cran: PHENIX | Projects | Ecosyste.ms: Papers

10.1016/j.str.2020.12.008

Using cryo-EM to understand antimycobacterial resistance in the catalase-peroxidase (KatG) from Mycobacterium tuberculosis
Cited by: 11
Author(s): Asma Munir, Michael T. Wilson, Steven W. Hardwick, Dimitri Y. Chirgadze, J.A.R. Worrall, Tom L. Blundell, Amanda K. Chaplin
Software Mentions: 2
Published: about 5 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: about 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 10 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: almost 13 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: over 7 years ago

10.1128/mBio.02660-18

Targeting Mannitol Metabolism as an Alternative Antimicrobial Strategy Based on the Structure-Function Study of Mannitol-1-Phosphate Dehydrogenase in Staphylococcus aureus
Cited by: 16
Author(s): Thanh H. Nguyen, Truc Kim, Hai Minh Ta, Won Sik Yeo, Joon‐Hwan Choi, Pushpak Mizar, Seung Seo Lee, Taeok Bae, Akhilesh Kumar Chaurasia, Kyeong Kyu Kim
Software Mentions: 2
Published: about 7 years ago

10.1128/mBio.01566-20

The Structure of the Cysteine-Rich Domain of Plasmodium falciparum P113 Identifies the Location of the RH5 Binding Site
Cited by: 5
Author(s): Ivan Campeotto, Francis Galaway, Shahid Mehmood, Lea Barfod, Doris Quinkert, Vinayaka Kotraiah, Timothy W. Phares, Katherine E. Wright, Ambrosius P. Snijders, Simon J. Draper, M.K. Higgins, Gavin J. Wright
Software Mentions: 2
Published: about 6 years ago

10.1007/s41048-018-0073-z

Significant expansion and red-shifting of fluorescent protein chromophore determined through computational design and genetic code expansion
Cited by: 6
Author(s): Li Wang, Xian Chen, Xuzhen Guo, Jiasong Li, Qi Liu, Fuying Kang, Xudong Wang, Cheng Hu, Haiping Li, Weimin Gong, Wei Zhuang, Liu Xiao-hong, Jiangyun Wang
Software Mentions: 2
Published: about 8 years ago

10.1128/mSphere.00108-21

Cryptic β-Lactamase Evolution Is Driven by Low β-Lactam Concentrations
Cited by: 16
Author(s): Christopher Fröhlich, João Alves Gama, Klaus Harms, Viivi H. A. Hirvonen, Bjarte Aarmo Lund, Marc W. van der Kamp, Pål Jarle Johnsen, Ørjan Samuelsen, Hanna‐Kirsti S. Leiros
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 11 years ago

10.1107/S2052252518013854

Structure-based mechanism of action of a viral poly(ADP-ribose) polymerase 1-interacting protein facilitating virus replication
Cited by: 7
Author(s): Woo Chang Chung, Junsoo Kim, Byung Chul Kim, Hye Ri Kang, Jonghyeon Son, Hosam Ki, Kwang Yeon Hwang, Mee Hyun Song
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0167755

Biophysical Studies of the Induced Dimerization of Human VEGF Receptor 1 Binding Domain by Divalent Metals Competing with VEGF-A
Cited by: 10
Author(s): Jonathan Gaucher, Marie Reille‐Seroussi, Nathalie Gagey‐Eilstein, Sylvain Broussy, Pascale Coric, Bili Seijo, Marie-Bernard Lascombe, Benoît Gautier, Wang-Quing Liu, Florent Huguenot, Nicolas Inguimbert, Serge Bouaziz, Michel Vidal, Isabelle Broutin
Software Mentions: 2
Published: almost 10 years ago

10.1107/S2052252518018274

A cytosine modification mechanism revealed by the structure of a ternary complex of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate
Cited by: 4
Author(s): Si Hoon Park, Se Won Suh, Hyun Kyu Song
Software Mentions: 2
Published: almost 8 years ago

10.1107/S2052252518001616

X-ray and cryo-EM structures of inhibitor-bound cytochromebc1complexes for structure-based drug discovery
Cited by: 20
Author(s): K. Amporndanai, Rachel M. Johnson, Paul M. O’Neill, Colin W. G. Fishwick, A.H. Jamson, Shaun Rawson, Stephen P. Muench, S.S. Hasnain, S.V. Antonyuk
Software Mentions: 2
Published: over 8 years ago

