Ecosyste.ms: Papers

10.1107/S2059798318017047

The crystal structure of the<i>N</i>-acetylglucosamine 2-epimerase from<i>Nostoc</i>sp. KVJ10 reveals the true dimer
Cited by: 5
Author(s): Marie Josée Haglund Halsør, U. Rothweiler, Bjørn Altermark, Inger Lin Uttakleiv Ræder
Software Mentions: 2
Published: almost 6 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

10.1371/journal.pone.0114903

An Integrative Computational Approach for Prioritization of Genomic Variants
Cited by: 7
Author(s): Inna Dubchak, Sandhya Balasubramanian, Sheng Wang, Cem Meyden, Dinanath Sulakhe, Alexander Poliakov, Daniela Börnigen, Bingqing Xie, Andrew Taylor, Jianzhu Ma, Alex R. Paciorkowski, Ghayda Mirzaa, Paul Dave, Gady Agam, Jinbo Xu, Lihadh Al‐Gazali, Christopher E. Mason, M. Elizabeth Ross, Natalia Maltsev, T. Conrad Gilliam
Software Mentions: 2
Published: almost 10 years ago

10.1107/S2059798318009397

High-pressure protein crystal structure analysis of <i>Escherichia coli</i> dihydrofolate reductase complexed with folate and NADP⁺
Cited by: 16
Author(s): T. Nagae, Hiroyuki Yamada, Nobuhisa Watanabe
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0154046

Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics
Cited by: 2
Author(s): Gloria Ruiz-Gómez, John C. Hawkins, Patrick Jenny, Georg Künze, Robert Wodtke, Reik Löser, Karim Fahmy, M. Teresa Pisabarro
Software Mentions: 2
Published: over 8 years ago

10.1107/S0907444913021811

SCEDS: protein fragments for molecular replacement in<i>Phaser</i>
Cited by: 16
Author(s): Airlie J. McCoy, Robert A. Nicholls, Thomas R. Schneider
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0067536

Towards Ligand Docking Including Explicit Interface Water Molecules
Cited by: 58
Author(s): Gordon Lemmon, Jens Meiler
Software Mentions: 2
Published: over 11 years ago

10.1107/S2059798319009574

Biochemical and structural explorations of α-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction
Cited by: 4
Author(s): Hsien‐Wei Yeh, Kuan Hung Lin, S.Y. Lyu, Yi Shan Li, Chun Man Huang, Yung Lin Wang, Hao Wei Shih, N.S. Hsu, Chang Jer Wu, Tsung Lin Li
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0021267

Expression of Enzymatically Inactive Wasp Venom Phospholipase A1 in Pichia pastoris
Cited by: 13
Author(s): Irina Borodina, Bettina M. Jensen, Tim Wagner, Maher Abou Hachem, Ib Søndergaard, Lars K. Poulsen
Software Mentions: 2
Published: over 13 years ago

10.3390/antib9020010

Ion Binding Properties of a Naturally Occurring Metalloantibody
Cited by: 0
Author(s): Elinaz Farokhi, Jonathan K. Fleming, M. Frank Erasmus, Aaron D Ward, Yunjin Wu, Maria Gaby Rivero de Gutiérrez, Jonathan M. Wojciak, Tom Huxford
Software Mentions: 2
Published: over 4 years ago

10.1107/S2059798315022482

Initiating heavy-atom-based phasing by multi-dimensional molecular replacement
Cited by: 3
Author(s): Bjørn Panyella Pedersen, Pontus Gourdon, Xiangyu Liu, Jesper Lykkegaard Karlsen, Poul Nissen
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

10.1371/journal.pone.0232757

Characterization of a human monoclonal antibody generated from a B-cell specific for a prefusion-stabilized spike protein of Middle East respiratory syndrome coronavirus
Cited by: 10
Author(s): Jang Hoon Choi, Hye Min Woo, Tae Young Lee, So Young Lee, Sang Mu Shim, Woo Jung Park, Jeong Sun Yang, Joo Ae Kim, Mi Ran Yun, Dae Won Kim, Sung Soon Kim, Yi Zhang, Wei Shi, Lingshu Wang, Barney S. Graham, John R. Mascola, Nanshuang Wang, Jason S. McLellan, Joo Yeon Lee, Hansaem Lee
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0081753

