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

10.7554/eLife.27829

Structure-based analysis of CysZ-mediated cellular uptake of sulfate
Cited by: 9
Author(s): Zahra Assur Sanghai, Qun Liu, Oliver B Clarke, Meagan Belcher Dufrisne, Pattama Wiriyasermkul, Maria Giese, Edgar Leal-Pinto, Brian Kloss, Shantelle Tabuso, J. Love, Marco Punta, Surajit Banerjee, Kanagalaghatta R. Rajashankar, Burkhard Rost, Diomedes E. Logothetis, Matthias Quick, Wayne A. Hendrickson, Filippo Mancia
Software Mentions: 3
Published: over 8 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

10.1016/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/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.0116688

Identification of STAT1 and STAT3 Specific Inhibitors Using Comparative Virtual Screening and Docking Validation
Cited by: 29
Author(s): Małgorzata Szeląg, Anna Czerwoniec, Joanna Wesoły, Hans A.R. Bluyssen
Software Mentions: 3
Published: over 11 years ago

10.3390/biomedicines9030249

In Silico Drug Repurposing by Structural Alteration after Induced Fit: Discovery of a Candidate Agent for Recovery of Nucleotide Excision Repair in Xeroderma Pigmentosum Group D Mutant (R683W)
Cited by: 4
Author(s): Yutaka Takaoka, Mika Ohta, Seiichiro Tateishi, Aki Sugano, Eiji Nakano, Kenji Miura, Takashi Suzuki, Chikako Nishigori
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-11-446

Fast and accurate protein substructure searching with simulated annealing and GPUs
Cited by: 44
Author(s): Alex Stivala, Peter J. Stuckey, Anthony Wirth
Software Mentions: 3
Published: about 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

10.3390/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

10.1186/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

10.7554/eLife.65339

Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein
Cited by: 12
Author(s): Xiangrong Chen, Yusuf Ali, Charlotte E L Fisher, Raquel Arribas-Bosacoma, Mohan B. Rajasekaran, Gareth Williams, Sarah Walker, Jessica R Booth, Jessica J. R. Hudson, S. Mark Roe, Laurence H. Pearl, Simon E. Ward, Frances M. G. Pearl, Antony W. Oliver
Software Mentions: 3
Published: over 5 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/s41598-018-37506-6

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

10.1371/journal.pone.0022201

A Computational-Experimental Approach Identifies Mutations That Enhance Surface Expression of an Oseltamivir-Resistant Influenza Neuraminidase
Cited by: 50
Author(s): Jesse D. Bloom, Jagannath S. Nayak, David Baltimore
Software Mentions: 3
Published: about 15 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

10.3390/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>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

10.1107/S2053230X20001466

Engineering the Fab fragment of the anti-IgE omalizumab to prevent Fab crystallization and permit IgE-Fc complex crystallization
Cited by: 4
Author(s): A.N. Mitropoulou, Tom Ceska, James T. Heads, Andrew J. Beavil, Alistair J. Henry, James M. McDonnell, Brian J. Sutton, Anna M. Davies
Software Mentions: 3
Published: over 6 years ago

10.1016/j.molcel.2018.12.023

Activation of the Endonuclease that Defines mRNA 3′ Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex
Cited by: 67
Author(s): C.P. Hill, Vytautė Boreikaitė, Aman Kumar, Ana Casañal, Peter Kubík, Gianluca Degliesposti, Sarah Maslen, Angelica Mariani, Ottilie von Loeffelholz, Mathias Girbig, Mark Skehel, Lori A. Passmore
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-24775-4

A molecular dynamics simulation study decodes the Zika virus NS5 methyltransferase bound to SAH and RNA analogue
Cited by: 22
Author(s): Chih-Hung Chuang, Shean‐Jaw Chiou, Tian−Lu Cheng, Yeng‐Tseng Wang
Software Mentions: 3
Published: over 8 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: over 15 years ago

10.1038/s41598-021-91494-8

Uncovering of cytochrome P450 anatomy by SecStrAnnotator
Cited by: 7
Author(s): Adam Midlik, Veronika Navrátilová, Taraka Ramji Moturu, Jaroslav Koča, Radka Svobodová, Karel Berka
Software Mentions: 3
Published: over 5 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: almost 9 years ago

10.6026/97320630015784

Molecular docking based virtual screening of the breast cancer target NUDT5
Cited by: 6
Author(s): Razia Sultana, Monjia Islam, Md Azizul Haque, Fatematuz Zuhura Evamoni, Zahid Mohammad Imran, Jabunnesa Khanom, Adnan Munim
Software Mentions: 3
Published: almost 7 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

