10.1371/journal.pone.0156067

Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana
Cited by: 0
Author(s): Yuan Xie, Li Mei, Wenrui Chang
Software Mentions: 3
Published: over 10 years ago

10.7554/eLife.56889

An ER translocon for multi-pass membrane protein biogenesis
Cited by: 68
Author(s): Philip T. McGilvray, S. Anghel, Arunkumar Sundaram, Frank Zhong, Michael J. Trnka, James R. Fuller, Hong Yu Hu, Alma L. Burlingame, Robert J. Keenan
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.41741

Crystal structure of a natural light-gated anion channelrhodopsin
Cited by: 30
Author(s): Hai Li, Chia‐Ying Huang, Elena G. Govorunova, Christopher T. Schafer, Oleg A. Sineshchekov, Meitian Wang, Lei Zheng, John L. Spudich
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.50175

Ligand recognition and gating mechanism through three ligand-binding sites of human TRPM2 channel
Cited by: 64
Author(s): Yongyang Huang, Becca Roth, Wei Lü, Juan Du
Software Mentions: 3
Published: about 7 years ago

10.7554/eLife.42426

TRIM28 promotes HIV-1 latency by SUMOylating CDK9 and inhibiting P-TEFb
Cited by: 61
Author(s): Xiancai Ma, Tao Yang, Yong Luo, Liyang Wu, Yawen Jiang, Sifa Zheng, Ting Pan, Bingfeng Liu, Guangyan Liu, Jun Li, Fei Yu, Zhangping He, Wanying Zhang, Jinyu Yang, Liting Liang, Yuanjun Guan, Xu Zhang, Linghua Li, Weiping Cai, Xiaoping Tang, Song Gao, Kai Deng, Hui Zhang
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms21228420

Methods and Applications of In Silico Aptamer Design and Modeling
Cited by: 59
Author(s): Andrey A. Buglak, А. В. Самохвалов, Anatoly V. Zherdev, Boris B. Dzantiev
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.bpj.2018.09.002

Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR
Cited by: 3
Author(s): Graham M. Saunders, Hannah E. Bruce Macdonald, Jonathan W. Essex, Syma Khalid
Software Mentions: 3
Published: almost 8 years ago

10.1016/j.yjsbx.2020.100031

In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors
Cited by: 1
Author(s): Jingxu Guo, A. Douangamath, Weixiao Song, Alun R. Coker, A. W. Edith Chan, Steve Wood, J.B. Cooper, E. Resnick, Nir London, F. von Delft
Software Mentions: 3
Published: over 6 years ago

10.1128/JVI.01664-19

Structure of Merkel Cell Polyomavirus Capsid and Interaction with Its Glycosaminoglycan Attachment Receptor
Cited by: 12
Author(s): Niklas Johannes Bayer, Dovile Januliene, Georg Zocher, Thilo Stehle, Arne Moeller, Bärbel S. Blaum
Software Mentions: 3
Published: almost 6 years ago

10.1007/s00792-013-0542-8

The role of disulfide bond in hyperthermophilic endocellulase
Cited by: 13
Author(s): Han-Woo Kim, Kazuhiko Ishikawa
Software Mentions: 3
Published: over 13 years ago

10.1016/j.molimm.2016.11.021

Room temperature structure of human IgG4-Fc from crystals analysed in situ
Cited by: 7
Author(s): Anna M. Davies, Theo Rispens, Pleuni Ooijevaar-de Heer, Rob C. Aalberse, Brian J. Sutton
Software Mentions: 3
Published: over 9 years ago

10.1016/j.molimm.2017.11.022

Crystal structures of murine and human Histamine-Releasing Factor (HRF/TCTP) and a model for HRF dimerisation in mast cell activation
Cited by: 12
Author(s): K.A. Dore, Jun‐ichi Kashiwakura, James M. McDonnell, Hannah Gould, Toshiaki Kawakami, Brian J. Sutton, Anna M. Davies
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0121415

Structural Models of Zebrafish (Danio rerio) NOD1 and NOD2 NACHT Domains Suggest Differential ATP Binding Orientations: Insights from Computational Modeling, Docking and Molecular Dynamics Simulations
Cited by: 31
Author(s): Jitendra Maharana, Bikash R. Sahoo, Aritra Bej, Itishree Jena, Arunima Parida, Jyoti Ranjan Sahoo, Budheswar Dehury, Mahesh Chandra Patra, Sushma Rani Martha, Sucharita Balabantray, Sukanta Kumar Pradhan, Bijay Kumar Behera
Software Mentions: 3
Published: over 11 years ago

