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

10.1074/jbc.RA119.010697

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

10.1016/j.jbc.2021.100700

ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis
Cited by: 8
Author(s): Jitender Mehla, George W. Liechti, Randy M. Morgenstein, J. Harry Caufield, Ali Hosseinnia, Alla Gagarinova, Sadhna Phanse, Norman Goodacre, Mary R. Brockett, Neha Sakhawalkar, Mohan Babu, Rong Xiao, Gaetano T. Montelione, S.M. Vorobiev, T. den Blaauwen, J.F. Hunt, Peter Uetz
Software Mentions: 3
Published: almost 6 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

10.3389/fpls.2019.00466

Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling
Cited by: 34
Author(s): Marius L. Theune, Ulrich Bloss, Luise H. Brand, Friederike Ladwig, Dierk Wanke
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2016.01810

The Eucalyptus Tonoplast Intrinsic Protein (TIP) Gene Subfamily: Genomic Organization, Structural Features, and Expression Profiles
Cited by: 9
Author(s): Marcela Iara Rodrigues, Agnes Alessandra Sekijima Takeda, Juliana Pereira Bravo, Ivan de Godoy Maia
Software Mentions: 3
Published: almost 10 years ago

10.3389/fpls.2016.00266

Identification and Characterization of the Sucrose Synthase 2 Gene (Sus2) in Durum Wheat
Cited by: 14
Author(s): Mariateresa Volpicella, Immacolata Fanizza, Claudia Leoni, Ágata Gadaleta, Domenica Nigro, B. Gattulli, Giacomo Mangini, Antonio Blanco, Luigi R. Ceci
Software Mentions: 3
Published: over 10 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

10.3389/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/frobt.2018.00133

Authenticity, Interactivity, and Collaboration in VR Learning Games
Cited by: 9
Author(s): Meredith Thompson, Annie Wang, Dan Roy, Eric Klopfer
Software Mentions: 3
Published: almost 8 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

10.3389/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

10.3389/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.2021.643728

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/fcimb.2020.00082

Francisella novicida Two-Component System Response Regulator BfpR Modulates iglC Gene Expression, Antimicrobial Peptide Resistance, and Biofilm Production
Cited by: 6
Author(s): Scott N. Dean, Morgan E. Milton, John Cavanagh, Monique L. van Hoek
Software Mentions: 3
Published: over 6 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

10.3389/fbioe.2020.00707

An (R)-Selective Transaminase From Thermomyces stellatus: Stabilizing the Tetrameric Form
Cited by: 18
Author(s): Christian M. Heckmann, L.J. Gourlay, Beatriz Domı́nguez, Francesca Paradisi
Software Mentions: 3
Published: over 6 years ago

10.1038/srep33553

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

10.3389/fcimb.2021.605589

Disseminated Talaromyces marneffei Infection in a Non-HIV Infant With a Homozygous Private Variant of RELB
Cited by: 9
Author(s): Xiaojuan Ding, Han Huang, Lili Zhao, Min Chen, Fang Peng, Bing Zhang, Xinyu Cui, Xiu‐An Yang
Software Mentions: 3
Published: over 5 years ago

10.1111/febs.13310

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

10.1007/s00792-013-0542-8

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

10.1371/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

10.1111/febs.15514

Structure‐based design of peptides that trigger <i>Streptococcus pneumoniae</i> cell death
Cited by: 11
Author(s): Sung-Min Kang, Chun Jin, Do-Hee Kim, Sung Jean Park, Sang-Woo Han, Bong-Jin Lee
Software Mentions: 3
Published: about 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

10.1074/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

10.1186/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: about 7 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

10.1016/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

10.1016/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

10.1186/1471-2105-13-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

10.1007/s00412-019-00700-0

The molecular basis of monopolin recruitment to the kinetochore
Cited by: 15
Author(s): Rebecca Plowman, Namit Singh, Eelco C. Tromer, Angel Payan, Eris Duro, Christos Spanos, Juri Rappsilber, Berend Snel, Geert J.P.L. Kops, K.D. Corbett, Adèle L. Marston
Software Mentions: 3
Published: over 7 years ago

10.1016/j.febslet.2015.11.030

Crystal structure of the Z-ring associated cell division protein ZapC from Escherichia coli
Cited by: 13
Author(s): Cristina Ortiz, Danguole Kureisaite-Ciziene, Florian Schmitz, Stephen H. McLaughlin, Miguel Vicente, Jan Löwe
Software Mentions: 3
Published: almost 11 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