10.1107/S0907444910007493

Features and development of Coot
Cited by: 21,554
Author(s): Paul Emsley, Bernhard Lohkamp, William G. Scott, Kevin Cowtan
Software Mentions: 2
Published: over 16 years ago

10.1107/S2052252515008969

Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser
Cited by: 21
Author(s): Maike Bublitz, Karol Nass, N.D. Drachmann, Anders J. Markvardsen, Matthias J. Gutmann, Thomas R. M. Barends, D. Mattle, Robert L. Shoeman, R. Bruce Doak, Sébastien Boutet, Marc Messerschmidt, M. Seibert, Garth J. Williams, L. Foucar, Linda Reinhard, Oleg Sitsel, J.L. Gregersen, Johannes Clausen, Thomas Boesen, Kamil Gotfryd, Kaituo Wang, Claus Olesen, Jesper Møller, Poul Nissen, Ilme Schlichting
Software Mentions: 2
Published: over 11 years ago

10.1042/BSR20140174

Structural characterization of the late competence protein ComFB from Bacillus subtilis
Cited by: 9
Author(s): Tatyana A. Sysoeva, Lukas B. Bane, Di Xiao, Baundauna Bose, Scott Chilton, Rachelle Gaudet, Briana M. Burton
Software Mentions: 2
Published: over 11 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: almost 11 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: almost 7 years ago

10.1083/jcb.201910059

Molecular basis of MKLP2-dependent Aurora B transport from chromatin to the anaphase central spindle
Cited by: 23
Author(s): Michela Serena, Ricardo Bastos, P.R. Elliott, Francis A. Barr
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1002832

The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors
Cited by: 179
Author(s): Keith P. Romano, Akbar Ali, Cihan Aydın, Djadé I. Soumana, Ayşegül Özen, Laura M. Deveau, C. N. Silver, Hong Cao, Alicia Newton, Christos J. Petropoulos, Wei Huang, Celia A. Schiffer
Software Mentions: 2
Published: over 14 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: over 7 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: about 7 years ago

10.1038/srep19981

Structural and functional attributes of malaria parasite diadenosine tetraphosphate hydrolase
Cited by: 12
Author(s): Amit Sharma, Manickam Yogavel
Software Mentions: 2
Published: over 10 years ago

10.1016/j.jbc.2021.100771

Structural basis of KdpD histidine kinase binding to the second messenger c-di-AMP
Cited by: 11
Author(s): Avijit Dutta, Mona Batish, Vijay Parashar
Software Mentions: 2
Published: almost 6 years ago

10.1107/S0907444913025250

Improvements in the order, isotropy and electron density of glypican-1 crystals by controlled dehydration
Cited by: 13
Author(s): W. Awad, Gabriel Svensson Birkedal, Marjolein M.G.M. Thunnissen, Katrin Mani, D.T. Logan
Software Mentions: 2
Published: almost 13 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: almost 9 years ago

10.1107/S2052252517008223

One enzyme, many reactions: structural basis for the various reactions catalyzed by naphthalene 1,2-dioxygenase
Cited by: 25
Author(s): D.J. Ferraro, Adam Okerlund, Eric N. Brown, S. Ramaswamy
Software Mentions: 2
Published: about 9 years ago

10.1107/S2052252518008217

Structural characterization of free-state and product-stateMycobacterium tuberculosismethionyl-tRNA synthetase reveals an induced-fit ligand-recognition mechanism
Cited by: 9
Author(s): Wei Wang, Bo Qin, Justyna Aleksandra Wojdyla, Meitian Wang, Xiaopan Gao, Sheng Cui
Software Mentions: 2
Published: over 8 years ago

10.1016/j.jbc.2021.100857

Oxalate decarboxylase uses electron hole hopping for catalysis
Cited by: 5
Author(s): Anthony J. Pastore, Ruijie D. Teo, Alvaro Montoya, M.J. Burg, Umar T. Twahir, Steven D. Bruner, David N. Beratan, Alexander Angerhofer
Software Mentions: 2
Published: over 5 years ago