10.1002/mgg3.267

A molecular analysis of the<i>GBA</i>gene in Caucasian South Africans with Parkinson's disease
Cited by: 13
Author(s): Melinda Barkhuizen, David G. Anderson, Francois H. van der Westhuizen, Anne Grobler
Software Mentions: 3
Published: over 9 years ago

10.1016/j.bpj.2018.03.040

Evaluating Anti-CD32b F(ab) Conformation Using Molecular Dynamics and Small-Angle X-Ray Scattering
Cited by: 3
Author(s): Emma J. Sutton, Richard T. Bradshaw, Christian M. Orr, Björn Frendéus, Gunilla Larsson, Ingrid Teige, Mark S. Cragg, Ivo Tews, Jonathan W. Essex
Software Mentions: 3
Published: about 8 years ago

10.1038/s42003-018-0063-1

Transient antibody-antigen interactions mediate the strain-specific recognition of a conserved malaria epitope
Cited by: 6
Author(s): Bankala Krishnarjuna, Toshihiko Sugiki, Rodrigo Morales, Jeffrey Seow, Toshimichi Fujiwara, Karyn L. Wilde, Raymond S. Norton, Christopher A. MacRaild
Software Mentions: 3
Published: over 8 years ago

10.1016/j.cell.2021.02.045

Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling
Cited by: 18
Author(s): R.A. Robinson, Samuel C. Griffiths, Lieke L van de Haar, Tomas Malinauskas, Eljo Y. van Battum, Pavol Zelina, Rebekka A. Schwab, Dimple Karia, L. Malinauskaite, Sara Brignani, Marleen H. van den Munkhof, O. Dudukcu, A.A. De Ruiter, Dianne M.A. van den Heuvel, B. Bishop, J. Elegheert, A. Radu Aricescu, R. Jeroen Pasterkamp, Christian Siebold
Software Mentions: 3
Published: over 5 years ago

10.1111/cea.12230

Human <scp>I</scp> g <scp>E</scp> against the major allergen <scp>B</scp> et v 1 – defining an epitope with limited cross‐reactivity between different <scp>PR</scp> ‐10 family proteins
Cited by: 20
Author(s): Mattias Levin, Anna M. Davies, Maria Liljekvist, Fredrika Carlsson, Hannah J. Gould, Brian J. Sutton, Mats Ohlin
Software Mentions: 3
Published: over 12 years ago

10.1038/s41421-020-00215-4

A novel multistage antiplasmodial inhibitor targeting Plasmodium falciparum histone deacetylase 1
Cited by: 20
Author(s): Zhenghui Huang, Ruoxi Li, Tongke Tang, Dazheng Ling, Manjiong Wang, Dandan Xu, Maoxin Sun, Lulu Zheng, Feng Zhu, Hui Min, Rachasak Boonhok, Yan Ding, Yang Wen, Zhong Chen, Xiaokang Li, Yuxi Chen, Taiping Liu, Jiping Han, Jun Miao, Qiang Fang, Yaming Cao, Yun Tang, Jie Cui, Wei Xu, Liwang Cui, Jin Zhu, Gary Wong, Jian Li, Lubin Jiang
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.cell.2020.10.004

SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses
Cited by: 394
Author(s): Abhik Banerjee, Mario R. Blanco, Emily A. Bruce, Drew D. Honson, Linlin M. Chen, Amy Chow, Prashant Bhat, Noah Ollikainen, Sofia A. Quinodoz, Colin Loney, Jasmine Thai, Zachary D. Miller, Aaron E. Lin, Madaline M Schmidt, Douglas G. Stewart, Daniel Goldfarb, Giuditta De Lorenzo, Suzannah J. Rihn, R.M. Voorhees, Jason Botten, Devdoot Majumdar, Mitchell Guttman
Software Mentions: 3
Published: almost 6 years ago

10.1038/s42003-021-02532-0

Modulation of Toll-like receptor 1 intracellular domain structure and activity by Zn2+ ions
Cited by: 7
Author(s): Владислав А. Лушпа, Marina V. Goncharuk, Cong Lin, Arthur O. Zalevsky, Irina A. Talyzina, Aleksandra Luginina, Daniil Vakhrameev, M.B. Shevtsov, Sergey A. Goncharuk, Alexander S. Arseniev, Valentin Borshchevskiy, Xiaohui Wang, K.S. Mineev
Software Mentions: 3
Published: about 5 years ago

10.1016/j.cell.2018.11.025

The Molecular Mechanism of Transport by the Mitochondrial ADP/ATP Carrier
Cited by: 206
Author(s): Jonathan J. Ruprecht, Martin King, Thomas Zögg, Antoniya A. Aleksandrova, Els Pardon, Paul G. Crichton, Jan Steyaert, Edmund R. S. Kunji
Software Mentions: 3
Published: over 7 years ago