10.1371/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

10.1371/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.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: almost 11 years ago

10.1371/journal.pone.0243085

Dissecting seed pigmentation-associated genomic loci and genes by employing dual approaches of reference-based and k-mer-based GWAS with 438 Glycine accessions
Cited by: 7
Author(s): Jin-Hyun Kim, Joo-Seok Park, Chang Kyu Lee, Min‐Gyun Jeong, Jiu Liang Xu, Yong-Soo Choi, Han‐Sung Jung, Hyunju Choi
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0232846

Diversity in kinetics correlated with structure in nano body-stabilized LacY
Cited by: 3
Author(s): Atul Kumar Johri, J. Finer-Moore, И. Н. Смирнова, Vladimir N. Kasho, Els Pardon, Jan Steyaert, H. Ronald Kaback, Robert M. Stroud
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0248887

Production and characterization of antibody against Opisthorchis viverrini via phage display and molecular simulation
Cited by: 0
Author(s): Sitthinon Siripanthong, Anchalee Techasen, Chanin Nantasenamat, Aijaz Ahmad Malik, Paiboon Sithithaworn, Chanvit Leelayuwat, Amonrat Jumnainsong
Software Mentions: 3
Published: over 5 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

10.1107/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

10.1371/journal.pone.0196484

Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches
Cited by: 71
Author(s): Abbas Khan, Muhammad Junaid, Aman Chandra Kaushik, Arif Ali, Syed Shujait Ali, Aamir Mehmood, Dong‐Qing Wei
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0080947

Crystal Structures of the Human G3BP1 NTF2-Like Domain Visualize FxFG Nup Repeat Specificity
Cited by: 43
Author(s): T. Vognsen, Ingvar R. Möller, Ole Kristensen
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0156067

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

10.1107/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

10.1128/AEM.00808-18

Shuffling the Neutral Drift of Unspecific Peroxygenase in Saccharomyces cerevisiae
Cited by: 24
Author(s): Javier Martín-Díaz, Carmen Paret, Eva García-Ruiz, Patricia Molina‐Espeja, Miguel Alcalde
Software Mentions: 3
Published: about 8 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.pgen.1008964

The evolution and functional divergence of the histone H2B family in plants
Cited by: 42
Author(s): Dazong Jiang, Michael Borg, Zdravko J. Lorković, Sean A. Montgomery, Akihisa Osakabe, Ramesh Yelagandula, Elin Axelsson, Frédéric Berger
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1009215

Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae
Cited by: 12
Author(s): Joshua J. Black, Richa Sardana, Ezzeddine W. Elmir, Arlen Johnson
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1009651

Functional and structural analyses of novel Smith-Kingsmore Syndrome-Associated MTOR variants reveal potential new mechanisms and predictors of pathogenicity
Cited by: 6
Author(s): Aaron D. Besterman, Thorsten Althoff, Peter Elfferich, Irma Gutierrez-Mejia, Joshua Sadik, Jonathan A. Bernstein, Yvette van Ierland, Anja A. Kattentidt-Mouravieva, Mark Nellist, Jeff Abramson, Julián A. Martínez-Agosto
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1008140

A steady-state model of microbial acclimation to substrate limitation
Cited by: 13
Author(s): John R. Casey, Michael J. Follows
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pcbi.1002708

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
Cited by: 908
Author(s): Eva Chovancová, Antonín Pavelka, Petr Beneš, Ondřej Strnad, Jan Brezovský, Barbora Kozlíková, Artur Góra, Vilém Šustr, Martin Klvaňa, Petr Medek, Lada Biedermannová, Jiří­ Sochor, Jiřı́ Damborský
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0083496

Exploration of Virtual Candidates for Human HMG-CoA Reductase Inhibitors Using Pharmacophore Modeling and Molecular Dynamics Simulations
Cited by: 17
Author(s): Maeng-Hyun Son, Ayoung Baek, Sugunadevi Sakkiah, Chanin Park, John Strouboulis, Keun Woo Lee
Software Mentions: 3
Published: almost 13 years ago