10.1107/S2052252519003622

A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography
Cited by: 21
Author(s): Raphaël de Wijn, O. Hennig, J Roche, S. Engilberge, K. Rollet, Pablo Fernández-Millán, Karl Brillet, Heike Betat, Mario Mörl, Alain Roussel, Éric Girard, Christoph Mueller-Dieckmann, Gavin C. Fox, V. Oliéric, José A. Gavira, Bernard Lorber, Claude Sauter
Software Mentions: 2
Published: over 7 years ago

10.1016/j.jbc.2021.100662

The molecular basis of spectral tuning in blue- and red-shifted flavin-binding fluorescent proteins
Cited by: 14
Author(s): Katrin Röllen, Joachim Granzin, Alina Remeeva, Mehdi D. Davari, Thomas Gensch, Vera V. Nazarenko, Kirill Kovalev, Andrey Bogorodskiy, Valentin Borshchevskiy, Stefanie Hemmer, Ulrich Schwaneberg, Valentin Gordeliy, Karl‐Erich Jaeger, Renu Batra‐Safferling, Ivan Gushchin, Ulrich Krauß
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.jbc.2021.100286

Pantoea stewartii WceF is a glycan biofilm-modifying enzyme with a bacteriophage tailspike-like fold
Cited by: 5
Author(s): Tobias Irmscher, Yvette Roske, Igor Gayk, Valentin Dunsing, Salvatore Chiantia, Udo Heinemann, Stefanie Barbirz
Software Mentions: 2
Published: almost 6 years ago

10.26508/lsa.201800187

The crystal structure of Staufen1 in complex with a physiological RNA sheds light on substrate selectivity
Cited by: 15
Author(s): Daniela Lazzaretti, L. Bandholz-Cajamarca, Christiane Emmerich, Kristina Schaaf, Claire Basquin, Uwe Irion, Fulvia Bono
Software Mentions: 2
Published: about 8 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: almost 11 years ago

10.1016/j.jbc.2021.100321

Structural characterization of HIV-1 matrix mutants implicated in envelope incorporation
Cited by: 5
Author(s): Gunnar N. Eastep, Ruba H. Ghanam, Todd Green, Jamil S. Saad
Software Mentions: 2
Published: almost 6 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 5 years ago

10.1016/j.jbc.2021.100684

Crystal structure of the catalytic domain of botulinum neurotoxin subtype A3
Cited by: 3
Author(s): Oneda Leka, Yufan Wu, Xiao Dan Li, Richard A. Kammerer
Software Mentions: 2
Published: almost 6 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: almost 8 years ago

10.1074/jbc.RA120.015050

KPC-2 β-lactamase enables carbapenem antibiotic resistance through fast deacylation of the covalent intermediate
Cited by: 11
Author(s): Shrenik Mehta, I. Furey, O.A. Pemberton, David M. Boragine, Yu Chen, Timothy Palzkill
Software Mentions: 2
Published: almost 6 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: almost 9 years ago

10.1107/S0907444913024608

Split green fluorescent protein as a modular binding partner for protein crystallization
Cited by: 27
Author(s): Hau B. Nguyen, Li Wei Hung, Todd O. Yeates, Thomas C. Terwilliger, Geoffrey S. Waldo
Software Mentions: 2
Published: almost 13 years ago

10.1074/jbc.RA120.016313

Active site metals mediate an oligomeric equilibrium in Plasmodium M17 aminopeptidases
Cited by: 2
Author(s): Tess R. Malcolm, Matthew J. Belousoff, Hariprasad Venugopal, Natalie A. Borg, N. Drinkwater, Sarah C. Atkinson, Sheena McGowan
Software Mentions: 2
Published: almost 6 years ago

10.1074/jbc.RA120.015444

Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors
Cited by: 15
Author(s): Sai Shashank Chavali, Sachitanand M. Mali, Jermaine L. Jenkins, Rudi Fasan, Joseph E. Wedekind
Software Mentions: 2
Published: almost 6 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: about 7 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: over 8 years ago