Heterologous Expression of Mycobacterial Esx Complexes in Escherichia coli for Structural Studies Is Facilitated by the Use of Maltose Binding Protein Fusions
Cited by: 22
Author(s): M.A. Arbing, Sammy Chan, L.R. Harris, E. Kuo, T. Zhou, Christine J. Ahn, Ludivine David NGuyen, Cyndi Qixin He, Jamie Lu, Phuong T. Menchavez, Ae Sun Shin, Thomas Holton, M.R. Sawaya, Duilio Cascio, David Eisenberg
Software Mentions: 2
Published: almost 11 years ago

10.1128/AAC.00123-20

Structure and Molecular Recognition Mechanism of IMP-13 Metallo-β-Lactamase
Cited by: 8
Author(s): Charlotte A Softley, Krzysztof Żak, Mark J. Bostock, Roberto Fino, Richard Xu Zhou, Marta Kolonko, Ramona Mejdi-Nitiu, Hannelore Meyer, Michael Sattler, Grzegorz M. Popowicz
Software Mentions: 2
Published: over 4 years ago

10.1107/S2059798315021683

<i>In meso in situ</i>serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures
Cited by: 89
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Nicole Howe, Lutz Vogeley, Xiangyu Liu, Rangana Warshamanage, T. Weinert, Ezequiel Panepucci, Brian K. Kobilka, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 2
Published: almost 9 years ago

10.1107/S1399004715018519

Sent packing: protein engineering generates a new crystal form of<i>Pseudomonas aeruginosa</i>DsbA1 with increased catalytic surface accessibility
Cited by: 5
Author(s): Róisín M. McMahon, M. Coincon, Stephanie Tay, Begoña Heras, Craig J. Morton, M.J. Scanlon, Jennifer L. Martin
Software Mentions: 2
Published: almost 9 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: about 5 years ago

10.1089/ars.2017.7104

Inhibition of Diverse DsbA Enzymes in Multi-DsbA Encoding Pathogens
Cited by: 33
Author(s): Makrina Totsika, Dimitrios Vagenas, Jason J. Paxman, Geqing Wang, Rabeb Dhouib, Pooja Sharma, Jennifer L. Martin, M.J. Scanlon, Begoña Heras
Software Mentions: 2
Published: about 6 years ago

10.3390/antiox10020152

Function and Regulation of Chloroplast Peroxiredoxin IIE
Cited by: 10
Author(s): Anna Dreyer, Patrick Treffon, Daniel Basiry, Anna Maria Józefowicz, Andrea Matros, Hans‐Peter Mock, Karl‐Josef Dietz
Software Mentions: 2
Published: almost 4 years ago

10.1107/S2059798316003065

A generic protocol for protein crystal dehydration using the HC1b humidity controller
Cited by: 14
Author(s): C.M.C. Lobley, James Sandy, Juan Sánchez-Weatherby, Marco Mazzorana, T. Krojer, Radosław P. Nowak, Thomas Sørensen
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0128225

Structural and Biochemical Characterization of the Francisella tularensis Pathogenicity Regulator, Macrophage Locus Protein A (MglA)
Cited by: 8
Author(s): Bonnie J. Cuthbert, Richard G. Brennan, Maria A. Schumacher
Software Mentions: 2
Published: over 9 years ago

10.3390/antiox8080240

Phlorotannins with Potential Anti-tyrosinase and Antioxidant Activity Isolated from the Marine Seaweed Ecklonia stolonifera
Cited by: 55
Author(s): Bandana Manandhar, Aditi Wagle, Su Hui Seong, Pradeep Paudel, Hyeung‐Rak Kim, Hyun Ah Jung, Jae Sue Choi
Software Mentions: 2
Published: over 5 years ago

10.1107/S2059798316001212

Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from<i>Klebsiella pneumoniae</i>and comparison with a related<i>Streptococcus pneumoniae</i>complex
Cited by: 25
Author(s): D. A. Veselkov, Ivan Laponogov, Xiao-Su Pan, Jogitha Selvarajah, Galyna B. Skamrova, Arthur Branstrom, Jana Narasimhan, J. V. N. Vara Prasad, L. Mark Fisher, Mark Sanderson
Software Mentions: 2
Published: over 8 years ago

