10.1371/journal.ppat.1009723

ACE2-lentiviral transduction enables mouse SARS-CoV-2 infection and mapping of receptor interactions
Cited by: 17
Author(s): Daniel J. Rawle, Thuy T. Le, Troy Dumenil, Kexin Yan, Bing Tang, Wilson Nguyen, Daniel Watterson, Naphak Modhiran, Jody Hobson‐Peters, Cameron Bishop, Andreas Suhrbier
Software Mentions: 3
Published: over 5 years ago

10.1186/1472-6807-11-33

Atomic resolution structure of EhpR: phenazine resistance in Enterobacter agglomerans Eh1087 follows principles of bleomycin/mitomycin C resistance in other bacteria
Cited by: 5
Author(s): Yu Song, A. Vit, Sean R. A. Devenish, H. K. Mahanty, Aymelt Itzen, Roger S. Goody, Wulf Blankenfeldt
Software Mentions: 3
Published: about 15 years ago

10.1371/journal.pone.0199585

Contact prediction is hardest for the most informative contacts, but improves with the incorporation of contact potentials
Cited by: 6
Author(s): John E. Holland, Qinxin Pan, Gevorg Grigoryan
Software Mentions: 3
Published: over 8 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: over 8 years ago

10.1371/journal.ppat.1008848

Chaperone-tip adhesin complex is vital for synergistic activation of CFA/I fimbriae biogenesis
Cited by: 1
Author(s): Libang He, Hao Wang, Yang Liu, Mei Kang, Tao Li, Changcheng Li, Aiping Tong, Yuanfeng Zhu, Yingjie Song, Stephen J. Savarino, Michael G. Prouty, Di Xia, Rui Bao
Software Mentions: 3
Published: about 6 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

10.1016/j.jbc.2021.100927

Beyond PKA: Evolutionary and structural insights that define a docking and dimerization domain superfamily
Cited by: 3
Author(s): Heather R. Dahlin, Ning Zheng, John D. Scott
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pcbi.1004068

Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data
Cited by: 34
Author(s): Kristen Fortney, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming‐Sound Tsao, Igor Jurišica
Software Mentions: 3
Published: over 11 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/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

10.1074/jbc.RA120.012788

Small molecule AX-024 reduces T cell proliferation independently of CD3ϵ/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain
Cited by: 10
Author(s): Kirsten Richter, Arne C. Rufer, Magali Muller, Dominique Burger, Fabio Casagrande, Tabea Grossenbacher, Sylwia Huber, Melanie N. Hug, Philipp Koldewey, Andrea D’Osualdo, Daniel Schlatter, Theodor Stoll, M.G. Rudolph
Software Mentions: 3
Published: over 6 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

10.1172/jci.insight.97018

Fine epitope signature of antibody neutralization breadth at the HIV-1 envelope CD4-binding site
Cited by: 16
Author(s): Hao Cheng, Sebastian K. Grimm, M.S.A. Gilman, Luc Christian Gwom, Devin Sok, Christopher Sundling, G. Donofrio, Gunilla B. Karlsson Hedestam, Mattia Bonsignori, Barton F. Haynes, Timothy Lahey, Isaac Maro, C. Fordham von Reyn, Miroslaw K. Gorny, Susan Zolla‐Pazner, Bruce D. Walker, Galit Alter, Dennis R. Burton, Merlin L. Robb, Shelly J. Krebs, Michael S. Seaman, Chris Bailey‐Kellogg, Margaret E. Ackerman
Software Mentions: 3
Published: over 8 years ago

10.1111/imm.13341

Modified recombinant human IgG1‐Fc is superior to natural intravenous immunoglobulin at inhibiting immune‐mediated demyelination
Cited by: 1
Author(s): Christine Baksmeier, Patricia A. Blundell, Julia Steckel, Verena Schultz, Quan Gu, Ana da Silva Filipe, Alain Kohl, Chris Linnington, Dongli Lu, Anne Dell, Stuart M. Haslam, Jiabin Wang, Dan Czajkowsky, Norbert Goebels, Richard J. Pleass
Software Mentions: 3
Published: over 5 years ago

