cran: PHENIX | Projects | Ecosyste.ms: Papers

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 12 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: about 14 years ago

10.1107/S2053230X15015939

An active site–tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase
Cited by: 7
Author(s): Jesse Murphy, Stefano Donini, T.J. Kappock
Software Mentions: 2
Published: almost 11 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

10.1107/S2059798319006831

Structural and functional characterization of CMP-N-acetylneuraminate synthetase fromVibrio cholerae
Cited by: 1
Author(s): Sucharita Bose, Debayan Purkait, Deepthi Joseph, Vinod Nayak, Ramaswamy Subramanian
Software Mentions: 2
Published: over 7 years ago

10.1107/S0907444912040590

Nearest-cell: a fast and easy tool for locating crystal matches in the PDB
Cited by: 13
Author(s): Varun Ramraj, Gwyndaf Evans, Jonathan M. Diprose, Robert Esnouf
Software Mentions: 2
Published: almost 14 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

10.1107/S1399004714001850

A conformational landscape for alginate secretion across the outer membrane ofPseudomonas aeruginosa
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: about 12 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: almost 11 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: about 9 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: about 7 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 14 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: about 10 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 12 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 17 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: about 8 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

10.1371/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 7 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 10 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 10 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

10.1371/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 14 years ago

10.1371/journal.pone.0066247

CD38 Structure-Based Inhibitor Design Using the N1-Cyclic Inosine 5′-Diphosphate Ribose Template
Cited by: 24
Author(s): Christelle Moreau, Qun Liu, Richard Graeff, Gerd K. Wagner, Mark Thomas, Joanna M. Swarbrick, Satoshi Shuto, Hon Cheung Lee, Quan Hao, Barry V. L. Potter
Software Mentions: 2
Published: about 13 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: almost 14 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 8 years ago

10.1371/journal.pone.0071866

The Tick-Derived Anticoagulant Madanin Is Processed by Thrombin and Factor Xa
Cited by: 19
Author(s): Ana C. Figueiredo, Daniele de Sanctis, Pedro José Barbosa Pereira
Software Mentions: 2
Published: about 13 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: almost 8 years ago

10.1371/journal.pone.0022337

The Crystal Structure of the Human Co-Chaperone P58IPK
Cited by: 19
Author(s): Maria Svärd, Ekaterina Biterova, Jean-Marie Bourhis, Jodie E. Guy
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0092249

Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6
Cited by: 20
Author(s): Keisuke Sugimoto, Masuo Senda, Daisuke Kasai, Masao Fukuda, Eiji Masai, Toshiya Senda
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0210842

Potent, multi-target serine protease inhibition achieved by a simplified β-sheet motif
Cited by: 7
Author(s): Xingchen Chen, Blake T. Riley, Simon J. de Veer, David E. Hoke, Jessica Van Haeften, Darren Leahy, Joakim E. Swedberg, Maria Brattsand, Perry J. Hartfield, Ashley M. Buckle, Jonathan M. Harris
Software Mentions: 2
Published: over 7 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: almost 13 years ago

10.1371/journal.pone.0177161

Structures of the inactive and active states of RIP2 kinase inform on the mechanism of activation
Cited by: 31
Author(s): Erika Pellegrini, Luca Signor, Saurabh Singh, Elisabetta Boeri Erba, Stephen Cusack
Software Mentions: 2
Published: over 9 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

10.3390/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 5 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 6 years ago

10.1371/journal.pone.0020864

Identification of the Allosteric Regulatory Site of Insulysin
Cited by: 36
Author(s): Nicholas Noinaj, Sonia K. Bhasin, Eun Suk Song, Kirsten E. Scoggin, María A. Juliano, Luiz Juliano, Louis B. Hersh, David W. Rodgers
Software Mentions: 2
Published: about 15 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 7 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 15 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