10.3390/antiox9020180

Pharmacological Targets of Kaempferol Within Inflammatory Pathways—A Hint Towards the Central Role of Tryptophan Metabolism
Cited by: 15
Author(s): Stefanie Hofer, Simon Geisler, Rebecca Lisandrelli, Huu Tung Nguyen, Markus Ganzera, Harald Schennach, Dietmar Fuchs, Julian E. Fuchs, Johanna M. Gostner, Katharina Kurz
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0119760

In Silico Screening for Novel Inhibitors of DNA Polymerase III Alpha Subunit of Mycobacterium tuberculosis (MtbDnaE2, H37Rv)
Cited by: 14
Author(s): Alka Jadaun, Raja Sudhakar D, Naidu Subbarao, Aparna Dixit
Software Mentions: 2
Published: over 9 years ago

10.1107/S2059798321006513

Exploring ligand dynamics in protein crystal structures with ensemble refinement
Cited by: 3
Author(s): Octav Caldararu, Vilhelm Ekberg, D.T. Logan, Esko Oksanen, Ulf Ryde
Software Mentions: 2
Published: over 3 years ago

10.1107/S2059798321002941

<i>UnityMol</i> prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments
Cited by: 13
Author(s): Xavier Martinez, Marc Baaden
Software Mentions: 2
Published: over 3 years ago

10.3390/antiox8010010

Structural and Biochemical Insights into the Reactivity of Thioredoxin h1 from Chlamydomonas reinhardtii
Cited by: 14
Author(s): Christophe Marchand, Simona Fermani, Jacopo Rossi, Libero Gurrieri, Daniele Tedesco, Julien Henri, Francesca Sparla, Paolo Bernardo Trost, Stéphane D. Lemaire, Mirko Zaffagnini
Software Mentions: 2
Published: almost 6 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: about 11 years ago

10.1016/j.cell.2020.01.010

Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody
Cited by: 89
Author(s): Philipp Schommers, Henning Gruell, Morgan E. Abernathy, My-Kim Tran, Adam S. Dingens, Harry B. Gristick, Christopher O. Barnes, Till Schoofs, Maike Schlotz, Kanika Vanshylla, Christoph Kreer, Daniela Weiland, Udo Holtick, Christof Scheid, Markus M. Valter, Marit J. van Gils, Rogier W. Sanders, Jörg Janne Vehreschild, Oliver A. Cornely, Clara Lehmann, Gerd Fätkenheuer, Michael S. Seaman, Jesse D Bloom, Pamela J. Björkman, Florian Klein
Software Mentions: 2
Published: almost 5 years ago

10.3390/antiox10040624

Natural Chain-Breaking Antioxidants and Their Synthetic Analogs as Modulators of Oxidative Stress
Cited by: 10
Author(s): V. D. Kancheva, Maria Antonietta Dettori, D. Fabbri, Petko Alov, Silvia Angelova, Adriana Slavova-Kazakova, Paola Carta, Valery A. Menshov, Olga I. Yablonskaya, Aleksei V. Trofimov, Ivanka Tsakovska, Luciano Saso
Software Mentions: 2
Published: over 3 years ago

10.3390/antiox10071112

Activation of Adenosine A1 Receptor in Ischemic Stroke: Neuroprotection by Tetrahydroxy Stilbene Glycoside as an Agonist
Cited by: 10
Author(s): Ling-Yu Ruan, Guanghui Li, Wenlong Zhao, Huihui Meng, Qi Zheng, Junsong Wang
Software Mentions: 2
Published: over 3 years ago

10.3390/antibiotics9030123

A Novel, Integron-Regulated, Class C β-Lactamase
Cited by: 12
Author(s): Maria-Elisabeth Böhm, Mohammad Reza Razavi, Carl-Fredrik Flach, D. G. Joakim Larsson
Software Mentions: 2
Published: over 4 years ago

10.1107/S0907444910007493

Features and development of <i>Coot</i>
Cited by: 21,554
Author(s): Paul Emsley, Bernhard Lohkamp, William G. Scott, Kevin Cowtan
Software Mentions: 2
Published: over 14 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 9 years ago