10.3390/molecules25153530

Flavonoids and Terpenoids with PTP-1B Inhibitory Properties from the Infusion of Salvia amarissima Ortega
Cited by: 14
Author(s): Eric D. Salinas-Arellano, Araceli Pérez-Vásquez, Isabel Rivero‐Cruz, Rafael Torres-Colín, Martín González-Andrade, Manuel Rangel‐Grimaldo, Rachel Mata
Software Mentions: 3
Published: about 6 years ago

10.3390/cancers13071618

Covalent Cysteine Targeting of Bruton’s Tyrosine Kinase (BTK) Family by Withaferin-A Reduces Survival of Glucocorticoid-Resistant Multiple Myeloma MM1 Cells
Cited by: 10
Author(s): Emilie Logie, Chandra Sekhar Chirumamilla, Claudina Pérez-Novo, Priyanka Shaw, Ken Declerck, Ajay Palagani, Savithri Rangarajan, Bart Cuypers, Nicolas De Neuter, Mobashar Hussain Urf Turabe Fazil, Navin Kumar Verma, Annemie Bogaerts, Kris Laukens, Fritz Offner, Pieter Van Vlierberghe, Xaveer Van Ostade, Wim Vanden Berghe
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-39984-8

Insights into the dynamic nature of the dsRNA-bound TLR3 complex
Cited by: 27
Author(s): Vijayakumar Gosu, Seung‐Woo Son, Donghyun Shin, Ki Duk Song
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-39588-2

The IKK-binding domain of NEMO is an irregular coiled coil with a dynamic binding interface
Cited by: 18
Author(s): Adam H. Barczewski, Michael J. Ragusa, Dale F. Mierke, Maria Pellegrini
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-40432-w

Reactive centre loop dynamics and serpin specificity
Cited by: 28
Author(s): Emilia M. Marijanovic, James Fodor, Blake T. Riley, Benjamin T. Porebski, Maurício G. S. Costa, Itamar Kass, David E. Hoke, Sheena McGowan, Ashley M. Buckle
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-37506-6

Mechanism of action of the moonlighting protein EfTu as a Substance P sensor in Bacillus cereus
Cited by: 9
Author(s): Awa Ndiaye, Valérie Borrel, Pierre‐Jean Racine, Thomas Clamens, Ségolène Depayras, Olivier Maillot, Béatrice Schaack, Sylvie Chevalier, Olivier Lesouhaitier, Marc Feuilloley
Software Mentions: 3
Published: over 7 years ago

10.3390/biom11070929

Discovery of Novel Allosteric Modulators Targeting an Extra-Helical Binding Site of GLP-1R Using Structure- and Ligand-Based Virtual Screening
Cited by: 7
Author(s): Qingtong Zhou, Wei Guo, Antao Dai, Xiaoqing Cai, Márton Vass, Chris de Graaf, Shui Wang, Suwen Zhao, Dehua Yang, Ming Wei Wang
Software Mentions: 3
Published: about 5 years ago

10.1016/j.dib.2016.01.016

Molecular determinants and interaction data of cyclic peptide inhibitor with the extracellular domain of TrkB receptor
Cited by: 5
Author(s): Nitin Chitranshi, Vivek Kumar Gupta, Yogita Dheer, Veer Bala Gupta, Roshana Vander Wall, Stuart L. Graham
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pcbi.1007892

Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans
Cited by: 2
Author(s): Chadi M. Saad-Roy, Nimalan Arinaminpathy, Ned S. Wingreen, Simon A. Levin, Joshua M. Akey, Bryan T. Grenfell
Software Mentions: 3
Published: about 6 years ago

10.1128/JVI.00828-17

Cooperation between Strain-Specific and Broadly Neutralizing Responses Limited Viral Escape and Prolonged the Exposure of the Broadly Neutralizing Epitope
Cited by: 35
Author(s): Colin Anthony, Talita York, Valerie Bekker, David Matten, Philippe Selhorst, Roux-Cil. Ferreria, Nigel Garrett, Salim S. Abdool Karim, Lynn Morris, Natasha T. Wood, Penny L. Moore, Carolyn Williamson
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-019-40564-z

Decline of transmissible gastroenteritis virus and its complex evolutionary relationship with porcine respiratory coronavirus in the United States
Cited by: 38
Author(s): Fangzhou Chen, Todd P. Knutson, Stephanie Rossow, Linda J. Saif, Douglas Marthaler
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-34508-2

“Infostery” analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations
Cited by: 16
Author(s): Yasaman Karami, Tristan Bitard‐Feildel, Élodie Laine, Alessandra Carbone
Software Mentions: 3
Published: almost 8 years ago

