10.1128/JVI.01127-19

Evolutionary Dynamics of Oropouche Virus in South America
Cited by: 14
Author(s): Bernardo Gutierrez, Emma L. Wise, Steven T. Pullan, Christopher Logue, Thomas A. Bowden, Marina Escalera-Zamudio, Gabriel Trueba, Márcio Roberto Teixeira Nunes, Nuno Rodrigues Faria, Oliver G. Pybus
Software Mentions: 4
Published: over 6 years ago

10.1007/s13205-014-0231-z

Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae
Cited by: 15
Author(s): Mohd Shahbaaz, Faizan Ahmad, Md. Imtaiyaz Hassan
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pcbi.1007219

Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
Cited by: 11
Author(s): Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini, Alessandro Paiardini
Software Mentions: 4
Published: almost 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

10.3390/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

10.3390/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/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/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

10.3390/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/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

10.3390/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/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

10.3390/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

10.7554/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

10.7554/eLife.03583

Structure and transport mechanism of the sodium/proton antiporter MjNhaP1
Cited by: 65
Author(s): Cristina Paulino, David Wöhlert, Ekaterina Kapotova, Özkan Yıldız, Werner Kühlbrandt
Software Mentions: 3
Published: almost 12 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

10.3390/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/ijms22189833

Searching for Biological Function of the Mysterious PA2504 Protein from Pseudomonas aeruginosa
Cited by: 0
Author(s): Joanna Drabinska, Kamil Steczkiewicz, Martyna Kujawa, Elżbieta Kraszewska
Software Mentions: 3
Published: about 5 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

10.7554/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.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

10.7554/eLife.60481

Identification of PARP-7 substrates reveals a role for MARylation in microtubule control in ovarian cancer cells
Cited by: 35
Author(s): Lori Parsons, Sridevi Challa, Bryan A. Gibson, Tulip Nandu, MiKayla S Stokes, Dan Huang, Jayanthi Lea, W. Lee Kraus
Software Mentions: 3
Published: over 5 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.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: almost 8 years ago

10.7554/eLife.46497

Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade
Cited by: 80
Author(s): Tom O. Delmont, Evan Kiefl, Ozsel Kilinc, Özcan C. Esen, Ismail Uysal, Michael S. Rappé, Steven Giovannoni, A. Murat Eren
Software Mentions: 3
Published: about 7 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

10.7554/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

10.7554/eLife.57861

Profiling of myristoylation in Toxoplasma gondii reveals an N-myristoylated protein important for host cell penetration
Cited by: 19
Author(s): Malgorzata Broncel, Caia Dominicus, Luis Vigetti, Stephanie D. Nofal, Edward Bartlett, Bastien Touquet, Alex Hunt, Bethan A. Wallbank, Stefania Federico, Stephen Matthews, J. M. Young, Edward W. Tate, Isabelle Tardieux, Moritz Treeck
Software Mentions: 3
Published: over 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

10.3390/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: about 5 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.46754

The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs
Cited by: 33
Author(s): Axelle Marchant, Angel F. Cisneros, Alexandre K. Dubé, Isabelle Gagnon‐Arsenault, Diana Ascencio, Honey A. Jain, Simon Aubé, Chris Eberlein, Daniel Evans-Yamamoto, Nozomu Yachie, Christian R. Landry
Software Mentions: 3
Published: about 7 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

10.1186/s12915-016-0311-0

Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation
Cited by: 18
Author(s): David S. Rabiger, Jennifer Taylor, Andrew Spriggs, Melanie L. Hand, Steven T. Henderson, Susan D. Johnson, Karsten Oelkers, Mária Hrmová, Keisuke Saito, Go Suzuki, Yasuhiko Mukai, Bernard J. Carroll, Anna M. Koltunow
Software Mentions: 3
Published: about 10 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

10.1016/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

10.1016/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

10.1002/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

10.1155/2014/162150

Evaluation of 11 Scoring Functions Performance on Matrix Metalloproteinases
Cited by: 10
Author(s): Jamal Shamsara
Software Mentions: 3
Published: almost 12 years ago

10.1107/S1399004714016241

Conformation-independent structural comparison of macromolecules with<i>ProSMART</i>
Cited by: 150
Author(s): Robert A. Nicholls, Marcus Fischer, Stuart McNicholas, Garib N. Murshudov
Software Mentions: 3
Published: about 12 years ago

10.1186/s12915-021-01102-4

High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding
Cited by: 9
Author(s): Hüseyin İlgü, Jean-Marc Jeckelmann, David Kalbermatter, Zöhre Ucurum, Thomas Lemmin, Dimitrios Fotiadis
Software Mentions: 3
Published: about 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