10.1007/s13361-018-1910-5

Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31
Cited by: 5
Author(s): Andrey Dyachenko, Sem Tamara, Albert J. R. Heck
Software Mentions: 3
Published: over 8 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

10.1093/gbe/evv046

OASes and STING: Adaptive Evolution in Concert
Cited by: 38
Author(s): Alessandra Mozzi, Chiara Pontremoli, Diego Forni, Mario Clerici, Nereo Bresolin, Rachele Cagliani, Manuela Sironi
Software Mentions: 3
Published: over 11 years ago

10.1186/s13104-015-1760-1

Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation
Cited by: 6
Author(s): Noriko Inoguchi, Kittichai Chaiseeda, Mamoru Yamanishi, Moon Ki Kim, Yunho Jang, M. Bajaj, Catherine P. Chia, Donald F. Becker, Hideaki Moriyama
Software Mentions: 3
Published: almost 11 years ago

10.1093/gbe/evaa038

The Evolution History of Fe–S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs
Cited by: 3
Author(s): Hui‐Meng Lu, Jing-Di Li, Yu-Dan Zhang, Xiaoli Lü, Chang Xu, Yuan Huang, Michael Gribskov
Software Mentions: 3
Published: over 6 years ago

10.3390/genes12050784

Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress
Cited by: 48
Author(s): Zahra Musavizadeh, Hamid Najafi-Zarrini, Seyed Kamal Kazemitabar, Seyyed Hamidreza Hashemi, Sahar Faraji, Gianni Barcaccia, Parviz Heidari
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-015-0478-5

New insights into the evolutionary history of plant sorbitol dehydrogenase
Cited by: 22
Author(s): Yuping Jia, D. Wong, Crystal Sweetman, John B. Bruning, Christopher M. Ford
Software Mentions: 3
Published: over 11 years ago

10.1093/gbe/evaa095

Molecular Evolutionary Analysis of Nematode Zona Pellucida (ZP) Modules Reveals Disulfide-Bond Reshuffling and Standalone ZP-C Domains
Cited by: 3
Author(s): Cameron J. Weadick
Software Mentions: 3
Published: over 6 years ago

10.3389/fmolb.2021.643728

Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction
Cited by: 1
Author(s): Ennys Gheyouche, Matthias Bagueneau, Gervaise Loirand, Bernard Offmann, Stéphane Téletchéa
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2016.00901

Reconstruction of the High-Osmolarity Glycerol (HOG) Signaling Pathway from the Halophilic Fungus Wallemia ichthyophaga in Saccharomyces cerevisiae
Cited by: 8
Author(s): Tilen Konte, Ulrich Terpitz, Ana Plemenitaš
Software Mentions: 3
Published: over 10 years ago

10.3389/fmolb.2020.603983

Identification of the Interactions Interference Between the PH and START Domain of CERT by Limonoid and HPA Inhibitors
Cited by: 1
Author(s): Mariem Ghoula, Axelle Le Marec, Christophe Magnan, Hervé Le Stunff, Olivier Taboureau
Software Mentions: 3
Published: almost 6 years ago

10.1107/S0907444910000302

Rapid model building of β-sheets in electron-density maps
Cited by: 4
Author(s): Thomas C. Terwilliger
Software Mentions: 3
Published: over 16 years ago

10.3389/fgene.2021.713224

Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress
Cited by: 18
Author(s): Ahmed H. El-Sappah, Rania G. Elbaiomy, Ahmed S. Elrys, Yu Wang, Yumin Zhu, Qiulan Huang, Yan Ke, Xingbo Zhao, Yun Li, Khaled A. El‐Tarabily, Jia Li
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2018.03192

Predictable Molecular Adaptation of Coevolving Enterococcus faecium and Lytic Phage EfV12-phi1
Cited by: 29
Author(s): Stephen Wandro, Andrew Oliver, Tara Gallagher, Claudia Weihe, Whitney England, Jennifer B. H. Martiny, Katrine Whiteson
Software Mentions: 3
Published: over 7 years ago