10.1016/j.molcel.2020.04.012

Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork
Cited by: 100
Author(s): Domagoj Baretić, Michael Jenkyn-Bedford, Valentina Aria, Giuseppe Cannone, Mark Skehel, Joseph T.P. Yeeles
Software Mentions: 3
Published: over 6 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

10.1074/mcp.RA120.002028

A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria
Cited by: 36
Author(s): Andreas Linden, Markus Deckers, Iwan Parfentev, Ralf Pflanz, Bettina Homberg, Piotr Neumann, Ralf Ficner, Peter Rehling, Henning Urlaub
Software Mentions: 3
Published: over 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

10.1016/j.jmb.2015.10.027

A Substrate Mimic Allows High-Throughput Assay of the FabA Protein and Consequently the Identification of a Novel Inhibitor of Pseudomonas aeruginosa FabA
Cited by: 6
Author(s): L. Moynié, Anthony G. Hope, Kara Finzel, J.W. Schmidberger, Stuart M. Leckie, Günter Schneider, Michael D. Burkart, Andrew D. Smith, David W. Gray, James H. Naismith
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0115082

Ethenoguanines Undergo Glycosylation by Nucleoside 2′-Deoxyribosyltransferases at Non-Natural Sites
Cited by: 10
Author(s): Wenjie Ye, Debajyoti Paul, Lina Gao, Jolita Šečkutė, R. Sangaiah, K. Jayaraj, Zhenfa Zhang, P.A. Kaminski, S.E. Ealick, Avram Gold, Louise M. Ball
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0243429

A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations
Cited by: 2
Author(s): Dimitrios A. Mitsikas, Nicholas M. Glykos
Software Mentions: 3
Published: almost 6 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

10.3389/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

10.1371/journal.pone.0182972

Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight
Cited by: 8
Author(s): Leslie Regad, Jean-Baptiste Chéron, Dhoha Triki, Caroline Senac, Delphine Flatters, Anne-Claude Camproux
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pntd.0008091

Trypanosomatid selenophosphate synthetase structure, function and interaction with selenocysteine lyase
Cited by: 4
Author(s): Marco Túlio Alves da Silva, Ivan Rosa e Silva, Lívia Maria Faim, Natália Karla Bellini, Murilo Leão Pereira, Ana Laura Lima, Teresa Cristina Leandro de Jesus, Fernanda Cristina Costa, Tatiana F. Watanabe, H.M. Pereira, Sandro Roberto Valentini, Cleslei Fernando Zanelli, Júlio César Borges, Márcio Vinícius Bertacini Dias, Júlia Pinheiro Chagas da Cunha, Bidyottam Mittra, Norma W. Andrews, Otávio Henrique Thiemann
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms21124378

Discovery of Isoplumbagin as a Novel NQO1 Substrate and Anti-Cancer Quinone
Cited by: 19
Author(s): Yen-Chi Tsao, Yu‐Jung Chang, Chun-Hsien Wang, Linyi Chen
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

10.7554/eLife.58362

Structural basis of mitochondrial translation
Cited by: 61
Author(s): Shintaro Aibara, Vivek P. Singh, A. Modelska, Alexey Amunts
Software Mentions: 3
Published: about 6 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

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: about 11 years ago

10.3390/v11020167

Genetic Evolution and Molecular Selection of the HE Gene of Influenza C Virus
Cited by: 25
Author(s): Wenyan Zhang, Letian Zhang, Wanting He, Xu Zhang, Baiqing Wen, Congcong Wang, Qiuhua Xu, Gairu Li, Jiyong Zhou, Michael Veit, Shuo Su
Software Mentions: 3
Published: over 7 years ago

10.1111/mpp.12868

Comparative transcriptome profiling uncovers a <i>Lilium regale</i> NAC transcription factor, <i>LrNAC35</i>, contributing to defence response against cucumber mosaic virus and tobacco mosaic virus
Cited by: 25
Author(s): Daoyang Sun, Xinguo Zhang, Qingyu Zhang, Xiaotong Ji, Yuping Jia, Hong Wang, Lixin Niu, Yanlong Zhang
Software Mentions: 3
Published: about 7 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

10.1111/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

10.1371/journal.ppat.1008394

Structural and functional insights into a novel two-component endolysin encoded by a single gene in Enterococcus faecalis phage
Cited by: 21
Author(s): Biao Zhou, Xiangkai Zhen, Huan Zhou, Feiyang Zhao, Chao Fan, Vanja Perčulija, Yigang Tong, Zhiqiang Mi, Songying Ouyang
Software Mentions: 3
Published: over 6 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

10.1038/s41598-018-27051-7

The crystal structure of monoacylglycerol lipase from M. tuberculosis reveals the basis for specific inhibition
Cited by: 19
Author(s): P. Aschauer, R. Zimmermann, Rolf Breinbauer, Tea Pavkov‐Keller, Monika Oberer
Software Mentions: 3
Published: over 8 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