10.1371/journal.pone.0170260

Targeted Deletion of a Plasmodium Site-2 Protease Impairs Life Cycle Progression in the Mammalian Host
Cited by: 5
Author(s): Konstantinos Koussis, Evi Goulielmaki, Anna Chalari, Chrislaine Withers‐Martinez, Inga Sidén‐Kiamos, Kai Matuschewski, Thanasis G. Loukeris
Software Mentions: 2
Published: almost 8 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

10.1107/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 9 years ago

10.1107/S2059798319010878

X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein
Cited by: 17
Author(s): Hiromi Yoshida, Katsuhiro Kojima, Masaki Shiota, Keiichi Yoshimatsu, Tomohiko Yamazaki, Stefano Ferri, Wakako Tsugawa, Shigehiro Kamitori, Koji Sode
Software Mentions: 2
Published: about 5 years ago

10.1128/AEM.00449-17

Rational Engineering of a Cold-Adapted α-Amylase from the Antarctic Ciliate Euplotes focardii for Simultaneous Improvement of Thermostability and Catalytic Activity
Cited by: 31
Author(s): Guang Yang, Hua Yang, Matteo Mozzicafreddo, Patrizia Ballarini, Sandra Pucciarelli, Cristina Miceli
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.0187628

Plant-type phytoene desaturase: Functional evaluation of structural implications
Cited by: 25
Author(s): Julian Koschmieder, M. Fehling-Kaschek, Patrick Schaub, Sandro Ghisla, Anton Brausemann, Jens Timmer, Peter Beyer
Software Mentions: 2
Published: almost 7 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

10.1371/journal.pone.0206143

Primary structures of different isoforms of buffalo pregnancy-associated glycoproteins (BuPAGs) during early pregnancy and elucidation of the 3-dimensional structure of the most abundant isoform BuPAG 7
Cited by: 7
Author(s): Masoud Lotfan, Suman Choudhary, Munna Lal Yadav, Sudarshan Kumar, Surender Singh, Shveta Bathla, Preeti Rawat, Jai K. Kaushik, Ashok Kumar Mohanty
Software Mentions: 2
Published: about 6 years ago

10.1107/S2059798318017825

Coping with strong translational noncrystallographic symmetry and extreme anisotropy in molecular replacement with <i>Phaser</i>: human Rab27a
Cited by: 8
Author(s): Mostafa Jamshidiha, Inmaculada Pérez‐Dorado, James W. Murray, Edward W. Tate, Ernesto Cota, Randy J. Read
Software Mentions: 2
Published: over 5 years ago

10.1038/cddis.2015.118

Conversion of cell-survival activity of Akt into apoptotic death of cancer cells by two mutations on the BIM BH3 domain
Cited by: 8
Author(s): J. S. Kim, Bonsu Ku, Tae Gyun Woo, Ah Young Oh, Youn-Sang Jung, Young‐Min Soh, Ji-Hyun Yeom, K. Lee, B. J. Park, Byung Ha Oh, Nam‐Chul Ha
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0092636

In-Silico Analysis of Binding Site Features and Substrate Selectivity in Plant Flavonoid-3-O Glycosyltransferases (F3GT) through Molecular Modeling, Docking and Dynamics Simulation Studies
Cited by: 12
Author(s): Ranu Sharma, Priyabrata Panigrahi, C.G. Suresh
Software Mentions: 2
Published: over 10 years ago

10.1038/s41419-020-2344-0

Deguelin suppresses non-small cell lung cancer by inhibiting EGFR signaling and promoting GSK3β/FBW7-mediated Mcl-1 destabilization
Cited by: 34
Author(s): Feng Gao, Xinfang Yu, Ming Li, Liqun Zhou, Wenbin Liu, Wei Li, Haidan Liu
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0096809

Calponin-Like Chd64 Is Partly Disordered
Cited by: 10
Author(s): Małgorzata Kozłowska, Aneta Tarczewska, Michał Jakób, Kamil Szpotkowski, Magdalena Wojtas, Grzegorz Rymarczyk, Andrzej Ożyhar
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0251067

Heterogeneous multimeric structure of isocitrate lyase in complex with succinate and itaconate provides novel insights into its inhibitory mechanism
Cited by: 4
Author(s): Sunghoon Kwon, Hye Lin Chun, Hyekyung Ha, So Yeon Lee, Hyun Ho Park
Software Mentions: 2
Published: over 3 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 9 years ago