10.3389/fmolb.2021.711975

Simulating PIP2-Induced Gating Transitions in Kir6.2 Channels
Cited by: 6
Author(s): Michael Bründl, Sarala Pellikan, Anna Stary-Weinzinger
Software Mentions: 3
Published: about 5 years ago

10.1093/gbe/evab125

Homology and Modular Evolution of CATCHR at the Origin of the Eukaryotic Endomembrane System
Cited by: 9
Author(s): Carlos Santana-Molina, Fernando Gutiérrez, Damien P. Devos
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-46756-x

Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India
Cited by: 31
Author(s): Asma Munir, Narender Kumar, Suresh Babu Ramalingam, Sembulingam Tamilzhalagan, Siva Kumar Shanmugam, Alangudi Natarajan Palaniappan, Dina Nair, Padma Priyadarshini, Mohan Natarajan, Srikanth Tripathy, Uma Devi Ranganathan, Sharon J. Peacock, Julian Parkhill, Tom L. Blundell, Sony Malhotra
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.ppat.1008476

Past and ongoing adaptation of human cytomegalovirus to its host
Cited by: 18
Author(s): Alessandra Mozzi, Matteo Biolatti, Rachele Cagliani, Diego Forni, Valentina Dell’Oste, Chiara Pontremoli, Chiara Vantaggiato, Diego Forni, Mario Clerici, Santo Landolfo, Manuela Sironi
Software Mentions: 3
Published: over 6 years ago

10.1155/2020/2758640

A Bioinformatics Research on Novel Mechanism of Compound Kushen Injection for Treating Breast Cancer by Network Pharmacology and Molecular Docking Verification
Cited by: 6
Author(s): Shuyu Liu, Xiaohong Hu, Xiaotian Fan, Ruiqi Jin, Wenqian Yang, Yifei Geng, Jiarui Wu
Software Mentions: 3
Published: about 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: almost 6 years ago

10.1186/s13072-016-0051-y

Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis
Cited by: 51
Author(s): Takashi Urahama, Akihito Harada, Kazuhira Maehara, Naoki Horikoshi, Koichi Sato, Yuko Sato, Koji Shiraishi, Norihiro Sugino, Akihisa Osakabe, Hiroaki Tachiwana, Wataru Kagawa, Hiroshi Kimurâ, Yasuyuki Ohkawa, Hitoshi Kurumizaka
Software Mentions: 3
Published: over 10 years ago

10.3389/fcimb.2021.730288

Identification of Natural Inhibitors Against SARS-CoV-2 Drugable Targets Using Molecular Docking, Molecular Dynamics Simulation, and MM-PBSA Approach
Cited by: 35
Author(s): Prem Prakash Kushwaha, Atul Kumar Singh, Tanya Bansal, Akansha Yadav, Kumari Sunita Prajapati, Mohd Shuaib, Shashank Kumar
Software Mentions: 3
Published: about 5 years ago

10.15252/emmm.201911592

STIM1‐mediated calcium influx controls antifungal immunity and the metabolic function of non‐pathogenic Th17 cells
Cited by: 22
Author(s): Sascha Kahlfuß, Ulrike Kaufmann, Axel R. Concepcion, Lucile Noyer, Dimitrius Raphael, Martin Vaeth, Jun J. Yang, Priya Pancholi, Máté Maus, James Muller, Lina Kozhaya, Alireza Khodadadi‐Jamayran, Zhengxi Sun, Patrick J. Shaw, Derya Unutmaz, Peter B. Stathopulos, Cori Feist, Scott Cameron, Stuart E. Turvey, Stefan Feske
Software Mentions: 3
Published: over 6 years ago

10.1038/celldisc.2016.51

Structural mechanism for the arginine sensing and regulation of CASTOR1 in the mTORC1 signaling pathway
Cited by: 33
Author(s): Zhongchao Gai, Qian Wang, Can Yang, Lei Wang, Wei Deng, Geng Wu
Software Mentions: 3
Published: almost 10 years ago