10.1371/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

10.7554/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

10.3389/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

10.1042/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

10.1093/ve/vev006

Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak
Cited by: 29
Author(s): Austin G. Meyer, Scott R. Spielman, Trevor Bedford, Claus O. Wilke
Software Mentions: 3
Published: almost 12 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

10.1016/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: over 8 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

10.1038/s41598-021-97871-7

Deep mutational scanning of the plasminogen activator inhibitor-1 functional landscape
Cited by: 7
Author(s): Zachary M. Huttinger, Laura M. Haynes, Andrew Yee, Colin A. Kretz, Matthew L. Holding, David Siemieniak, Daniel A. Lawrence, David Ginsburg
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-25346-3

Critical amino acids for the insecticidal activity of Vip3Af from Bacillus thuringiensis: Inference on structural aspects
Cited by: 26
Author(s): Núria Banyuls, Carmen Sara Hernández‐Rodríguez, Jeroen Van Rie, Juan Ferré
Software Mentions: 3
Published: over 8 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

10.1371/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

10.1093/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

10.1093/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

10.3389/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

10.1016/j.str.2017.01.002

Crystal Structure of the Heterotrimeric Integrin-Binding Region of Laminin-111
Cited by: 28
Author(s): David Pulido, Sadaf-Ahmahni Hussain, Erhard Hohenester
Software Mentions: 3
Published: over 9 years ago

10.1016/j.str.2017.12.005

Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa
Cited by: 27
Author(s): Osman Salih, Shaoda He, Sara Planamente, Lasse Stach, James T. MacDonald, Eleni Manoli, S.H.W. Scheres, Alain Filloux, Paul S. Freemont
Software Mentions: 3
Published: over 8 years ago

10.1016/j.molcel.2017.09.027

A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants
Cited by: 54
Author(s): Mads Gabrielsen, Lori Buetow, Mark A. Nakasone, Syed Feroj Ahmed, Gary Sibbet, Brian O. Smith, Wei Zhang, Sachdev S. Sidhu, Danny T. Huang
Software Mentions: 3
Published: about 9 years ago

10.1074/mcp.RA119.001839

Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker
Cited by: 32
Author(s): Karl A.T. Makepeace, Yassene Mohammed, Elena L. Rudashevskaya, Evgeniy V. Petrotchenko, F.-Nora Vögtle, Chris Meisinger, Albert Sickmann, Christoph H. Borchers
Software Mentions: 3
Published: over 6 years ago

10.1016/j.jmb.2013.10.039

Structural Determinants of Unique Properties of Human IgG4-Fc
Cited by: 95
Author(s): Anna M. Davies, Theo Rispens, Pleuni Ooijevaar-de Heer, Hannah J. Gould, Royston Jefferis, Rob C. Aalberse, Brian J. Sutton
Software Mentions: 3
Published: over 12 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

10.7554/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

10.3389/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/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

10.1371/journal.pntd.0006180

Inhibitors of Trypanosoma cruzi Sir2 related protein 1 as potential drugs against Chagas disease
Cited by: 9
Author(s): Luís Gaspar, Ross P.. Coron, Paul Kong Thoo Lin, David Costa, Begoña Pérez-Cabezas, Joana Tavares, Meritxell Roura-Ferrer, Isbaal Ramos, C. Ronin, Louise L. Major, Fabrice Ciesielski, Iain K. Pemberton, Jane MacDougall, Paola Ciapetti, Terry Smith, Anabela Cordeiro-da-Silva
Software Mentions: 3
Published: over 8 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

10.3390/ijms22062861

In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila, Persephonella marina, Thermosulfidibacter takaii, and Thermus thermophilus
Cited by: 5
Author(s): Colleen Varaidzo Manyumwa, Özlem Tastan Bishop
Software Mentions: 3
Published: over 5 years ago

10.1155/2013/185282

Elucidation of Novel Structural Scaffold in Rohu TLR2 and Its Binding Site Analysis with Peptidoglycan, Lipoteichoic Acid and Zymosan Ligands, and Downstream MyD88 Adaptor Protein
Cited by: 20
Author(s): Bikash R. Sahoo, Madhubanti Basu, Bichitrananda Swain, Manas Ranjan Dikhit, P. Jayasankar, Mrinal Samanta
Software Mentions: 3
Published: almost 14 years ago

10.15252/msb.20209840

From chemoproteomic‐detected amino acids to genomic coordinates: insights into precise multi‐omic data integration
Cited by: 7
Author(s): Maria Palafox, Heta S Desai, Valerie A. Arboleda, Keriann M. Backus
Software Mentions: 3
Published: over 5 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