10.1371/journal.pone.0062252

Crystal Structures of a Plant Trypsin Inhibitor from Enterolobium contortisiliquum (EcTI) and of Its Complex with Bovine Trypsin
Cited by: 30
Author(s): Dongwen Zhou, Yara Aparecida Lobo, Isabel de Fátima Correia Batista, Rafael Marques-Porto, Alla Gustchina, Maria Luíza Vilela Oliva, Alexander Wlodawer
Software Mentions: 2
Published: over 13 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

10.1371/journal.pone.0040066

The Crystal Structures of Dystrophin and Utrophin Spectrin Repeats: Implications for Domain Boundaries
Cited by: 27
Author(s): M. Muthu, Kylie A. Richardson, Andrew J. Sutherland-Smith
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0091232

Molecular Recognition of the Neurotransmitter Acetylcholine by an Acetylcholine Binding Protein Reveals Determinants of Binding to Nicotinic Acetylcholine Receptors
Cited by: 34
Author(s): Jeppe Olsen, Thomas Balle, Michael Gajhede, Philip K. Ahring, J.S. Kastrup
Software Mentions: 2
Published: over 12 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: about 6 years ago

10.1107/S2059798316001212

Structure of a quinolone-stabilized cleavage complex of topoisomerase IV fromKlebsiella pneumoniaeand comparison with a relatedStreptococcus pneumoniaecomplex
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: over 10 years ago

10.1371/journal.pone.0241912

Molecular analysis of cyclic α-maltosyl-(1→6)-maltose binding protein in the bacterial metabolic pathway
Cited by: 2
Author(s): Masanori Kohno, T. Arakawa, Naoki Sunagawa, Tetsuya Mori, Kiyohiko Igarashi, Tetsuya Nishimoto, Shinya Fushinobu
Software Mentions: 2
Published: almost 6 years ago

10.1107/S2059798317015236

The crystal structure of theYersinia pestisiron 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: almost 9 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: almost 10 years ago

10.1371/journal.pone.0124272

LucY: A Versatile New Fluorescent Reporter Protein
Cited by: 4
Author(s): M.E. Auldridge, Heidi B. Cao, Satyabrata Sen, Laura Franz, C.A. Bingman, Ragothaman M. Yennamalli, George N. Phillips, David A. Mead, Eric J. Steinmetz
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0140953

Activity Augmentation of Amphioxus Peptidoglycan Recognition Protein BbtPGRP3 via Fusion with a Chitin Binding Domain
Cited by: 4
Author(s): Wenjie Wang, Cheng Wang, Ming Luo, Qingyu Yan, Gino Yu, Qiong Li, Dong Cao, Shengfeng Huang, Anlong Xu, Roy A. Mariuzza, Yuxing Chen, Cong‐Zhao Zhou
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0174284

Structural insights into the regulation of Bacillus subtilis SigW activity by anti-sigma RsiW
Cited by: 19
Author(s): Shankar Raj Devkota, Eunju Kwon, Soonhoi Ha, Hyeun Wook Chang, Dong Young Kim
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0155846

The Crystal Structure of the YknZ Extracellular Domain of ABC Transporter YknWXYZ from Bacillus amyloliquefaciens
Cited by: 9
Author(s): Yongbin Xu, Jianyun Guo, Lulu Wang, Rui Jiang, Xiaoling Jin, Jing Liu, Fan Sheng-di, Chunshan Quan, Nam‐Chul Ha
Software Mentions: 2
Published: over 10 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: over 8 years ago

10.1371/journal.pone.0089027

Distinct Structural Features of the Peroxide Response Regulator from Group A Streptococcus Drive DNA Binding
Cited by: 13
Author(s): Chang Hong Lin, Shi-Yu Chao, Michal Hammel, Jay C. Nix, Hsiao-Ling Tseng, Chih-Cheng Tsou, Chun-Hsien Fei, Huo-Sheng Chiou, U‐Ser Jeng, Yee‐Shin Lin, Woei‐Jer Chuang, Jiunn-Jong Wu, Shuying Wang
Software Mentions: 2
Published: over 12 years ago

10.1107/S2059798315021683

In meso in situserial 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 10 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: almost 11 years ago