10.15252/emmm.201911210

Glufosinate constrains synchronous and metachronous metastasis by promoting anti‐tumor macrophages
Cited by: 27
Author(s): Alessio Menga, Marina Serra, Simona Todisco, Carla Riera-Domingo, Ummi Ammarah, Manuel Ehling, Erika M. Palmieri, Maria Antonietta Di Noia, Rosanna Gissi, Maria Favia, Ciro Leonardo Pierri, Paolo E. Porporato, Alessandra Castegna, Massimiliano Mazzone
Software Mentions: 3
Published: about 6 years ago

10.3389/fchem.2020.597495

Exploring the Allosteric Mechanism of Src Homology-2 Domain-Containing Protein Tyrosine Phosphatase 2 (SHP2) by Molecular Dynamics Simulations
Cited by: 4
Author(s): Quan Wang, Wencheng Zhao, Xueqi Fu, Qing‐Chuan Zheng
Software Mentions: 3
Published: almost 6 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

10.1107/S0907444912001308

Towards automated crystallographic structure refinement with <i>phenix.refine</i>
Cited by: 4,334
Author(s): Pavel V. Afonine, Ralf W. Grosse‐Kunstleve, Nathaniel Echols, Jeffrey J. Headd, Nigel W. Moriarty, Marat Mustyakimov, Thomas C. Terwilliger, Alexandre Urzhumtsev, Peter H. Zwart, Paul D. Adams
Software Mentions: 3
Published: over 14 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: almost 8 years ago

10.3390/cancers13143418

Phosphorylation of OGFOD1 by Cell Cycle-Dependent Kinase 7/9 Enhances the Transcriptional Activity of RNA Polymerase II in Breast Cancer Cells
Cited by: 1
Author(s): Han Teo Lee, Il Hwan Lee, Jaehwan Kim, Sang-Ho Lee, Sojung Kwak, Min Young Suh, In Kyeom Hwang, Bu Gyeong Kang, Sun Shin, Byung Il Lee, Sang Eun Lee, Jinmi Choi, Jae Seok Roe, Eun Jung Cho, Hong Duk Youn
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0236894

A chemical interpretation of protein electron density maps in the worldwide protein data bank
Cited by: 5
Author(s): Sen Yao, Hunter N. B. Moseley
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/cddis.2017.487

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2
Cited by: 20
Author(s): M. Merski, Cátia Moreira, Rui M.V. Abreu, María J. Ramos, Pedro A. Fernandes, L. Miguel Martins, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro
Software Mentions: 3
Published: almost 9 years ago

10.3389/fgene.2020.568052

Whole-Exome Sequencing of Discordant Monozygotic Twin Families for Identification of Candidate Genes for Microtia-Atresia
Cited by: 7
Author(s): Xinmiao Fan, Ping Lu, Hao Sun, Yu‐Shan Chen, Pu Wang, Tao Liu, Rui Jiang, Xuegong Zhang, Xiaowei Chen
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0140934

Rubisco Activase Is Also a Multiple Responder to Abiotic Stresses in Rice
Cited by: 40
Author(s): Yue Chen, Xiaoman Wang, Li Zhou, Yi He, Dun Wang, Yanhua Qi, Dongxiang Jiang
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0043245

A Bioinformatic Strategy for the Detection, Classification and Analysis of Bacterial Autotransporters
Cited by: 62
Author(s): Nemin Celik, Chaille T Webb, Denisse L. Leyton, Kathryn E. Holt, Eva Heinz, Rebecca J. Gorrell, Terry Kwok, Thomas Naderer, Richard A. Strugnell, Terence P. Speed, Rohan D. Teasdale, Vladimir A Likić, Trevor Lithgow
Software Mentions: 3
Published: about 14 years ago

10.1186/1471-2164-10-611

Identification of novel aspartic proteases from Strongyloides ratti and characterisation of their evolutionary relationships, stage-specific expression and molecular structure
Cited by: 15
Author(s): Luciane V. Mello, Helen O’Meara, Daniel J. Rigden, Steve Paterson
Software Mentions: 3
Published: almost 18 years ago