10.3390/ijms21207683

Hydroxylation of Antitubercular Drug Candidate, SQ109, by Mycobacterial Cytochrome P450
Cited by: 12
Author(s): Sergey Bukhdruker, Tatsiana Varaksa, Irina Grabovec, Egor Marin, Polina Shabunya, Maria Kadukova, Sergei Grudinin, Anton Kavaleuski, Anastasiia Gusach, Andrei A. Gilep, Valentin Borshchevskiy, Natallia Strushkevich
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0083496

Exploration of Virtual Candidates for Human HMG-CoA Reductase Inhibitors Using Pharmacophore Modeling and Molecular Dynamics Simulations
Cited by: 17
Author(s): Maeng-Hyun Son, Ayoung Baek, Sugunadevi Sakkiah, Chanin Park, John Strouboulis, Keun Woo Lee
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-018-33193-5

Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas
Cited by: 10
Author(s): Hong‐Hsiang Guan, Yin-Cheng Hsieh, Po‐Chun Lin, Yen‐Chieh Huang, Masato Yoshimura, Liying Chen, Shao-Kang Chen, Phimonphan Chuankhayan, Chien-Chih Lin, Nai-Chi Chen, Atsushi Nakagawa, Sunney I. Chan, Chun‐Jung Chen
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-36267-6

The reduced activity of PP-1α under redox stress condition is a consequence of GSH-mediated transient disulfide formation
Cited by: 7
Author(s): Simranjit Singh, Simon Lämmle, Heiko Giese, Susanne Kämmerer, Stefanie Meyer-Roxlau, Ezzaldin Ahmed Alfar, Hassan Dihazi, Kaomei Guan, Ali El‐Armouche, Florian Richter
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-32040-x

The potential HLA Class I-restricted epitopes derived from LeIF and TSA of Leishmania donovani evoke anti-leishmania CD8+ T lymphocyte response
Cited by: 20
Author(s): Manas Ranjan Dikhit, Sushmita Das, Vijaya Mahantesh, Akhilesh Kumar, Ashish Kumar Singh, Budheswar Dehury, Ajaya Kumar Rout, Vahab Ali, Ganesh Chandra Sahoo, Roshan Kamal Topno, Krishna Pandey, Vidya Nand Rabi Das, Sanjiva Bimal, Pradeep Das
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.59753

Structures of diverse poxin cGAMP nucleases reveal a widespread role for cGAS-STING evasion in host–pathogen conflict
Cited by: 29
Author(s): J.B. Eaglesham, Kacie McCarty, Philip J. Kranzusch
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-29865-x

EPO does not promote interaction between the erythropoietin and beta-common receptors
Cited by: 18
Author(s): Karen S. Cheung Tung Shing, Sophie E. Broughton, Tracy L. Nero, Kevin R. Gillinder, Melissa Ilsley, Hayley S. Ramshaw, Angel F. Lopez, Michael D. W. Griffin, Michael W. Parker, Andrew C. Perkins, Urmi Dhagat
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-33068-9

Spider silk proteome provides insight into the structural characterization of Nephila clavipes flagelliform spidroin
Cited by: 26
Author(s): José Roberto Aparecido dos Santos-Pinto, Helen Andrade Arcuri, Franciele Grego Esteves, Mário Sérgio Palma, Gert Lübec
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-37699-w

The EZH2 SANT1 domain is a histone reader providing sensitivity to the modification state of the H4 tail
Cited by: 15
Author(s): Tyler Weaver, Jiachen Liu, Katelyn E. Connelly, Chris Coble, Katayoun Varzavand, Emily C. Dykhuizen, Catherine A. Musselman
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-40323-0

Molecular cloning, GTP recognition mechanism and tissue-specific expression profiling of myxovirus resistance (Mx) protein in Labeo rohita (Hamilton) after Poly I:C induction
Cited by: 14
Author(s): Basanta Kumar Das, Pragyan Roy, Ajaya Kumar Rout, Deepak Ranjan Sahoo, Soumya Prasad Panda, Sushmita Pattanaik, Budheswar Dehury, Bijay Kumar Behera, Sudhansu Sekhar Mishra
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-01640-4

Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern
Cited by: 7
Author(s): L. Xue, Qingping Wu, Ruimin Dong, Weiping Cai, Haoming Wu, Moutong Chen, Gang Chen, Juan Wang, Jumei Zhang
Software Mentions: 3
Published: about 9 years ago

10.1038/srep13652

Dimeric interactions and complex formation using direct coevolutionary couplings
Cited by: 72
Author(s): Ricardo Nascimento dos Santos, Faruck Morcos, Biman Jana, Adriano D. Andricopulo, José N. Onuchic
Software Mentions: 3
Published: about 11 years ago