10.1038/s41421-018-0073-7

Coxsackievirus A10 atomic structure facilitating the discovery of a broad-spectrum inhibitor against human enteroviruses
Cited by: 25
Author(s): Jinhuan Chen, Xiaohua Ye, Xueyang Zhang, Zhiyuan Zhu, Xiang Zhang, Zhijian Xu, Zhanyu Ding, Gang Zou, Renjie Li, Liangliang Kong, Wen Jiang, Weiliang Zhu, Cong Yao, Zhong Huang
Software Mentions: 2
Published: almost 6 years ago

10.1007/s00253-017-8161-4

Trichoderma reesei xylanase 5 is defective in the reference strain QM6a but functional alleles are present in other wild-type strains
Cited by: 8
Author(s): Jonas Ramoni, Martina Marchetti‐Deschmann, Verena Seidl‐Seiboth, Bernhard Schink
Software Mentions: 2
Published: over 7 years ago

10.1107/S205979831801519X

Iron–sulfur clusters have no right angles
Cited by: 15
Author(s): Nigel W. Moriarty, Paul D. Adams
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0082484

Structure-Based Analysis of A19D, a Variant of Transthyretin Involved in Familial Amyloid Cardiomyopathy
Cited by: 5
Author(s): Priscila S. Ferreira, Oliveira Sant’Anna, Nathalia Varejão, Cristina Ferreira Lima, Sérgio A. P. Novis, Renata V. Barbosa, Concy M. Caldeira, Franklin David Rumjanek, Salvador Ventura, Márcia Waddington Cruz, Débora Foguel
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0008949

An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome
Cited by: 26
Author(s): Danny A. Bitton, Duncan L. Smith, Yvonne Connolly, Paul J. Scutt, Crispin Miller
Software Mentions: 2
Published: almost 15 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.0115409

Characterization of M. tuberculosis SerB2, an Essential HAD-Family Phosphatase, Reveals Novel Properties
Cited by: 12
Author(s): Gaya P. Yadav, Sonal Shree, Ruchi Maurya, Niyati Rai, Diwakar Singh, Kirti Srivastava, Ravishankar Ramachandran
Software Mentions: 2
Published: almost 10 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.0105984

Cleavage Specificity Analysis of Six Type II Transmembrane Serine Proteases (TTSPs) Using PICS with Proteome-Derived Peptide Libraries
Cited by: 46
Author(s): Olivier Barré, Antoine Dufour, Ulrich Eckhard, Reinhild Kappelhoff, François Béliveau, Richard Leduc, Christopher M. Overall
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0050769

Using RosettaLigand for Small Molecule Docking into Comparative Models
Cited by: 38
Author(s): Kristian Kaufmann, Jens Meiler
Software Mentions: 2
Published: almost 12 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/S090744491302252X

Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2
Cited by: 53
Author(s): Naoki Horikoshi, Koichi Sato, Keisuke Shimada, Yasuhiro Arimura, Akihisa Osakabe, Hiroaki Tachiwana, Yoko Hayashi‐Takanaka, W. Iwasaki, Wataru Kagawa, Masahiko Harata, Hiroshi Kimurâ, Hitoshi Kurumizaka
Software Mentions: 2
Published: about 11 years ago

10.1038/s42003-019-0562-8

Identification of an amphipathic peptide sensor of the Bacillus subtilis fluid membrane microdomains
Cited by: 5
Author(s): Yiping Jiang, Xin Dai, Mingming Qin, Zhihong Guo
Software Mentions: 2
Published: over 5 years ago

10.1107/S1399004714018732

Structural basis for the recognition of muramyltripeptide by<i>Helicobacter pylori</i>Csd4, a<scp>D</scp>,<scp>L</scp>-carboxypeptidase controlling the helical cell shape
Cited by: 19
Author(s): Hyoun Sook Kim, Jieun Kim, Ha Na Im, Doo Ri An, Mijoon Lee, Dušan Hesek, Shahriar Mobashery, Jin Young Kim, Kun Cho, Hye Jin Yoon, Byung Woo Han, Byung Il Lee, Se Won Suh
Software Mentions: 2
Published: about 10 years ago