10.7554/eLife.36656

Dynamics of human protein kinase Aurora A linked to drug selectivity
Cited by: 35
Author(s): Warintra Pitsawong, Vanessa Buosi, Renee Otten, Roman V. Agafonov, Adelajda Zorba, Nadja Kern, Steffen Kutter, Günther Kern, R.A.P. Padua, Xavier Méniche, Dorothee Kern
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0192488

The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity
Cited by: 7
Author(s): Igor Sabljić, Marko Tomin, Mihaela Matovina, Iva Sučec, Ana Tomašić Paić, Antonija Tomić, Marija Abramić, Sanja Tomić
Software Mentions: 2
Published: over 8 years ago

10.1074/jbc.RA120.013649

Molecular basis for histone H3 “K4me3-K9me3/2” methylation pattern readout by Spindlin1
Cited by: 13
Author(s): Fan Zhao, Yunan Liu, Xuantao Su, Jieun Lee, Yinglin Song, Daliang Wang, Kai Ge, Juntao Gao, Michael Q. Zhang, Haitao Li
Software Mentions: 2
Published: almost 6 years ago

10.1074/jbc.RA120.014005

Structural comparisons of host and African swine fever virus dUTPases reveal new clues for inhibitor development
Cited by: 6
Author(s): Rui Liang, Gang Wang, Ding Zhang, Gang Ye, Mengxia Li, Yuejun Shi, Jiale Shi, Huanchun Chen, Guiqing Peng
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.jbc.2021.100957

The endopeptidase of the maize-affecting Marafivirus type member maize rayado fino virus doubles as a deubiquitinase
Cited by: 5
Author(s): Ankoor Patel, Jessica A.M. McBride, Brian L. Mark
Software Mentions: 2
Published: about 5 years ago

10.1074/jbc.RA118.007285

A low-potential terminal oxidase associated with the iron-only nitrogenase from the nitrogen-fixing bacterium Azotobacter vinelandii
Cited by: 19
Author(s): Febin Varghese, B.V. Kabasakal, Charles A. R. Cotton, Julia Schumacher, A. William Rutherford, Andrea Fantuzzi, James W. Murray
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.03239

How lamina-associated polypeptide 1 (LAP1) activates Torsin
Cited by: 89
Author(s): Brian A Sosa, F. Esra Demircioglu, James Z. Chen, Jessica R. Ingram, Hidde L. Ploegh, Thomas Schwartz
Software Mentions: 2
Published: about 12 years ago

10.1074/jbc.RA119.008610

Alternative folding to a monomer or homopolymer is a common feature of the type 1 pilus subunit FimA from enteroinvasive bacteria
Cited by: 7
Author(s): Dawid Zyla, A.E. Prota, Guido Capitani, Rudi Glockshuber
Software Mentions: 2
Published: over 7 years ago

10.1186/1756-0500-5-626

Crystal structures of wild-type and mutated cyclophilin B that causes hyperelastosis cutis in the American quarter horse
Cited by: 8
Author(s): Sergei P. Boudko, Yoshihiro Ishikawa, Thomas F. Lerch, Jay C. Nix, Michael S. Chapman, Hans Peter Bächinger
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0188005

Crystal structures of ternary complexes of archaeal B-family DNA polymerases
Cited by: 36
Author(s): H.M. Kropp, Karin Betz, Johannes Wirth, Kay Diederichs, Andreas Marx
Software Mentions: 2
Published: almost 9 years ago

10.1107/S2059798317000067

AceDRG: a stereochemical description generator for ligands
Cited by: 228
Author(s): Fei Long, Robert A. Nicholls, Paul Emsley, Saulius Graǽulis, Andrius Merkys, Antanas Vaitkus, Garib N. Murshudov
Software Mentions: 2
Published: over 9 years ago

10.1016/j.molcel.2021.02.021

Structural basis for conformational equilibrium of the catalytic spliceosome
Cited by: 21
Author(s): Max E. Wilkinson, Sebastian M. Fica, Wojciech P. Galej, Kiyoshi Nagai
Software Mentions: 2
Published: over 5 years ago