10.1107/S2059798316007695

<i>Ab initio</i>phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus
Cited by: 3
Author(s): Masato Yoshimura, Nai Chi Chen, Hongbing Guan, Phimonphan Chuankhayan, Chi‐Chang Lin, Atsushi Nakagawa, Chun‐Jung Chen
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0077995

Structural and Enzymatic Characterization of the Phosphotriesterase OPHC2 from Pseudomonas pseudoalcaligenes
Cited by: 52
Author(s): Guillaume Gotthard, Julien Hiblot, Daniel H. González, Mikael Elias, Éric Chabrière
Software Mentions: 3
Published: almost 13 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

10.1107/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.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.1005294

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations
Cited by: 8
Author(s): Andrew F. Neuwald, Stephen F. Altschul
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pcbi.1007892

Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans
Cited by: 2
Author(s): Chadi M. Saad-Roy, Nimalan Arinaminpathy, Ned S. Wingreen, Simon A. Levin, Joshua M. Akey, Bryan T. Grenfell
Software Mentions: 3
Published: over 6 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: almost 7 years ago

10.1371/journal.pone.0214440

A DNA aptamer reveals an allosteric site for inhibition in metallo-β-lactamases
Cited by: 17
Author(s): Nazmul H Khan, Anthony A. Bui, Yang Xiao, R. Bryan Sutton, Robert W. Shaw, Benjamin J. Wylie, Michael P. Latham
Software Mentions: 3
Published: over 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

10.1371/journal.pbio.3000654

Cryo-EM structures of the human PA200 and PA200-20S complex reveal regulation of proteasome gate opening and two PA200 apertures
Cited by: 22
Author(s): Hongxin Guan, Youwang Wang, Ting Yu, Yini Huang, Mianhuan Li, Abdullah F. U. H. Saeed, Vanja Perčulija, Daliang Li, Jia Xiao, Dongmei Wang, Ping Zhu, Songying Ouyang
Software Mentions: 3
Published: over 6 years ago

10.3390/medsci7060074

In Silico Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts
Cited by: 0
Author(s): P. Sneha, Urmi Shah, S. Balaji
Software Mentions: 3
Published: over 7 years ago

10.1074/jbc.M115.671586

Structure and Function of the Escherichia coli Tol-Pal Stator Protein TolR
Cited by: 30
Author(s): Justyna Aleksandra Wojdyla, Erin E. Cutts, Renata Kaminska, Grigorios Papadakos, Jonathan T. S. Hopper, Phillip J. Stansfeld, David Staunton, Carol V. Robinson, Colin Kleanthous
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pbio.1001994

Thermodynamic System Drift in Protein Evolution
Cited by: 74
Author(s): Kathryn M. Hart, Michael J. Harms, Bryan H. Schmidt, Carolyn Elya, Joseph W. Thornton, Susan Marqusee
Software Mentions: 3
Published: almost 12 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

10.3389/fmicb.2020.582437

Role of BgaA as a Pneumococcal Virulence Factor Elucidated by Molecular Evolutionary Analysis
Cited by: 5
Author(s): M. Yamaguchi, Moe Takemura, Kõtarõ Higashi, Kana Goto, Yujiro Hirose, Tomoko Sumitomo, Masao Nakata, Narikazu Uzawa, Shigetada Kawabata
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2017.00048

Porphyromonas gingivalis Uses Specific Domain Rearrangements and Allelic Exchange to Generate Diversity in Surface Virulence Factors
Cited by: 37
Author(s): Stuart G. Dashper, Helen Mitchell, Christine A. Seers, Simon Gladman, Torsten Seemann, Dieter Bulach, P. Scott Chandry, Keith J. Cross, Steven M. Cleal, Eric C. Reynolds
Software Mentions: 3
Published: over 9 years ago

10.1074/jbc.M116.730382

Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases
Cited by: 14
Author(s): Marco Igor Valencia-Sánchez, Annia Rodríguez‐Hernández, Ruben Ferreira, Hugo A. Santamaría-Suárez, Marcelino Arciniega, Anne-Catherine Dock-Brégeon, Dino Moras, Brice Beinsteiner, Haydyn D. T. Mertens, Dmitri I. Svergun, Luis G. Brieba, Morten Grøtli, Alfredo Torres‐Larios
Software Mentions: 3
Published: over 10 years ago