10.1038/s42003-018-0236-y

The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release
Cited by: 19
Author(s): Heidi B. Cao, Mu Gao, Hongyi Zhou, Jeffrey Skolnick
Software Mentions: 2
Published: almost 6 years ago

10.1038/s42003-018-0203-7

Structural basis for activation of plasma-membrane Ca2+-ATPase by calmodulin
Cited by: 28
Author(s): Julius Nitsche, Inokentijs Josts, Johannes Heidemann, Haydyn D. T. Mertens, Selma Maric, Martine Moulin, Michael Haertlein, Sebastian Büsch, V. Trevor Forsyth, Dmitri I. Svergun, Charlotte Uetrecht, Henning Tidow
Software Mentions: 2
Published: almost 6 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

10.1107/S2059798320008049

Fragment-based determination of a proteinase K structure from MicroED data using <i>ARCIMBOLDO_SHREDDER</i>
Cited by: 12
Author(s): Logan S. Richards, Claudia Millán, Jennifer Miao, Michael W. Martynowycz, M.R. Sawaya, Tamir Gonen, Rafael J. Borges, Isabel Usón, José A. Rodríguez
Software Mentions: 2
Published: over 4 years ago

10.1038/s42003-018-0262-9

Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters
Cited by: 19
Author(s): Yong Wei, Zi Jian Xiong, Jun Li, Chunxia Zou, Christopher W. Cairo, John S. Klassen, Gilbert G. Privé
Software Mentions: 2
Published: almost 6 years ago

10.1107/S0907444912039042

Structure of the catalytic domain of the<i>Salmonella</i>virulence factor SseI
Cited by: 16
Author(s): Shyam S. Bhaskaran, C. Erec Stebbins
Software Mentions: 2
Published: about 12 years ago

10.1038/s42003-021-02326-4

Structure-based insights into evolution of rhodopsins
Cited by: 13
Author(s): Dmitrii Zabelskii, Natalia I. Dmitrieva, Oleksandr Volkov, Vitaly Shevchenko, Kirill Kovalev, Taras Balandin, Dmytro Soloviov, Roman Astashkin, Egor V. Zinovev, Alexey Alekseev, Ekaterina Round, Vitaly Polovinkin, Igor Chizhov, Andrey Rogachev, Ivan Okhrimenko, Valentin Borshchevskiy, Vladimir Chupin, Georg Büldt, Natalia Yutin, Ernst Bamberg, Eugene V. Koonin, Valentin Gordeliy
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0209420

Deciphering the ATP-binding mechanism(s) in NLRP-NACHT 3D models using structural bioinformatics approaches
Cited by: 22
Author(s): Jitendra Maharana, Debashis Panda, Sachinandan De
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2091-12-59

Delineation of the Pasteurellaceae-specific GbpA-family of glutathione-binding proteins
Cited by: 8
Author(s): Bjorn Vergauwen, Ruben Van der Meeren, Ann Dansercoer, Savvas N. Savvides
Software Mentions: 2
Published: almost 14 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

10.1038/s42003-020-01640-7

Molecular basis of IRGB10 oligomerization and membrane association for pathogen membrane disruption
Cited by: 8
Author(s): Hyekyung Ha, Hye Lin Chun, So Yeon Lee, Jin Ho Jeong, Yeon-Gil Kim, Hyun Ho Park
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2091-12-12

The Peroxisomal Targeting Signal 1 in sterol carrier protein 2 is autonomous and essential for receptor recognition
Cited by: 9
Author(s): Chris Williams, Nicole Schueller, Colin A. Thompson, Marlene van den Berg, Simon D. van Haren, Ralf Erdmann, Charles S. Bond, Ben Distel, Wolfgang Schliebs, Matthias Wilmanns, Will A. Stanley
Software Mentions: 2
Published: over 13 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

10.1371/journal.pone.0029406

Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII
Cited by: 21
Author(s): Melanie I. Stefan, David P. Marshall, Nicolas Le Novère
Software Mentions: 2
Published: almost 13 years ago