10.1074/jbc.RA118.003857

The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel
Cited by: 33
Author(s): Stephanie J. Ward, Hayley E. Gratton, Peni Indrayudha, Camille Michavila, Rishov Mukhopadhyay, Sigrun K. Maurer, Simon G. Caulton, Jonas Emsley, Ingrid Dreveny
Software Mentions: 2
Published: almost 8 years ago

10.1074/jbc.M117.816348

Exceptionally high-affinity Ras binders that remodel its effector domain
Cited by: 33
Author(s): John H. McGee, So Youn Shim, Seung-Joo Lee, Paige Swanson, Sam Y. Jiang, Michael A. Durney, Gregory L. Verdine
Software Mentions: 2
Published: over 8 years ago

10.1016/j.molcel.2017.08.020

Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling
Cited by: 146
Author(s): Martin A. Michel, Kirby N. Swatek, Manuela K. Hospenthal, David Komander
Software Mentions: 2
Published: about 9 years ago

10.1074/jbc.M117.809657

Prodomain–growth factor swapping in the structure of pro-TGF-β1
Cited by: 29
Author(s): Bo Zhao, Shutong Xu, Xiao Dong, Chafen Lu, Timothy A. Springer
Software Mentions: 2
Published: over 8 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 6 years ago

10.1074/jbc.RA118.005405

InhA, the enoyl-thioester reductase from Mycobacterium tuberculosis forms a covalent adduct during catalysis
Cited by: 15
Author(s): Bastian Vögeli, Raoul Rosenthal, Gabriele Stoffel, T. Wagner, Patrick Kiefer, Niña Socorro Cortina, Seigo Shima, Tobias J. Erb
Software Mentions: 2
Published: almost 8 years ago

10.1186/1741-7007-9-48

Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1
Cited by: 49
Author(s): Alexei Korennykh, Pascal F. Egea, А.A. Коростелев, J. Finer-Moore, Robert M. Stroud, Chao Zhang, Kevan M. Shokat, Peter Walter
Software Mentions: 2
Published: over 15 years ago

10.1107/S2059798317016618

Molecular architectures of benzoic acid-specific type III polyketide synthases
Cited by: 11
Author(s): Charles Stewart, Kate Woods, Greg Macias, Andrew C. Allan, Roger P. Hellens, Joseph P. Noel
Software Mentions: 2
Published: almost 9 years ago

10.1074/jbc.M117.797811

Discovery of a microbial transglutaminase enabling highly site-specific labeling of proteins
Cited by: 42
Author(s): Wojtek Steffen, Fu Chong Ko, Jigar Patel, Victor I. Lyamichev, Thomas Albert, Jörg Benz, M.G. Rudolph, Frank Bergmann, Thomas Streidl, Peter Kratzsch, Mara Boenitz-Dulat, Tobias Oelschlaegel, Michael Schraeml
Software Mentions: 2
Published: about 9 years ago

10.1107/S2059798316016910

Strategies for carbohydrate model building, refinement and validation
Cited by: 45
Author(s): Jon Agirre
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.09832

Dna2 nuclease-helicase structure, mechanism and regulation by Rpa
Cited by: 89
Author(s): Chun Zhou, Sergei Pourmal, Nikola P. Pavletich
Software Mentions: 2
Published: almost 11 years ago

10.1107/S0907444910001502

Detection and correction of underassigned rotational symmetry prior to structure deposition
Cited by: 12
Author(s): Billy K. Poon, Ralf W. Grosse‐Kunstleve, Peter H. Zwart, Nicholas K. Sauter
Software Mentions: 2
Published: over 16 years ago

10.7554/eLife.01496

Crystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803
Cited by: 66
Author(s): Yuval Mazor, Daniel Nataf, Hila Toporik, Nathan Nelson
Software Mentions: 2
Published: over 12 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 8 years ago

10.1107/S1399004715009438

High-resolution crystal structures of the solubilized domain of porcine cytochromeb5
Cited by: 3
Author(s): Yu Hirano, Shigenobu Kimura, Taro Tamada
Software Mentions: 2
Published: over 11 years ago