10.1038/s41598-017-08747-8

Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters
Cited by: 56
Author(s): Venkata Krishnan Ramaswamy, Attilio Vittorio Vargiu, Giuliano Malloci, Jürg Dreier, Paolo Ruggerone
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.ppat.1005165

Structure Elucidation of Coxsackievirus A16 in Complex with GPP3 Informs a Systematic Review of Highly Potent Capsid Binders to Enteroviruses
Cited by: 19
Author(s): Luigi De Colibus, Xiangxi Wang, Aloys Tijsma, Johan Neyts, John A. B. Spyrou, Jingshan Ren, Jonathan M. Grimes, Gerhard Puerstinger, Pieter Leyssen, Elizabeth E. Fry, Zihe Rao, David I. Stuart
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.ppat.1003403

The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence
Cited by: 65
Author(s): Anne Marie Hansen, Raghothama Chaerkady, Jyoti Sharma, J. Javier Díaz-Mejía, Nidhi Tyagi, Santosh Renuse, Harrys K.C. Jacob, Sneha M. Pinto, Nandini A. Sahasrabuddhe, Min‐Sik Kim, Bernard Delanghe, Narayanaswamy Srinivasan, Andrew Emili, James B. Kaper, Akhilesh Pandey
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pcbi.1006722

Identifying individual risk rare variants using protein structure guided local tests (POINT)
Cited by: 8
Author(s): Rachel West, Wenbin Lu, Daniel M. Rotroff, Mélaine A. Kuenemann, Sheng Mao Chang, Michael C. Wu, Michael J. Wagner, John B. Buse, Alison A. Motsinger‐Reif, Denis Fourches, Jung Ying Tzeng
Software Mentions: 3
Published: over 7 years ago

10.1126/sciadv.aaq0762

Structures of monomeric and oligomeric forms of the <i>Toxoplasma gondii</i> perforin-like protein 1
Cited by: 28
Author(s): Ni Tien, Sophie I. Williams, Saša Rezelj, Gregor Anderluh, K. Harlos, Phillip J. Stansfeld, Robert J.C. Gilbert
Software Mentions: 3
Published: over 8 years ago

10.1111/febs.13310

Inter‐domain electron transfer in cellobiose dehydrogenase: modulation by <scp>pH</scp> and divalent cations
Cited by: 49
Author(s): Daniel Kracher, Kawah Zahma, Christopher Schulz, Christoph Sygmund, Lo Gorton, Roland Ludwig
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-017-08842-w

Exploring Leishmania secretory proteins to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach
Cited by: 226
Author(s): Nazia Khatoon, Rajan Kumar Pandey, Vijay Kumar Prajapati
Software Mentions: 3
Published: about 9 years ago

10.1016/j.jbc.2021.101061

A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase
Cited by: 7
Author(s): Emily Chen, Krystle Reiss, Dilip Shah, R Manjula, Brandon Allen, Eva Murphy, James W. Murphy, Víctor S. Batista, Vineet Bhandari, Elias Lolis, George P. Lisi
Software Mentions: 3
Published: about 5 years ago

10.1074/jbc.RA119.010697

Structural basis of cell-surface signaling by a conserved sigma regulator in Gram-negative bacteria
Cited by: 3
Author(s): Jaime L. Jensen, Beau D. Jernberg, Sangita C. Sinha, Christopher L. Colbert
Software Mentions: 3
Published: over 6 years ago

10.1016/j.jbc.2021.100384

Bacillus subtilis YngB contributes to wall teichoic acid glucosylation and glycolipid formation during anaerobic growth
Cited by: 8
Author(s): Chih-Hung Wu, Jeanine Rismondo, Rhodri M. L. Morgan, Yang Shen, Martin J. Loessner, Gérald Larrouy-Maumus, Paul S. Freemont, Angelika Gründling
Software Mentions: 3
Published: over 5 years ago

10.3389/frobt.2018.00133

Authenticity, Interactivity, and Collaboration in VR Learning Games
Cited by: 9
Author(s): Meredith Thompson, Annie Wang, Dan Roy, Eric Klopfer
Software Mentions: 3
Published: over 7 years ago

10.1534/g3.119.400224

Contraction of the ROS Scavenging Enzyme Glutathione<i>S</i>-Transferase Gene Family in Cetaceans
Cited by: 11
Author(s): Ran Tian, Inge Seim, Wenhua Ren, Shixia Xu
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pcbi.1004805

Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications
Cited by: 73
Author(s): Vaclav Cvicek, William A. Goddard, Ravinder Abrol
Software Mentions: 3
Published: over 10 years ago