10.1371/journal.pone.0133033

Identification of Interactions between Abscisic Acid and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase
Cited by: 16
Author(s): Marek Gałka, Nandhakishore Rajagopalan, Leann Buhrow, Ken M. Nelson, Jacek Switala, Adrian J. Cutler, David R. J. Palmer, P.C. Loewen, Suzanne R. Abrams, Michèle C. Loewen
Software Mentions: 2
Published: about 11 years ago

10.1107/S1399004715017927

MeshAndCollect: 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: almost 11 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 9 years ago

10.1371/journal.pone.0085940

Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site
Cited by: 47
Author(s): Young Do Kwon, Judith M. LaLonde, Yongping Yang, Mark A. Elban, Akihiro Sugawara, Joel R. Courter, David M. Jones, Amos B. Smith, Asim K. Debnath, Peter D. Kwong
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0087267

Crystal Structure of Arginine Methyltransferase 6 from Trypanosoma brucei
Cited by: 23
Author(s): Chongyuan Wang, Yuwei Zhu, Jiajia Chen, Xu Li, Junxia Peng, Jiajing Chen, Yang Zou, Zhiyong Zhang, Hongtao Jin, Pengyuan Yang, Jihui Wu, Liwen Niu, Qingguo Gong, Maikun Teng, Yunyu Shi
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0050055

Tolerance of Protein Folding to a Circular Permutation in a PDZ Domain
Cited by: 13
Author(s): Greta Hultqvist, Avinash S. Punekar, Angela Morrone, N. Celestine, Åke Engström, M. Selmer, Stefano Gianni, Per Jemth
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0196751

Assigning crystallographic electron densities with free energy calculations—The case of the fluoride channel Fluc
Cited by: 2
Author(s): Igor Ariz-Extreme, Jochen S. Hub
Software Mentions: 2
Published: over 8 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: about 12 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: almost 7 years ago

10.1371/journal.pone.0094166

Biochemical Properties and Atomic Resolution Structure of a Proteolytically Processed β-Mannanase from Cellulolytic Streptomyces sp. SirexAA-E
Cited by: 16
Author(s): Taichi E. Takasuka, Justin Acheson, C.M. Bianchetti, Ben M. Prom, Lai F. Bergeman, Adam J. Book, Cameron R. Currie, Brian G. Fox
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0204703

Structural and biochemical characterization of the Cutibacterium acnes exo-β-1,4-mannosidase that targets the N-glycan core of host glycoproteins
Cited by: 11
Author(s): Tom Reichenbach, Dayanand Kalyani, Rosaria Gandini, Olov Svartström, Henrik Aspeborg, Christina Divne
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0184627

Structure-based design, synthesis and crystallization of 2-arylquinazolines as lipid pocket ligands of p38α MAPK
Cited by: 10
Author(s): Mike Bührmann, Bianca Wiedemann, Matthias Müller, Julia Hardick, Mary Ecke, Daniel Rauh
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0121764

Stability of the Octameric Structure Affects Plasminogen-Binding Capacity of Streptococcal Enolase
Cited by: 13
Author(s): Amanda J. Cork, Daniel Ericsson, Ruby H. P. Law, Lachlan W. Casey, Eugene Valkov, Carlo Bertozzi, Anna Stamp, Blagojce Jovcevski, J. Andrew Aquilina, James C. Whisstock, Mark J. Walker, Boštjan Kobe
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0032070

Recognition of Anesthetic Barbiturates by a Protein Binding Site: A High Resolution Structural Analysis
Cited by: 13
Author(s): Simon Oakley, L.S. Vedula, Weiming Bu, Qing Cheng Meng, Xi Jin, Renyu Liu, Roderic G. Eckenhoff, Patrick J. Loll
Software Mentions: 2
Published: over 14 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: over 11 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 9 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: over 12 years ago

10.1371/journal.pone.0096198

Structural Basis for the Site-Specific Incorporation of Lysine Derivatives into Proteins
Cited by: 16
Author(s): Veronika Flügel, Milan Vrábel, Sabine Schneider
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0146457

