry, Eric C. Long, Margaret Taylor, Rosemary Russell
Software Mentions: 2
Published: over 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: 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: about 10 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: over 8 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: over 12 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: over 9 years ago
10.1371/journal.pntd.0004132
Structural and Functional Characterization of the Enantiomers of the Antischistosomal Drug Oxamniquine
Cited by: 18
Author(s): Alexander B. Taylor, Livia Pica‐Mattoccia, C. Polcaro, Enrica Donati, Xiaoguang Cao, Annalisa Basso, Алессандра Гуиди, Anastasia R. Rugel, S. Holloway, Timothy J. Anderson, P. John Hart, Donato Cioli, Philip T. LoVerde
Software Mentions: 2
Published: about 9 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: about 15 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: over 13 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: almost 4 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: about 14 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: about 5 years ago
10.1107/S090744491200251X
<i>JLigand</i>: a graphical tool for the <i>CCP</i>4 template-restraint library
Cited by: 353
Author(s): А. А. Лебедев, Paul G. Young, Michail N. Isupov, Olga V. Moroz, A.A. Vagin, Garib N. Murshudov
Software Mentions: 2
Published: over 12 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: over 8 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: over 5 years ago