10.1107/S1399004715005210

<i>In meso in situ</i> serial X-ray crystallography of soluble and membrane proteins
Cited by: 98
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Ezequiel Panepucci, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 3
Published: over 11 years ago

10.1107/S0907444910029690

Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from <i>Bacillus anthracis</i>
Cited by: 19
Author(s): Ekaterina Morgunova, Boris Illarionov, Sabine Saller, Aleksander Popov, Thota Sambaiah, Adelbert Bacher, Mary Cushman, Markus Fischer, Rudolf Ladenstein
Software Mentions: 3
Published: about 16 years ago

10.1371/journal.pone.0165020

Genome-Wide Analysis, Classification, Evolution, and Expression Analysis of the Cytochrome P450 93 Family in Land Plants
Cited by: 32
Author(s): Hongwu Du, Feng Ran, Hongli Dong, Jing Wen, Jiana Li, Zhe Liang
Software Mentions: 3
Published: almost 10 years ago

10.1107/S0907444910000272

Rapid chain tracing of polypeptide backbones in electron-density maps
Cited by: 5
Author(s): Thomas C. Terwilliger
Software Mentions: 3
Published: over 16 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

10.1371/journal.pone.0150634

Computational Identification Raises a Riddle for Distribution of Putative NACHT NTPases in the Genome of Early Green Plants
Cited by: 4
Author(s): Preeti Arya, Vishal Acharya
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0097817

Exploring the Functional Residues in a Flavin-Binding Fluorescent Protein Using Deep Mutational Scanning
Cited by: 12
Author(s): HyeonSeok Shin, Yoobok Cho, Donghui Choe, Yu‐Jin Jeong, Suhyung Cho, Sun Chang Kim, Byung-Kwan Cho
Software Mentions: 3
Published: over 12 years ago

10.1107/S0907444911056058

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in<i>BUSTER</i>
Cited by: 529
Author(s): Oliver S. Smart, Thomas Womack, Claus Flensburg, Peter M. Keller, W. A. Paciorek, A. Sharff, Clemens Vonrhein, G. Bricogne
Software Mentions: 3
Published: over 14 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

10.1186/s12864-018-4605-1

Genome-wide transcriptional analyses in Anopheles mosquitoes reveal an unexpected association between salivary gland gene expression and insecticide resistance
Cited by: 26
Author(s): Alison T. Isaacs, Henry Mawejje, Sean Tomlinson, Daniel J. Rigden, Martin J. Donnelly
Software Mentions: 3
Published: over 8 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

10.1371/journal.pone.0172743

Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin
Cited by: 35
Author(s): Akshay Sridhar, Gregory A. Ross, Philip C. Biggin
Software Mentions: 3
Published: over 9 years ago

10.15252/embj.2021107985

Neutralization of SARS‐CoV‐2 by highly potent, hyperthermostable, and mutation‐tolerant nanobodies
Cited by: 56
Author(s): Thomas Güttler, Metin Aksu, Antje Dickmanns, Kim M. Stegmann, Kathrin Gregor, Renate Rees, Waltraud Taxer, Oleh Rymarenko, Jürgen Schünemann, Christian Dienemann, Philip Gunkel, Bianka Mußil, Jens Krull, Ulrike Teichmann, Uwe Groß, Volker C. Cordes, Matthias Dobbelstein, Dirk Görlich
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0088229

Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts
Cited by: 29
Author(s): Dallas Thomas, Abdul G. Lone, L. Brent Selinger, Eduardo N. Taboada, Richard R. E. Uwiera, D. Wade Abbott, G. Douglas Inglis
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0082341

Targeting a Cross-Reactive Gly m 5 Soy Peptide as Responsible for Hypersensitivity Reactions in a Milk Allergy Mouse Model
Cited by: 21
Author(s): Renata Curciarello, Paola Lorena Smaldini, Ángela María Candreva, Vicente Ferreira González, Gustavo Parisi, Ana Cauerhff, Ivana Analía Barrios, Luis Enrique Bruno Blanch, Carlos A. Fossati, Silvana Petruccelli, Guillermo Horacio Docena
Software Mentions: 3
Published: almost 13 years ago