The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex
Cited by: 14
Author(s): N. Silva-Martin, María I. Daudén, Sebastian Glatt, N.A. Hoffmann, Panagiotis L. Kastritis, Peer Bork, Martin Beck, Christoph W. Müller
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0206260

Crystal structure and functional characterization of a cold-active acetyl xylan esterase (PbAcE) from psychrophilic soil microbe Paenibacillus sp.
Cited by: 21
Author(s): Sunha Park, Woo-Kyoung Yoo, Chang Woo Lee, Chang-Sung Jeong, Seung Chul Shin, Han-Woo Kim, Hyun Park, Kyeong Kyu Kim, T. Doohun Kim, Jun Hyuck Lee
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0242383

The crystal structure of mouse IRG1 suggests that cis-aconitate decarboxylase has an open and closed conformation
Cited by: 4
Author(s): Hye Lin Chun, So Yeon Lee, Ki-Hwa Kim, Chang Sup Lee, Tae‐Jin Oh, Hyun Ho Park
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12900-014-0024-y

Structural insights into Escherichia coli polymyxin B resistance protein D with X-ray crystallography and small-angle X-ray scattering
Cited by: 9
Author(s): Hang-Hyun Jo, Eui Young Jeong, Jinseong Jeon, Changill Ban
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0080298

Diversification of Fungal Specific Class A Glutathione Transferases in Saprotrophic Fungi
Cited by: 37
Author(s): Yann Mathieu, P. Prosper, F. Favier, Luc Harvengt, Claude Didierjean, Jean‐Pierre Jacquot, Mélanie Morel‐Rouhier, Éric Gelhaye
Software Mentions: 2
Published: almost 13 years ago

10.1186/1472-6807-12-13

Crystal structure of the Yersinia enterocolitica type III secretion chaperone SycD in complex with a peptide of the minor translocator YopD
Cited by: 25
Author(s): Madeleine Schreiner, Hartmut H. Niemann
Software Mentions: 2
Published: over 14 years ago

10.1107/S1399004713033634

Multi-PAS domain-mediated protein oligomerization of PpsR fromRhodobacter sphaeroides
Cited by: 11
Author(s): Udo Heintz, Anton Meinhart, Andreas Winkler
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0026021

Structural and Biochemical Studies of Human 4-hydroxy-2-oxoglutarate Aldolase: Implications for Hydroxyproline Metabolism in Primary Hyperoxaluria
Cited by: 49
Author(s): Travis J. Riedel, Lynnette C. Johnson, John Knight, Roy R. Hantgan, Ross P. Holmes, W. Todd Lowther
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0098551

Identification of NAD(P)H Quinone Oxidoreductase Activity in Azoreductases from P. aeruginosa: Azoreductases and NAD(P)H Quinone Oxidoreductases Belong to the Same FMN-Dependent Superfamily of Enzymes
Cited by: 50
Author(s): Ali Ryan, Elise Kaplan, Jean‐Christophe Nebel, Elena Polycarpou, Vincenzo Crescente, E.D. Lowe, Gail M. Preston, Edith Sim
Software Mentions: 2
Published: about 12 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

10.1186/1472-6807-14-3

Crystal structures of the human Dysferlin inner DysF domain
Cited by: 25
Author(s): Altin Sula, A.R. Cole, Corin Yeats, Christine A. Orengo, Nicholas H. Keep
Software Mentions: 2
Published: over 12 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: almost 11 years ago

10.1371/journal.pone.0033524

Carbohydrate Recognition by an Architecturally Complex α-N-Acetylglucosaminidase from Clostridium perfringens
Cited by: 42
Author(s): E. Ficko-Blean, C.P. Stuart, M.D.L. Suits, Melissa Cid, Matthew B. Tessier, Robert J. Woods, A.B. Boraston
Software Mentions: 2
Published: over 14 years ago

10.1186/1472-6807-12-32

Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme’s active site closure
Cited by: 22
Author(s): Jaeok Park, Yih‐Shyan Lin, Joris W. De Schutter, Youla S. Tsantrizos, Albert M. Berghuis
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12900-015-0030-8