10.1038/s41598-020-60768-y

Complex approach for analysis of snake venom α-neurotoxins binding to HAP, the high-affinity peptide
Cited by: 9
Author(s): Denis S. Kudryavtsev, Valentin М. Tabakmakher, Gleb S. Budylin, N. S. Egorova, Roman G. Efremov, Igor A. Ivanov, Svetlana Yu. Belukhina, Artjom V. Jegorov, Igor E. Kasheverov, Elena V. Kryukova, Irina V. Shelukhina, Evgeny A. Shirshin, Nadezhda G. Zhdanova, Maxim N. Zhmak, Victor I. Tsetlin
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-64034-z

Comparative Analyses of the Conformational Dynamics Between the Soluble and Membrane-Bound Cytokine Receptors
Cited by: 7
Author(s): Chao‐Yie Yang
Software Mentions: 3
Published: over 6 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

10.1038/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

10.1038/s41598-019-52825-y

A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser
Cited by: 2
Author(s): Si Hoon Park, Jaehyun Park, Sang Jae Lee, Woo Seok Yang, Sehan Park, Kyungdo Kim, Zee Yong Park, Hyun Kyu Song
Software Mentions: 3
Published: almost 7 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

10.1107/S2059798321003533

Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum
Cited by: 4
Author(s): Leona Švecová, Lars Østergaard, Tereza Skálová, Kirk Schnorr, T. Kovaľ, Petr Kolenko, Jan Stránský, David Sedlák, Jarmila Dušková, Mária Trundová, Jindřich Hašek, Jan Dohnálek
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-10-153

Tableau-based protein substructure search using quadratic programming
Cited by: 11
Author(s): Alex Stivala, Anthony Wirth, Peter J. Stuckey
Software Mentions: 3
Published: over 17 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

10.1038/s41598-017-10085-8

Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq
Cited by: 14
Author(s): Eike C. Schulz, Markus Seiler, Cecilia Zuliani, Franka Voigt, Vladimir Rybin, Vivian Pogenberg, Norbert Mücke, Matthias Wilmanns, Toby J. Gibson, O. Barábas
Software Mentions: 3
Published: about 9 years ago

10.1107/S2059798319003991

Structural analysis of a replication protein encoded by a plasmid isolated from a multiple sclerosis patient
Cited by: 5
Author(s): Turgay Kilic, A. Popov, Amelie Burk-Körner, A.D. Koromyslova, Harald zur Hausen, Timo Bund, Grant S. Hansman
Software Mentions: 3
Published: over 7 years ago

10.1107/S0907444911035943

High-resolution structure of a retroviral protease folded as a monomer
Cited by: 22
Author(s): Mirosław Gilski, Maciej Kazmierczyk, Szymon Krzywda, Helena Zábranská, Seth Cooper, Zoran Popović, Firas Khatib, Frank DiMaio, James Thompson, David Baker, Iva Pichová, Mariusz Jaskólski
Software Mentions: 3
Published: almost 15 years ago

10.1186/1471-2105-13-S14-S13

High-Throughput parallel blind Virtual Screening using BINDSURF
Cited by: 142
Author(s): Irene Sánchez-Linares, Horacio Pérez‐Sánchez, José M. Cecilia, José M. García
Software Mentions: 3
Published: about 14 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/s41598-018-25346-3

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

10.7554/eLife.22964

Dilation of fusion pores by crowding of SNARE proteins
Cited by: 54
Author(s): Zhenyong Wu, Oscar Bello, Sathish Thiyagarajan, Sarah M. Auclair, Wensi Vennekate, Shyam S. Krishnakumar, Ben O’Shaughnessy, Erdem Karatekin
Software Mentions: 3
Published: over 9 years ago

10.1073/pnas.1911776116

Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection
Cited by: 14
Author(s): Fiona Whelan, Aleix Lafita, Samuel C. Griffiths, R.E.M. Cooper, J.L. Whittingham, J.P. Turkenburg, Iain W. Manfield, Alexander N. St John, Emanuele Paci, Alex Bateman, Jennifer R. Potts
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.ppat.1009775

Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses
Cited by: 10
Author(s): Sofia Banchenko, Ferdinand Krupp, Christine Gotthold, Jörg Bürger, Andrea Graziadei, Francis J. O’Reilly, Ludwig Sinn, Olga Ruda, Juri Rappsilber, C.M.T. Spahn, Thorsten Mielke, Ian A. Taylor, David Schwefel
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-15-87

Estimation of protein function using template-based alignment of enzyme active sites
Cited by: 13
Author(s): Brett R. Hanson, Charles Westin, Mario De Rosa, Alexander Grier, Mikhail Osipovitch, Madolyn L. MacDonald, Greg J. Dodge, Paule M Boli, Cyprian Corwin, Haeja Kessler, Talia McKay, H. J. Bernstein, P. Craig
Software Mentions: 3
Published: over 12 years ago

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

10.1107/S1399004715004241

Using support vector machines to improve elemental ion identification in macromolecular crystal structures
Cited by: 4
Author(s): Nader Morshed, Nathaniel Echols, Paul D. Adams
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.ppat.1009016