10.3390/genes12010034

Biological Regulatory Network (BRN) Analysis and Molecular Docking Simulations to Probe the Modulation of IP3R Mediated Ca2+ Signaling in Cancer
Cited by: 2
Author(s): Humaira Ismatullah, Ishrat Jabeen, Muhammad Saeed
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.ppat.1002085

The N-Terminus of the RNA Polymerase from Infectious Pancreatic Necrosis Virus Is the Determinant of Genome Attachment
Cited by: 34
Author(s): Stephen C. Graham, L. Peter Sarin, Mohammad W. Bahar, Robert A. Myers, David I. Stuart, Dennis H. Bamford, Jonathan M. Grimes
Software Mentions: 3
Published: about 15 years ago

10.1038/s41598-018-29058-6

Structural determinants of specificity and regulation of activity in the allosteric loop network of human KLK8/neuropsin
Cited by: 7
Author(s): Mekdes Debela, Viktor Magdolen, Wolfgang Skala, Brigitta Elsässer, Eric L. Schneider, Charles S. Craik, Martin L. Biniossek, Oliver Schilling, Wolfram Bode, Hans Brandstetter, Peter Goettig
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-019-40762-9

Meta-analysis suggests evidence of novel stress-related pathway components in Orsay virus - Caenorhabditis elegans viral model
Cited by: 3
Author(s): Prachi Mishra, Jessica Ngo, Jahanshah Ashkani, Frédéric Pio
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.4728

Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain from <i>Mycobacterium tuberculosis</i>
Cited by: 5
Author(s): Mingjing Yu, Chao Dou, Yijun Gu, Wei Cheng
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1005294

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations
Cited by: 8
Author(s): Andrew F. Neuwald, Stephen F. Altschul
Software Mentions: 3
Published: over 9 years ago

10.1038/srep38564

Structure and dynamics of a constitutively active neurotensin receptor
Cited by: 55
Author(s): Brian E. Krumm, Sangbae Lee, Supriyo Bhattacharya, Istvan Botos, Courtney F. White, Haijuan Du, Nagarajan Vaidehi, Reinhard Grisshammer
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep33553

Crystal structures of the bifunctional tRNA methyltransferase Trm5a
Cited by: 7
Author(s): Caiyan Wang, Qian Jia, Ran Chen, Yuming Wei, Juntao Li, Jie Ma, Wei Xie
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-018-19991-x

Thermal stabilization of the deglycating enzyme Amadoriase I by rational design
Cited by: 18
Author(s): Federica Rigoldi, Stefano Donini, Francesca Giacomina, Federico Sorana, Alberto Redaelli, Tiziano Bandiera, Emilio Parisini, Alfonso Gautieri
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.ppat.1009566

Characterization of changes in the hemagglutinin that accompanied the emergence of H3N2/1968 pandemic influenza viruses
Cited by: 4
Author(s): Johanna West, Juliane Röder, Tatyana Matrosovich, Jana Beicht, Jan Baumann, Nancy Mounogou Kouassi, Jennifer Doedt, Nicolai V. Bovin, Gianpiero Zamperin, Michele Gastaldelli, Annalisa Salviato, Francesco Bonfante, Sergei L. Kosakovsky Pond, Sander Herfst, Ron A. M. Fouchier, Jochen Wilhelm, Hans‐Dieter Klenk, Mikhail Matrosovich
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms221910493

Discovery and Validation of Lmj_04_BRCT Domain, a Novel Therapeutic Target: Identification of Candidate Drugs for Leishmaniasis
Cited by: 6
Author(s): José Peña-Guerrero, Celia Fernández-Rubio, Aroia Burguete-Mikeo, Rima El-Dirany, Alfonso T. García-Sosa, Paul A. Nguewa
Software Mentions: 3
Published: almost 5 years ago

10.3390/md18070349

Interactions of the α3β2 Nicotinic Acetylcholine Receptor Interfaces with α-Conotoxin LsIA and its Carboxylated C-terminus Analogue: Molecular Dynamics Simulations
Cited by: 3
Author(s): Jierong Wen, David J. Adams, Andrew Hung
Software Mentions: 3
Published: about 6 years ago

10.3390/life5021264

The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets
Cited by: 14
Author(s): Birgit Märtens, G.A. Bezerra, Mathias Josef Kreuter, Irina Grishkovskaya, Andrea Manica, Valentina Arkhipova, Kristina Djinović-Carugo, Udo Bläsi
Software Mentions: 3
Published: over 11 years ago

10.3390/ijms22168631

The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales
Cited by: 5
Author(s): Marie-Caroline Müller, T. Wagner
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms20225574