10.3390/pharmaceutics13040554

Artocarpin Targets Focal Adhesion Kinase-Dependent Epithelial to Mesenchymal Transition and Suppresses Migratory-Associated Integrins in Lung Cancer Cells
Cited by: 10
Author(s): Nongyao Nonpanya, Kittipong Sanookpan, Nicharat Sriratanasak, Chanida Vinayanuwattikun, Duangdao Wichadakul, Boonchoo Sritularak, Pithi Chanvorachote
Software Mentions: 3
Published: over 5 years ago

10.1111/tpj.12935

Hetero‐trans‐β‐glucanase, an enzyme unique to <i>Equisetum</i> plants, functionalizes cellulose
Cited by: 46
Author(s): Thomas J. Simmons, Kyle E. Mohler, Claire Holland, Florence Goubet, Lenka Franková, Douglas R. Houston, Andrew Hudson, Frank Meulewaeter, Stephen C. Fry
Software Mentions: 3
Published: about 11 years ago

10.3390/md16100386

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

10.1371/journal.pbio.1001512

Conformational Change-Induced Repeat Domain Expansion Regulates Rap Phosphatase Quorum-Sensing Signal Receptors
Cited by: 56
Author(s): Vijay Parashar, Philip D. Jeffrey, Matthew B. Neiditch
Software Mentions: 3
Published: over 13 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.pbio.3000958

Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome
Cited by: 14
Author(s): Kai Ehrenbolger, Nathan Jespersen, Himanshu Sharma, Yuliya Y. Sokolova, Yuri S. Tokarev, Charles R. Vossbrinck, Jonas Barandun
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pcbi.1008568

Rosetta design with co-evolutionary information retains protein function
Cited by: 10
Author(s): Samuel Schmitz, Moritz Ertelt, Rainer Merkl, Jens Meiler
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-32040-x

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

10.1371/journal.pone.0167978

Using the Amino Acid Network to Modulate the Hydrolytic Activity of β-Glycosidases
Cited by: 12
Author(s): Fábio K. Tamaki, Diorge P. Souza, Valquiria P. Souza, Cecília M. Ikegami, Chuck S. Farah, Sandro R. Marana
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-018-33068-9

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

10.1038/s41598-018-37506-6

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

10.3390/molecules26041134

Establishing an Analogue Based In Silico Pipeline in the Pursuit of Novel Inhibitory Scaffolds against the SARS Coronavirus 2 Papain-Like Protease
Cited by: 9
Author(s): Roxanna Hajbabaie, Matthew T. Harper, Taufiq Rahman
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-40892-0

Steered molecular dynamic simulations of conformational lock of Cu, Zn-superoxide dismutase
Cited by: 11
Author(s): Bao-Lin Xiao, Yan-Na Ning, Nan-Nan Niu, Di Li, Ali Akbar Moosavi-Movahedi, Nader Sheibani, Jun Hong
Software Mentions: 3
Published: over 7 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

10.7554/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

10.15252/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

10.7554/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

10.1107/S205225251900246X

Subatomic resolution X-ray structures of green fluorescent protein
Cited by: 24
Author(s): Kiyotsugu Takaba, Yang Tai, Haruhiko Eki, Hoang Anh Dao, Yuya Hanazono, Kazuya Hasegawa, Kunio Miki, Kazuki Takeda
Software Mentions: 3
Published: over 7 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

10.7554/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

10.26508/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

10.1371/journal.pone.0023779

Evolutionary Pathways of the Pandemic Influenza A (H1N1) 2009 in the UK
Cited by: 38
Author(s): Mónica Galiano, Paul‐Michael Agapow, Catherine Thompson, Steven G. Platt, Anthony Underwood, Joanna Ellis, Richard Myers, Jonathan Green, Maria Zambon
Software Mentions: 3
Published: about 15 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

10.1038/s41598-019-46094-y

Human Corneal Expression of SLC4A11, a Gene Mutated in Endothelial Corneal Dystrophies
Cited by: 23
Author(s): Deepti Malhotra, Sampath K. Loganathan, Anthony M. Chiu, Chris M. Lukowski, Joseph R. Casey
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-39984-8

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

10.1371/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

10.1371/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

10.3390/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.pcbi.1007747

ProteinVR: Web-based molecular visualization in virtual reality
Cited by: 40
Author(s): Kevin C. Cassidy, Jan Šefčík, Yogindra Raghav, Alexander Chang, Jacob D. Durrant
Software Mentions: 3
Published: over 6 years ago