10.3390/molecules23010111

Characterization of Two VAO-Type Flavoprotein Oxidases from Myceliophthora thermophila
Cited by: 7
Author(s): Alessandro Ferrari, H.J. Rozeboom, Aniek S.C. Vugts, Martijn J. Koetsier, R.J. Floor, Marco W. Fraaije
Software Mentions: 2
Published: almost 9 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
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Author(s): Laurel Jones, Michael Tynes, Paul Smith
Software Mentions: 2
Published: about 7 years ago

10.1074/jbc.RA118.004227

Oxidative cyclization of N-methyl-dopa by a fungal flavoenzyme of the amine oxidase family
Cited by: 3
Author(s): Majd Lahham, Tea Pavkov‐Keller, Michael Fuchs, Johannes Niederhauser, Gabriel Chalhoub, Bastian Daniel, Wolfgang Kroutil, Karl Gruber, Peter Macheroux
Software Mentions: 2
Published: almost 8 years ago

10.1107/S1399004714022755

Structural implications of the C-terminal tail in the catalytic and stability properties of manganese peroxidases from ligninolytic fungi
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Author(s): Elena Fernández‐Fueyo, Sandra Acebes, Francisco J. Ruíz-Dueñas, Marı́a Jesús Martı́nez, Antonio Romero, F.J. Medrano, Vı́ctor Guallar, Ángel T. Martı́nez
Software Mentions: 2
Published: almost 12 years ago

10.1016/j.jbc.2021.101001

Structural and functional analysis of gum arabic l-rhamnose-α-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family
Cited by: 3
Author(s): Tatsuya Kondo, Miyu Kichijo, Akiho Maruta, Makoto Nakaya, Shigeo Takenaka, T. Arakawa, Shinya Fushinobu, Tatsuji Sakamoto
Software Mentions: 2
Published: about 5 years ago

10.1038/srep22127

In-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth
Cited by: 7
Author(s): Akira Nakamura, Jun Ohtsuka, Tatsuki Kashiwagi, Nobutaka Numoto, Noriyuki Hirota, Takahiro Ode, Hidehiko Okada, Koji Nagata, Motosuke Kiyohara, E Suzuki, Akiko Kita, Hitoshi Wada, Masaru Tanokura
Software Mentions: 2
Published: over 10 years ago

10.1016/j.str.2020.03.013

Interactions of a Bacterial RND Transporter with a Transmembrane Small Protein in a Lipid Environment
Cited by: 45
Author(s): Dijun Du, Arthur Neuberger, Mona W. Orr, Catherine E. Newman, Pin-Chia Hsu, Firdaus Samsudin, Andrzej Harris, Leana M. Ramos, Mekdes Debela, Syma Khalid, Gisela Storz, Ben F. Luisi
Software Mentions: 2
Published: over 6 years ago

10.1186/s12915-019-0698-5

Crystal structure of diamondback moth ryanodine receptor Repeat34 domain reveals insect-specific phosphorylation sites
Cited by: 18
Author(s): Tong Xu, Zhiguang Yuchi
Software Mentions: 2
Published: about 7 years ago

10.1107/S1399004714027114

Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes
Cited by: 12
Author(s): S.O. Dahms, Magnus C. Mayer, Dirk Roeser, Gerd Multhaup, Manuel E. Than
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 12 years ago

10.1107/S2053230X18002236

Crystal structure of theMSMEG_4306gene product fromMycobacterium smegmatis
Cited by: 1
Author(s): Adarsh Kumar, Subramanian Karthikeyan
Software Mentions: 2
Published: over 8 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 11 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 16 years ago

10.1107/S2053230X14003355

A range of C∊3–C∊4 interdomain angles in IgE Fc accommodate binding to its receptor CD23
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Author(s): B. Dhaliwal, M.O.Y. Pang, Daopeng Yuan, Andrew J. Beavil, Brian J. Sutton
Software Mentions: 2
Published: over 12 years ago

10.1107/S2059798316000401

An overview of heavy-atom derivatization of protein crystals
Cited by: 40
Author(s): A.C.W. Pike, Elspeth F. Garman, T. Krojer, Frank von Delft, E.P. Carpenter
Software Mentions: 2
Published: over 10 years ago