Establishing Computational Approaches Towards Identifying Malarial Allosteric Modulators: A Case Study of Plasmodium falciparum Hsp70s
Cited by: 10
Author(s): Arnold Amusengeri, Lindy Astl, Kevin A. Lobb, Gennady M. Verkhivker, Özlem Tastan Bishop
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms20225734

A Single Synonymous Variant (c.354G&gt;A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity
Cited by: 23
Author(s): Ryan Hunt, Gaya Hettiarachchi, Upendra Katneni, Nancy Hernandez, David D. Holcomb, Jacob Kames, Redab Alnifaidy, Brian C. Lin, Nobuko Hamasaki-Katagiri, Aaron Wesley, Tal Kafri, Christina Morris, Laura Bouché, Maria Panico, Tal Schiller, Juan C. Ibla, Haim Bar, Amra Ismail, Howard R. Morris, Anton A. Komar
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms19113340

Physical Background of the Disordered Nature of “Mutual Synergetic Folding” Proteins
Cited by: 6
Author(s): Csaba Magyar, Anikó Mentes, Erzsébet Fichó, Miklós Cserző, István Simon
Software Mentions: 3
Published: almost 8 years ago

10.1107/S090744491104978X

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from <i>Corynebacterium glutamicum</i>
Cited by: 26
Author(s): Axel T. Brunger, Debanu Das, Ashley M. Deacon, Joanna C Grant, Thomas C. Terwilliger, Randy J. Read, Paul D. Adams, Michael Levitt, Gunnar F. Schröder
Software Mentions: 3
Published: over 14 years ago

10.3390/ijms19030916

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations
Cited by: 2
Author(s): Long‐Can Mei, Yanping Zhou, Lizhe Zhu, Changlin Liu, Zhuo Wu, Fangkui Wang, Ge‐Fei Hao, Di Yu, Hong Yuan, Yanfang Cui
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms20040884

Identification and Evaluation of Inhibitors of Lipase from Malassezia restricta using Virtual High-Throughput Screening and Molecular Dynamics Studies
Cited by: 67
Author(s): Shahid Ali, Faez Iqbal Khan, Taj Mohammad, Dongming Lan, Md. Imtaiyaz Hassan, Yonghua Wang
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms21082764

Structural Characterization of Carbonic Anhydrase VIII and Effects of Missense Single Nucleotide Variations to Protein Structure and Function
Cited by: 11
Author(s): Taremekedzwa Allan Sanyanga, Özlem Tastan Bishop
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.28842

Cyclic di-GMP differentially tunes a bacterial flagellar motor through a novel class of CheY-like regulators
Cited by: 59
Author(s): Jutta Nesper, Isabelle Hug, Setsu Kato, Chee-Seng Hee, Judith Habazettl, Pablo Manfredi, Stephan Grzesiek, Tilman Schirmer, Thierry Emonet, Urs Jenal
Software Mentions: 3
Published: almost 9 years ago

10.3390/biom10091286

Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2
Cited by: 13
Author(s): Faez Iqbal Khan, Fakhrul Hassan, Razique Anwer, Jia‐Xun Feng, Dakun Lai
Software Mentions: 3
Published: about 6 years ago

10.3390/biom10050744

Structure–Activity Relationship Study Reveals the Molecular Basis for Specific Sensing of Hydrophobic Amino Acids by the Campylobacter jejuni Chemoreceptor Tlp3
Cited by: 13
Author(s): Mohammad Firoz Khan, Mayra A. Machuca, Mohammad Mizanur Rahman, Cengiz Koç, Raymond S. Norton, Brian J. Smith, Anna Roujeinikova
Software Mentions: 3
Published: over 6 years ago

10.1107/S2053273316010731

Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm
Cited by: 9
Author(s): Hongxing He, Hengrui Fang, Mitchell D. Miller, George N. Phillips, W. P. Su
Software Mentions: 3
Published: about 10 years ago

10.7554/eLife.60552

Cryo-EM analysis of PIP2 regulation in mammalian GIRK channels
Cited by: 43
Author(s): Yiming Niu, Xiao Tao, Kouki K Touhara, Roderick MacKinnon
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.22037

Operon mRNAs are organized into ORF-centric structures that predict translation efficiency
Cited by: 119
Author(s): David H Burkhardt, Silvi Rouskin, Yan Zhang, Gene-Wei Li, Jonathan S. Weissman, Carol A. Gross
Software Mentions: 3
Published: over 9 years ago

10.1107/S2059798320001679

<i>ALEPH</i>: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation
Cited by: 15
Author(s): Ana María Medina, Josep Triviño, Rafael J. Borges, Claudia Millán, Isabel Usón, Massimo Sammito
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.59018