10.1155/2019/1205942

PIM1, CYP1B1, and HSPA2 Targeted by Quercetin Play Important Roles in Osteoarthritis Treatment by<i> Achyranthes bidentata</i>
Cited by: 7
Author(s): Dujun Ma, Yu Tian, Liping Peng, Lixin Wang, Zhouwei Liao, Wenming Xu
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0058333

Structural Insights into Putative Molybdenum Cofactor Biosynthesis Protein C (MoaC2) from Mycobacterium tuberculosis H37Rv
Cited by: 2
Author(s): Vijay Kumar Srivastava, Shubra Srivastava, Ashish Arora, J. Venkatesh Pratap
Software Mentions: 3
Published: over 13 years ago

10.1186/s40360-017-0128-7

Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects
Cited by: 42
Author(s): Matthieu Chartier, Louis–Philippe Morency, María Inés Zylber, Rafaël Najmanovich
Software Mentions: 3
Published: over 9 years ago

10.1186/s12860-020-00328-4

Identification of biomarkers for the accurate and sensitive diagnosis of three bacterial pneumonia pathogens using in silico approaches
Cited by: 7
Author(s): Olalekan Olanrewaju Bakare, Marshall Keyster, Ashley Pretorius
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0229467

Discovery of antitumor lectins from rainforest tree root transcriptomes
Cited by: 3
Author(s): Atip Lawanprasert, Caitlin A. Guinan, Erica A. Langford, Carly E. Hawkins, Janna N. Sloand, Howard W. Fescemyer, Matthew R. Aronson, Jacob A. Halle, James H. Marden, Scott H. Medina
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.620472

Case Report: Novel RPGRIP1L Gene Mutations Identified by Whole Exome Sequencing in a Patient With Multiple Primary Tumors
Cited by: 0
Author(s): Jianghong Guo, Yu Ye, Zhuqing Ji, Ming Yao, Xiaotian Xia, Xiaofeng Sha, Ming‐De Huang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0039550

On the Structure and Function of the Phytoene Desaturase CRTI from Pantoea ananatis, a Membrane-Peripheral and FAD-Dependent Oxidase/Isomerase
Cited by: 74
Author(s): Patrick Schaub, Qiuju Yu, Sandra Gemmecker, Pierre Poussin-Courmontagne, J. Mailliot, A.G. McEwen, Sandro Ghisla, Salim Al‐Babili, Jean Cavarelli, Peter Beyer
Software Mentions: 3
Published: over 14 years ago

10.3389/fmicb.2020.01100

Characterization of a Novel Functional Trimeric Catechol 1,2-Dioxygenase From a Pseudomonas stutzeri Isolated From the Gulf of Mexico
Cited by: 16
Author(s): Julieta Rodríguez-Salazar, Arisbeth G Almeida-Juarez, Katya Ornelas-Ocampo, Sofía Millán-López, Enrique Raga-Carbajal, José Luis Rodríguez-Mejía, Luis Felipe Muriel-Millán, Elizabeth Ernestina Godoy-Lozano, Nancy Rivera-Gómez, E. Rudiño-Piñera, Liliana Pardo-López
Software Mentions: 3
Published: over 6 years ago

10.1107/S1399004715004514

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams
Cited by: 112
Author(s): Nicolas Coquelle, Aaron S. Brewster, U. Kapp, Anastasya Shilova, Britta Weinhausen, Manfred Burghammer, J.P. Colletier
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0257206

Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease
Cited by: 4
Author(s): R. V. Sriram Uday, Rajdip Misra, Annaram Harika, Sandip Dolui, Achintya Saha, Samir Kumar Pal, V. Ravichandiran, Nakul C. Maiti
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0232959

Crystal structure of Thermus thermophilus methylenetetrahydrofolate dehydrogenase and determinants of thermostability
Cited by: 7
Author(s): Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele
Software Mentions: 3
Published: over 6 years ago