10.1074/jbc.M116.743948

The Mechanism by Which Arabinoxylanases Can Recognize Highly Decorated Xylans
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Author(s): Aurore Labourel, Lucy I. Crouch, Joana L. A. Brás, Adam Jackson, Artur Rogowski, Joe Gray, Madhav P. Yadav, Bernard Henrissat, Carlos M. G. A. Fontes, Harry J. Gilbert, Shabir Najmudin, Arnaud Baslé, Fiona Cuskin
Software Mentions: 2
Published: about 10 years ago

10.1186/s12915-017-0372-8

Ion- and water-binding sites inside an occluded hourglass pore of a trimeric intracellular cation (TRIC) channel
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Author(s): Xiaomin Ou, Jing Guo, Long Wang, Hongxin Yang, Xiuying Liu, Jianyuan Sun, Zhongfan Liu
Software Mentions: 2
Published: over 9 years ago

10.3390/v7122946

Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone
Cited by: 43
Author(s): Carmela Garcia-Doval, José R. Castón, Daniel Luque, Meritxell Granell, José M. Otero, Antonio L. Llamas‐Saiz, Madalena Renouard, P. Boulanger, Mark J. van Raaij
Software Mentions: 2
Published: almost 11 years ago

10.1107/S2053230X18000250

Structure of a Talaromyces pinophilus GH62 arabinofuranosidase in complex with AraDNJ at 1.25 Å resolution
Cited by: 4
Author(s): Olga V. Moroz, L.F. Sobala, E.V. Blagova, Travis Coyle, Wei Peng, Kristian B. R. M. Krogh, Keith A. Stubbs, K.S. Wilson, G.J. Davies
Software Mentions: 2
Published: over 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: almost 9 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 9 years ago

10.7554/eLife.35677

Specific Eph receptor-cytoplasmic effector signaling mediated by SAM–SAM domain interactions
Cited by: 30
Author(s): Yue Wang, Yuan Shang, Jianchao Li, Weidi Chen, Gang Li, Jun Wan, Wei Liu, Mingjie Zhang
Software Mentions: 2
Published: over 8 years ago

10.1186/s12915-015-0167-8

Role of electrostatic interactions for ligand recognition and specificity of peptide transporters
Cited by: 47
Author(s): Rajendra Boggavarapu, Jean-Marc Jeckelmann, Daniel Harder, Zöhre Ucurum, Dimitrios Fotiadis
Software Mentions: 2
Published: about 11 years ago

10.1074/jbc.M115.672790

Agonistic Human Antibodies Binding to Lecithin-Cholesterol Acyltransferase Modulate High Density Lipoprotein Metabolism
Cited by: 29
Author(s): Ruwanthi N. Gunawardane, Preston Fordstrom, Derek E. Piper, Stephanie Masterman, Sophia Siu, Dongming Liu, M Ichael S. Brown, Mei Lü, Jie Tang, Richard Zhang, Janet Cheng, Andrew J. Gates, David Meininger, Janice Chan, Tim Carlson, Nigel Walker, Margrit Schwarz, John Delaney, Mingyue Zhou
Software Mentions: 2
Published: over 10 years ago

10.1107/S2052252515021259

Rapid experimental SAD phasing and hot-spot identification with halogenated fragments
Cited by: 26
Author(s): J.D. Bauman, Jerry Joe Ebow Kingsley Harrison, Eddy Arnold
Software Mentions: 2
Published: almost 11 years ago

10.1074/jbc.M116.748160

Ligand-bound Structures and Site-directed Mutagenesis Identify the Acceptor and Secondary Binding Sites of Streptomyces coelicolor Maltosyltransferase GlgE
Cited by: 11
Author(s): Karl Syson, Clare E. M. Stevenson, Farzana Miah, J. Elaine Barclay, Minhong Tang, Andrii Gorelik, Abdur Rashid, David M. Lawson, Stephen Bornemann
Software Mentions: 2
Published: about 10 years ago

10.3390/v12080812

Structural and Biological Basis of Alphacoronavirus nsp1 Associated with Host Proliferation and Immune Evasion
Cited by: 17
Author(s): Zhou Shen, Yiling Yang, Siqi Yang, Guangxu Zhang, Shaobo Xiao, Zhen F. Fu, Guiqing Peng
Software Mentions: 2
Published: over 6 years ago

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Papers Mentioning PHENIX 2,287