10.1002/ana.24073

<i>GRIN2B</i> mutations in west syndrome and intellectual disability with focal epilepsy
Cited by: 176
Author(s): Johannes R. Lemke, Rik Hendrickx, Kirsten Geider, Bodo Laube, Michael Schwake, Robert J. Harvey, Victoria M. James, Alex Pepler, Isabelle Steiner, Konstanze Hörtnagel, John Neidhardt, Susanne Ruf, Markus Wolff, Deborah Bartholdi, Roberto Caraballo, Konrad Platzer, Arvid Suls, Peter De Jonghe, Saskia Biskup, Sarah Weckhuysen
Software Mentions: 2
Published: almost 11 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

10.1038/s42003-020-01283-8

Structural role of essential light chains in the apicomplexan glideosome
Cited by: 8
Author(s): Samuel Pažický, Karthikeyan Dhamotharan, Karol Kaszuba, Haydyn D. T. Mertens, Tim‐Wolf Gilberger, Dmitri I. Svergun, Jan Kosiński, Ulrich Weininger, Christian Löw
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0103099

In Silico Modeling of Human α2C-Adrenoreceptor Interaction with Filamin-2
Cited by: 11
Author(s): Marcin Pawłowski, Saras Saraswathi, Hanaa K. B. Motawea, Maqsood A. Chotani, Andrzej Kloczkowski
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0041710

Predicting HLA Class I Non-Permissive Amino Acid Residues Substitutions
Cited by: 21
Author(s): T.A. Binkowski, Susana R. Marino, A. Joachimiak
Software Mentions: 2
Published: over 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: about 11 years ago

10.1016/j.csbj.2021.08.012

Computationally grafting an IgE epitope onto a scaffold: Implications for a pan anti-allergy vaccine design
Cited by: 1
Author(s): Sari Sabban
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.csbj.2021.06.006

A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis
Cited by: 13
Author(s): P. Gupta, S.E. Thomas, Shaymaa A. Zaidan, Maria A. Pasillas, J. Cory-Wright, Víctor Sebastián-Pérez, Ailidh Burgess, Emma Cattermole, C. Meghir, Chris Abell, Anthony G. Coyne, William R. Jacobs, Tom L. Blundell, Sangeeta Tiwari, V. Mendes
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2105-9-554

ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family
Cited by: 9
Author(s): Alberto I. Roca, Albert E. Almada, Aaron Abajian
Software Mentions: 2
Published: almost 16 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.0245358

Insights into structure and dynamics of extracellular domain of Toll-like receptor 5 in Cirrhinus mrigala (mrigala): A molecular dynamics simulation approach
Cited by: 8
Author(s): Ajaya Kumar Rout, Varsha Acharya, Diptimayee Maharana, Budheswar Dehury, Sheela Rani Udgata, Rajkumar Jena, Bhaskar Behera, Pranaya Kumar Parida, Bijay Kumar Behera
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0017624

Structure and Function of the First Full-Length Murein Peptide Ligase (Mpl) Cell Wall Recycling Protein
Cited by: 24
Author(s): Debanu Das, Mireille Hervé, Julie Feuerhelm, Carol L. Farr, Hsiu‐Ju Chiu, Marc‐André Elsliger, Mark W. Knuth, Heath E. Klock, Mitchell D. Miller, Adam Godzik, Scott A. Lesley, Ashley M. Deacon, Dominique Mengin‐Lecreulx, Ian A. Wilson
Software Mentions: 2
Published: over 13 years ago

10.1016/j.csbj.2021.05.035

Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker
Cited by: 6
Author(s): N.M. Hoitsma, Timothy H. Click, Pratul K. Agarwal, Bret Freudenthal
Software Mentions: 2
Published: almost 4 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 6 years ago

10.1371/journal.pone.0196642

Structure of frequency-interacting RNA helicase from Neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance
Cited by: 9
Author(s): Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean Johnson
Software Mentions: 2
Published: over 6 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.0195355

Solution scattering study of the Bacillus subtilis PgdS enzyme involved in poly-γ-glutamic acids degradation
Cited by: 1
Author(s): Jumei Zeng, Yipeng Jin, Zhongchuan Liu
Software Mentions: 2
Published: over 6 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

10.1186/1471-2105-12-207

HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information
Cited by: 39
Author(s): Rong Liu, Jianjun Hu
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0130888

Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies
Cited by: 16
Author(s): Shannon E. Hill, Rebecca K. Donegan, Elaine Nguyen, Tanay M. Desai, Raquel L. Lieberman
Software Mentions: 2
Published: over 9 years ago