10.1186/s12860-020-00290-1

Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease
Cited by: 4
Author(s): Pierre Laville, Sandrine Fartek, Natacha Cerisier, Delphine Flatters, Michel Petitjean, Leslie Regad
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0246915

Experimental and molecular predictions of the adjuvanticity of snail mucin on hepatitis B vaccine in albino mice
Cited by: 2
Author(s): Parker Elijah Joshua, Cynthia Ogochukwu Nwauzor, Damian Chukwu Odimegwu, Uzochukwu Gospel Ukachukwu, Rita Onyekachukwu Asomadu, Timothy Prince Chidike Ezeorba
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0217164

Three genetically distinct ferlaviruses have varying effects on infected corn snakes (Pantherophis guttatus)
Cited by: 7
Author(s): Michael Pees, Volker Schmidt, Tibor Papp, Ákos Gellért, Maha Diekan Abbas, J. Matthias Starck, Annkatrin Neul, Rachel E. Marschang
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-48849-z

Modelling of substrate access and substrate binding to cephalosporin acylases
Cited by: 6
Author(s): Virgilio F. Ferrario, Mona Fischer, Yushan Zhu, Jürgen Pleiss
Software Mentions: 3
Published: about 7 years ago

10.1186/s13071-020-04476-6

Major SCP/TAPS protein expansion in Lucilia cuprina is associated with novel tandem array organisation and domain architecture
Cited by: 1
Author(s): Yair D J Prawer, Andreas J. Stroehlein, Neil D. Young, Shilpa Kapoor, Ross S. Hall, Razi Ghazali, Philip Batterham, Robin B. Gasser, Trent Perry, Clare A. Anstead
Software Mentions: 3
Published: almost 6 years ago

10.12688/wellcomeopenres.14438.2

Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum
Cited by: 5
Author(s): Mary Dias, Chitra Pattabiraman, Shilpa Siddappa, Malali Gowda, Anita Shet, Derek J. Smith, Barbara Muehlemann, Krishnapriya Tamma, Tom Solomon, Terry C. Jones, Sudhir Krishna
Software Mentions: 3
Published: over 7 years ago

10.3390/molecules25040904

Understanding the Pyrimethamine Drug Resistance Mechanism via Combined Molecular Dynamics and Dynamic Residue Network Analysis
Cited by: 26
Author(s): Arnold Amusengeri, Rolland Bantar Tata, Özlem Tastan Bishop
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pntd.0007868

Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance
Cited by: 93
Author(s): Yogesh Hooda, Mohammad Saiful Islam Sajib, Hafizur Rahman, Stephen P. Luby, Joseph Bondy‐Denomy, Mathuram Santosham, Jason R Andrews, Samir K. Saha, Senjuti Saha
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.ppat.1002957

De novo GTP Biosynthesis Is Critical for Virulence of the Fungal Pathogen Cryptococcus neoformans
Cited by: 53
Author(s): Carl A. Morrow, Eugene Valkov, Anna Stamp, Eve W. L. Chow, I. Russel Lee, Ania Wronski, Simon J. Williams, Jennifer Hill, Julianne T. Djordjevic, Ulrike Kappler, Boštjan Kobe, James S. Fraser
Software Mentions: 3
Published: almost 14 years ago

10.1186/1471-2105-15-72

Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis
Cited by: 8
Author(s): Carlos Mata-Munguía, Martha Escoto-Delgadillo, Blanca Miriam Torres-Mendoza, M.E. Flores-Soto, Mildred Vázquez-Torres, Francisco Javier Gálvez-Gastélum, Arturo Viniegra‐Osorio, Marcelo Castillero-Manzano, Eduardo Vázquez-Valls
Software Mentions: 3
Published: over 12 years ago

10.1074/jbc.RA118.004469

Discovery of peptide ligands targeting a specific ubiquitin-like domain–binding site in the deubiquitinase USP11
Cited by: 24
Author(s): Anastasios Spiliotopoulos, Lia Blokpoel Ferreras, Ruth M Densham, Simon G. Caulton, Ben C. Maddison, Joanna R. Morris, James E. Dixon, Kevin C. Gough, Ingrid Dreveny
Software Mentions: 3
Published: almost 8 years ago