Crystal structure and biophysical characterization of the nucleoside diphosphate kinase from Leishmania braziliensis
Cited by: 6
Author(s): P.S. Vieira, P.O. Giuseppe, Mário Tyago Murakami, Arthur Henrique Cavalcante de Oliveira
Software Mentions: 2
Published: over 11 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

10.1186/s12900-015-0037-1

Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase
Cited by: 8
Author(s): Norbert Schormann, Surajit Banerjee, Robert P. Ricciardi, Debasish Chattopadhyay
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1002484

Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1
Cited by: 22
Author(s): Takehiro Nishimura, Guillaume Molinard, Tom J. Petty, Larissa Broger, Caroline Gabus, Thanos D. Halazonetis, Stéphane Thore, Jerzy Paszkowski
Software Mentions: 2
Published: over 14 years ago

10.1107/S2059798319000081

Engineered variants provide new insight into the structural properties important for activity of the highly dynamic, trimeric protein disulfide isomerase ScsC from Proteus mirabilis
Cited by: 5
Author(s): Emily Furlong, Fabian Kurth, Lakshmanane Premkumar, Andrew E. Whitten, Jennifer L. Martin
Software Mentions: 2
Published: over 7 years ago

10.1186/1472-6807-7-45

Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly
Cited by: 35
Author(s): Norbert Schormann, Alexei Grigorian, Alexandra B. Samal, Krishnan Raman, Lawrence J. DeLucas, Debasish Chattopadhyay
Software Mentions: 2
Published: about 19 years ago

10.1107/S2059798317003400

Estimation of the protein–ligand interaction energy for model building and validation
Cited by: 10
Author(s): Daria A. Beshnova, Joana Pereira, Victor S. Lamzin
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pntd.0005374

Structure of SALO, a leishmaniasis vaccine candidate from the sand fly Lutzomyia longipalpis
Cited by: 10
Author(s): Oluwatoyin A. Asojo, Alan Kelleher, Zhuyun Liu, Jeroen Pollet, Elissa M. Hudspeth, Wanderson Rezende, Mallory Jo Groen, Christopher A. Seid, Maha Abdeladhim, Shannon E. Townsend, Waldionê de Castro, Antonio Ferreira Mendes-Sousa, Daniella Castanheira Bartholomeu, Ricardo Toshio Fujiwara, María Elena Bottazzi, Peter J. Hotez, Bin Zhan, Fabiano Oliveira, Shaden Kamhawi, Jesús G. Valenzuela
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0081904

New Conformational State of NHERF1-CXCR2 Signaling Complex Captured by Crystal Lattice Trapping
Cited by: 10
Author(s): Yuanyuan Jiang, Guorong Lu, Laura Trescott, Yuning Hou, Xiaoqing Guan, Shuo Wang, Angelique Stamenkovich, J.S. Brunzelle, Nualpun Sirinupong, Chunying Li, Zhe Yang
Software Mentions: 2
Published: over 12 years ago

10.1107/S0907444912024420

Experimental phasing using zinc anomalous scattering
Cited by: 22
Author(s): Sun Mi Shin, Young Jun An, Chang-Sung Jeong, Min Kyu Kim, Sung Gyu Lee, Kwang Hoon Lee, Byung Ha Oh
Software Mentions: 2
Published: about 14 years ago

10.1186/1472-6807-14-17

Characterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3
Cited by: 36
Author(s): Catherine Leettola, Mary Jane Knight, Duilio Cascio, Sigrid Hoffman, James U. Bowie
Software Mentions: 2
Published: about 12 years ago

10.1107/S2059798315010268

Data collection with a tailored X-ray beam size at 2.69 Å wavelength (4.6 keV): sulfur SAD phasing of Cdc23Nterm
Cited by: 9
Author(s): Michele Cianci, Matthew R. Groves, David Barford, Thomas R. Schneider
Software Mentions: 2
Published: over 10 years ago

Projects: cran: PHENIX

Science Score: 75/100

Penalties:

Papers Mentioning PHENIX 2,287