Structural insights into loss of function of a pore forming toxin and its role in pneumococcal adaptation to an intracellular lifestyle
Cited by: 10
Author(s): Dilip Badgujar, Anjali Anil, Angharad E Green, Manalee Vishnu Surve, Shilpa Madhavan, Alison J. Beckett, Ian A. Prior, Barsa Kanchan Jyotshna Godsora, Sanket B. Patil, Prachi More, Shruti Guha Sarkar, Andrea M. Mitchell, Rinti Banerjee, Prashant S. Phale, Timothy J. Mitchell, Daniel R. Neill, Prasenjit Bhaumik, Anirban Banerjee
Software Mentions: 3
Published: almost 6 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

10.1007/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

10.1186/1471-2105-9-352

Alignment of protein structures in the presence of domain motions
Cited by: 48
Author(s): Roberto Mosca, Barbara Brannetti, Thomas R. Schneider
Software Mentions: 3
Published: about 18 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.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

10.1186/1471-2105-11-155

Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity
Cited by: 13
Author(s): Zong Hong Zhang, Hwee Kuan Lee, Ivana Mihalek
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.ppat.1009431

High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19
Cited by: 29
Author(s): Sung Hee Ko, Elham Bayat Mokhtari, Prakriti Mudvari, Sydney Stein, Christopher D. Stringham, Danielle A. Wagner, Sabrina Ramelli, Marcos J. Ramos‐Benitez, Jeffrey R Strich, Richard T. Davey, Tongqing Zhou, John Misasi, Peter D. Kwong, Daniel S. Chertow, Nancy J. Sullivan, Eli Boritz
Software Mentions: 3
Published: over 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

10.1107/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

10.1186/s12859-019-3120-y

RNA 3D structure prediction guided by independent folding of homologous sequences
Cited by: 18
Author(s): Marcin Magnus, Kalli Kappel, Rhiju Das, Janusz M. Bujnicki
Software Mentions: 3
Published: almost 7 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: about 5 years ago

10.1107/S2059798320000443

Extending the scope of coiled-coil crystal structure solution by <i>AMPLE</i> through improved <i>ab initio</i> modelling
Cited by: 7
Author(s): Jens M. H. Thomas, Ronan Keegan, Daniel J. Rigden, Owen R. Davies
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/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

10.1186/1471-2105-15-72

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

10.1107/S090744491301576X

Complex structure of type VI peptidoglycan muramidase effector and a cognate immunity protein
Cited by: 17
Author(s): Tianyu Wang, Jingjin Ding, Ying Zhang, Dacheng Wang, Wei Liu
Software Mentions: 3
Published: about 13 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

10.1371/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

10.1038/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

10.1186/s12859-016-0898-8

Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Cited by: 22
Author(s): Ruben Cloete, Ekow Oppon, Edwin Murungi, Wolf‐Dieter Schubert, Alan Christoffels
Software Mentions: 3
Published: over 10 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

10.1126/sciadv.aav8421

HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C
Cited by: 44
Author(s): M Collier, T. Reid Alderson, Carin Pamela de Villiers, D Nicholls, Heidi Y. Gastall, Timothy M. Allison, Matteo T. Degiacomi, Jiang He, Georg Mlynek, Dieter O. Fürst, Peter F.M. van der Ven, Kristina Djinović-Carugo, Andrew J. Baldwin, Hugh Watkins, Katja Gehmlich, Justin L. P. Benesch
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-48155-8

Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site
Cited by: 11
Author(s): Carsten Krichel, Christina Möckel, Oliver Schillinger, Pitter F. Huesgen, Heinrich Sticht, Birgit Strodel, Oliver H. Weiergräber, Dieter Willbold, Philipp Neudecker
Software Mentions: 3
Published: about 7 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

10.3389/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/S1399004714027011

Three-dimensional structures of<i>Plasmodium falciparum</i>spermidine synthase with bound inhibitors suggest new strategies for drug design
Cited by: 12
Author(s): J. Sprenger, Bo Svensson, J.C. Halander, Jannette Carey, Lo Persson, Salam Al-Karadaghi
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-020-58138-9

Structural characterization and in-silico analysis of Momordica charantia 7S globulin for stability and ACE inhibition
Cited by: 26
Author(s): Pooja Kesari, Shivendra Pratap, Poonam Dhankhar, Vikram Dalal, Manisha Mishra, Pradyumna Kumar Singh, Harsh Chauhan, Pravindra Kumar
Software Mentions: 3
Published: over 6 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

10.3389/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

10.3389/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

10.1093/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

10.1107/S2059798317007707

DNA conformational transitions inferred from re-evaluation ofm|Fo| −D|Fc| electron-density maps
Cited by: 3
Author(s): Tomoko Sunami, Toshiyuki Chatake, Hidetoshi Kono
Software Mentions: 3
Published: over 9 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.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