10.3389/fcvm.2020.00008

Protein Subdomain Enrichment of NUP155 Variants Identify a Novel Predicted Pathogenic Hotspot
Cited by: 2
Author(s): Riley J Leonard, Claudia C. Preston, Melanie E Gucwa, Yohannes Afeworki Tecleab, Arielle Selya, Randolph S. Faustino
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-017-1541-z

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP
Cited by: 24
Author(s): Julia Koehler Leman, Sergey Lyskov, Richard Bonneau
Software Mentions: 3
Published: over 9 years ago

10.3390/molecules24142610

Local Interaction Density (LID), a Fast and Efficient Tool to Prioritize Docking Poses
Cited by: 4
Author(s): Célien Jacquemard, Viet-Khoa Tran-Nguyen, Malgorzata N. Drwal, Didier Rognan, Esther Kellenberger
Software Mentions: 3
Published: about 7 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: almost 10 years ago

10.3390/ijms21176185

Characterization of Two Novel Variants of the Steroidogenic Acute Regulatory Protein Identified in a Girl with Classic Lipoid Congenital Adrenal Hyperplasia
Cited by: 3
Author(s): Efstathios Katharopoulos, Natascia Di Iorgi, Paula Fernández-Álvarez, Amit V. Pandey, Michael Groessl, Shraddha Dubey, Núria Camats, Flavia Napoli, Giuseppa Patti, Marilea Lezzi, Mohamad Maghnie, Christa E. Flück
Software Mentions: 3
Published: about 6 years ago

10.1042/BJ20141324

Comparative structural analysis of the caspase family with other clan CD cysteine peptidases
Cited by: 61
Author(s): Karen McLuskey, Jeremy C. Mottram
Software Mentions: 3
Published: over 11 years ago

10.26508/lsa.202101152

The structure and flexibility analysis of the <i>Arabidopsis</i> synaptotagmin 1 reveal the basis of its regulation at membrane contact sites
Cited by: 8
Author(s): Juan Luis Benavente, Dritan Siliqi, Lourdes Infantes, Laura Lagartera, Alberto Mills, Federico Gago, Noemı́ Ruiz-López, Miguel A. Botella, María José Sánchez-Barrena, Armando Albert
Software Mentions: 3
Published: about 5 years ago

10.1074/jbc.M114.621789

Complex Structure and Biochemical Characterization of the Staphylococcus aureus Cyclic Diadenylate Monophosphate (c-di-AMP)-binding Protein PstA, the Founding Member of a New Signal Transduction Protein Family
Cited by: 47
Author(s): Ivan Campeotto, Yong Everett Zhang, Miroslav Mladenov, Paul S. Freemont, Angelika Gründling
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0147097

CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking
Cited by: 9
Author(s): Lei Hua, Yang Song, Namhee Kim, Christian Laing, Jianli Wang, Tamar Schlick
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1002598

Broad-Specificity mRNA–rRNA Complementarity in Efficient Protein Translation
Cited by: 13
Author(s): Pamela A. Barendt, Najaf A. Shah, Gregory A. Barendt, Casim A. Sarkar
Software Mentions: 3
Published: over 14 years ago

10.1128/mSphere.00454-21

A Novel Phage Infecting <i>Alteromonas</i> Represents a Distinct Group of Siphophages Infecting Diverse Aquatic Copiotrophs
Cited by: 16
Author(s): Ruijie Ma, Jiayong Lai, Xiaowei Chen, Long Wang, Yue Yang, Shuzhen Wei, Nianzhi Jiao, Rui Zhang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0004978

Nonstructural Proteins Are Preferential Positive Selection Targets in Zika Virus and Related Flaviviruses
Cited by: 52
Author(s): Manuela Sironi, Diego Forni, Mario Clerici, Rachele Cagliani
Software Mentions: 3
Published: about 10 years ago