10.1371/journal.pone.0080210

Comparative Sequence, Structure and Redox Analyses of Klebsiella pneumoniae DsbA Show That Anti-Virulence Target DsbA Enzymes Fall into Distinct Classes
Cited by: 25
Author(s): Fabian Kurth, Kieran Rimmer, Lakshmanane Premkumar, Biswaranjan Mohanty, Wilko Duprez, Maria A. Halili, Stephen R. Shouldice, Begoña Heras, David P. Fairlie, M.J. Scanlon, Jennifer L. Martin
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pntd.0000115

Characterization of the Entamoeba histolytica Ornithine Decarboxylase-Like Enzyme
Cited by: 16
Author(s): Anupam Jhingran, Prasad K. Padmanabhan, Sushma Singh, Krishanpal Anamika, Abhijeet Bakre, Sudha Bhattacharya, Alok Bhattacharya, Narayanaswamy Srinivasan, Rentala Madhubala
Software Mentions: 3
Published: almost 19 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

10.1107/S1600576720002423

Application of a high-throughput microcrystal delivery system to serial femtosecond crystallography
Cited by: 21
Author(s): Donghyeon Lee, Sehan Park, Keondo Lee, Jang Woo Kim, Gisu Park, Ki Hyun Nam, Sangwon Baek, Wan Kyun Chung, Jong‐Lam Lee, Yunje Cho, Jaehyun Park
Software Mentions: 3
Published: over 6 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

10.1038/s41598-018-21667-5

Structure based function-annotation of hypothetical protein MGG_01005 from Magnaporthe oryzae reveals it is the dynein light chain orthologue of dynlt1/3
Cited by: 2
Author(s): Guorui Li, Jinguang Huang, Jun Yang, Dan He, Chao Wang, Xiaoxuan Qi, Ian A. Taylor, Junfeng Liu, You-Liang Peng
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-021-94019-5

Multi-omics integration of methyltransferase-like protein family reveals clinical outcomes and functional signatures in human cancer
Cited by: 26
Author(s): Ion J. Campeanu, Yuanyuan Jiang, Lanxin Liu, Maksymilian Pilecki, Alvina Najor, Era Cobani, Morenci Manning, Xiaohong Mary Zhang, Zeng-Quan Yang
Software Mentions: 3
Published: about 5 years ago

10.3390/v12010105

Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111
Cited by: 8
Author(s): Aaron E. Lin, William E. Diehl, Yíngyún Caì, Courtney Finch, Chidiebere Akusobi, Robert N. Kirchdoerfer, Laura Bollinger, Stephen F. Schaffner, Elizabeth Brown, Erica Ollmann Saphire, Kristian G. Andersen, Jens H. Kuhn, Jeremy Luban, Pardis C. Sabeti
Software Mentions: 3
Published: over 6 years ago

10.1093/gbe/evu235

Albuminoid Genes: Evolving at the Interface of Dispensability and Selection
Cited by: 12
Author(s): Alessandra Mozzi, Diego Forni, Rachele Cagliani, Jacopo Vertemara, Nereo Bresolin, Manuela Sironi
Software Mentions: 3
Published: almost 12 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

10.1371/journal.pone.0143245

Coevolution Analysis of HIV-1 Envelope Glycoprotein Complex
Cited by: 9
Author(s): Reda Rawi, Khalid Kunji, Abdelali Haoudi, Halima Bensmail
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0241754

Emergence of a novel chikungunya virus strain bearing the E1:V80A substitution, out of the Mombasa, Kenya 2017-2018 outbreak
Cited by: 9
Author(s): Fredrick Eyase, Solomon Langat, Irina Maljkovic Berry, Francis Mulwa, Albert Nyunja, James Mu, Samuel Owaka, Samson Limbaso, Victor Ofula, Hellen Koka, Edith Koskei, Joel Lutomiah, Richard G. Jarman, Rosemary Sang
Software Mentions: 3
Published: almost 6 years ago

10.1155/2021/6696012

Active Learning and the Potential of Neural Networks Accelerate Molecular Screening for the Design of a New Molecule Effective against SARS-CoV-2
Cited by: 3
Author(s): Yassine Rabhi, Makrem Mrabet, Farhat Fnaiech
Software Mentions: 3
Published: over 5 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.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

10.1371/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.0201509

Hydroxycholesterol binds and enhances the anti-viral activities of zebrafish monomeric c-reactive protein isoforms
Cited by: 11
Author(s): Melissa Belló-Pérez, Alberto Falcó, Beatriz Novoa, Luis Pérez, Julio Coll
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0233689

The crystal structures of Thermus thermophilus CMP kinase complexed with a phosphoryl group acceptor and donor
Cited by: 3
Author(s): Ryosuke Mega, Noriko Nakagawa, Seiki Kuramitsu, Ryoji Masui
Software Mentions: 3
Published: over 6 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

10.1172/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