Structural ordering of the Plasmodium berghei circumsporozoite protein repeats by inhibitory antibody 3D11
Cited by: 10
Author(s): Iga Kucharska, Elaine Thai, Ananya Srivastava, John L. Rubinstein, Régis Pomès, Jean-Philippe Julien
Software Mentions: 3
Published: almost 6 years ago

10.3390/biom11030458

A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of Leishmania donovani
Cited by: 18
Author(s): Emmanuel Broni, Samuel K. Kwofie, Seth O. Asiedu, Whelton A. Miller, Michael D. Wilson
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.70560

Processing of the ribosomal ubiquitin-like fusion protein FUBI-eS30/FAU is required for 40S maturation and depends on USP36
Cited by: 5
Author(s): Jasmin van den Heuvel, Caroline Ashiono, Ludovic Gillet, Kerstin Dörner, Emanuel Wyler, Ivo Zemp, Ulrike Kutay
Software Mentions: 3
Published: about 5 years ago

10.3390/md16100386

Kororamides, Convolutamines, and Indole Derivatives as Possible Tau and Dual-Specificity Kinase Inhibitors for Alzheimer’s Disease: A Computational Study
Cited by: 25
Author(s): Laura Llorach-Parés, Alfons Nonell-Canals, Conxita Àvila, Melchor Sánchez-Martínez
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.22693

The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels
Cited by: 77
Author(s): A. J. Miles, Stephen P. Burr, GL Grice, James A. Nathan
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms17060897

Functional Characterization of Soybean Glyma04g39610 as a Brassinosteroid Receptor Gene and Evolutionary Analysis of Soybean Brassinosteroid Receptors
Cited by: 16
Author(s): Suna Peng, Peng Tao, Feng Xu, Aiping Wu, Weige Huo, Jinxiang Wang
Software Mentions: 3
Published: over 10 years ago

10.1016/j.jmb.2015.08.023

Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain
Cited by: 9
Author(s): Nora Cronin, Jing Yang, Ziguo Zhang, Kiran Kulkarni, Leifu Chang, Hiroyuki Yamano, David Barford
Software Mentions: 3
Published: almost 11 years ago

10.1016/j.jmb.2016.12.004

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures
Cited by: 307
Author(s): Harry Jubb, Alícia P. Higueruelo, Bernardo Ochoa‐Montaño, William R. Pitt, David B. Ascher, Tom L. Blundell
Software Mentions: 3
Published: over 9 years ago

10.1016/j.jmb.2018.05.019

Proteomic and Biochemical Comparison of the Cellular Interaction Partners of Human VPS33A and VPS33B
Cited by: 20
Author(s): Morag R. Hunter, Geoffrey G. Hesketh, Tomasz H. Benedyk, Anne‐Claude Gingras, Stephen C. Graham
Software Mentions: 3
Published: about 8 years ago

10.1107/S205225252000072X

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals
Cited by: 31
Author(s): Alexander M. Wolff, I.D. Young, Raymond G. Sierra, Aaron S. Brewster, Michael W. Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, J.T. Biel, Sergio Carbajo, Aina E. Cohen, S.V. Cortez, Ana González, Tsuneo Hino, Dohyun Im, Jake Koralek, Minoru Kubo, Tomas S. Lazarou, Takashi Nomura, Shigeki Owada, Avi J. Samelson, Tomoyuki Tanaka, R. Tanaka, Erin Thompson, H. van den Bedem, R.A. Woldeyes, Fumiaki Yumoto, Zhao Wei, Kensuke Tono, Sébastien Boutet, So Iwata, Tamir Gonen, Nicholas K. Sauter, James S. Fraser, Michael C. Thompson
Software Mentions: 3
Published: over 6 years ago

10.1128/mBio.03066-19

How Bacterial Chemoreceptors Evolve Novel Ligand Specificities
Cited by: 45
Author(s): José A. Gavira, Vadim M. Gumerov, Míriam Rico-Jiménez, Marharyta Petukh, Amit A. Upadhyay, Álvaro Ortega, Miguel A. Matilla, Igor B. Zhulin, Tino Krell
Software Mentions: 3
Published: over 6 years ago

10.1155/2014/162150

Evaluation of 11 Scoring Functions Performance on Matrix Metalloproteinases
Cited by: 10
Author(s): Jamal Shamsara
Software Mentions: 3
Published: over 11 years ago

10.1002/jmr.2696

The evolutionary characteristics and structural biology of <i>Gallus</i> toll-like receptor 21
Cited by: 6
Author(s): Hongping Wu, Hai Wang, Weibo Jiang, Zhengxing Lian
Software Mentions: 3
Published: over 8 years ago