10.1038/s41598-017-01640-4

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

10.1038/s41598-017-08842-w

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

10.1128/mBio.00373-17

Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus
Cited by: 243
Author(s): Simon J. Anthony, Kirsten Gilardi, Vineet D. Menachery, Tracey Goldstein, Benard Ssebide, R. Mbabazi, Isamara Navarrete-Macias, Eliza Liang, Heather L. Wells, Alan C. Hicks, Alexandra Petrosov, Denis K. Byarugaba, Kari Debbink, Kenneth H. Dinnon, Trevor Scobey, Scott H. Randell, Boyd Yount, Michael R. Cranfield, Christine K. Johnson, Ralph S. Baric, W. Ian Lipkin, Jonna A. K. Mazet
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms20081996

Two Sides of the Coin: Ezrin/Radixin/Moesin and Merlin Control Membrane Structure and Contact Inhibition
Cited by: 45
Author(s): Katharine A. Michie, Adam Bermeister, Neil O. Robertson, Sophia C. Goodchild, Paul M. G. Curmi
Software Mentions: 3
Published: over 7 years ago

10.1016/j.yjsbx.2020.100031

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

10.1371/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

10.1371/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/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

10.1016/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

10.1016/j.jbc.2021.100927

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

10.1371/journal.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

10.3390/genes12010034

Biological Regulatory Network (BRN) Analysis and Molecular Docking Simulations to Probe the Modulation of IP3R Mediated Ca2+ Signaling in Cancer
Cited by: 2
Author(s): Humaira Ismatullah, Ishrat Jabeen, Muhammad Saeed
Software Mentions: 3
Published: almost 6 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

10.1074/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

10.3389/fpls.2019.00293

Phylogenetic Distribution and Diversity of Bacterial Pseudo-Orthocaspases Underline Their Putative Role in Photosynthesis
Cited by: 17
Author(s): Marina Klemenčič, Johannes Asplund-Samuelsson, Marko Dolinar, Christiane Funk
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.2019.00070

Mechanism Underlying Heat Stability of the Rice Endosperm Cytosolic ADP-Glucose Pyrophosphorylase
Cited by: 6
Author(s): Seon‐Kap Hwang, S. S. Singh, Jitendra Maharana, S. N. Kalita, Aytuğ Tuncel, Tanmayee Rath, Debashis Panda, Mahendra Kumar Modi, Thomas W. Okita
Software Mentions: 3
Published: over 7 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

10.1074/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

10.1371/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

10.3389/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

10.1107/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/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

10.3389/fimmu.2021.664877

Ovine CD14- an Immune Response Gene Has a Role Against Gastrointestinal Nematode Haemonchus contortus—A Novel Report
Cited by: 6
Author(s): Kavita Rawat, Aruna Pal, Sandipan Banerjee, Abantika Pal, S. C. Mandal, Subhasis Batabyal
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-13-S4-S16

Intuitive representation of surface properties of biomolecules using BioBlender
Cited by: 59
Author(s): Raluca Andrei, Marco Callieri, Maria Francesca Zini, Tiziana Loni, Giuseppe Maraziti, Mike Pan, Monica Zoppè
Software Mentions: 3
Published: over 14 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

10.3389/fcvm.2020.00008

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

10.3389/fimmu.2018.02086

The Diversity of Mammalian Hemoproteins and Microbial Heme Scavengers Is Shaped by an Arms Race for Iron Piracy
Cited by: 6
Author(s): Alessandra Mozzi, Diego Forni, Mario Clerici, Rachele Cagliani, Manuela Sironi
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2017.02034

Molecular Insight into the Acryloyl-CoA Hydration by AcuH for Acrylate Detoxification in Dimethylsulfoniopropionate-Catabolizing Bacteria
Cited by: 10
Author(s): Hai‐Yan Cao, Peng Wang, Fei Xu, Ping‐Yi Li, Bin-Bin Xie, Qi‐Long Qin, Yuzhong Zhang, Chunyang Li, Xiu-Lan Chen
Software Mentions: 3
Published: almost 9 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

10.1186/1471-2105-11-446

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

10.1016/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

10.1007/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.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

10.1186/1471-2105-15-72

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

10.1186/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

10.1186/1471-2105-13-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/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

10.3389/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: about 6 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.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

10.1371/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

10.1107/S2059798320001679

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

10.1371/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

10.1371/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

10.1371/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

10.1074/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

10.1371/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.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/S0907444912001308

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

10.1371/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.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

10.1128/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.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.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.pcbi.1006722

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

10.1371/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: about 6 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

10.1371/journal.pcbi.1003478

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor
Cited by: 69
Author(s): Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, Brian M. Baker
Software Mentions: 3
Published: over 12 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.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

10.1371/journal.pcbi.1004981

Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation
Cited by: 28
Author(s): Dario Corrada, Anatoly A. Soshilov, Michael S. Denison, Laura Bonati
Software Mentions: 3
Published: over 10 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

10.3390/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

10.3390/biom10050744

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

10.1093/ve/vev006

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

10.1038/srep38564

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

10.1098/rsob.200237

Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential
Cited by: 55
Author(s): J.G.M. Rack, Valentina Zorzini, Zihan Zhu, M. Schuller, Dragana Ahel, Ivan Ahel
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2020.568052

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

10.3390/molecules26061793

Quantum Chemical Microsolvation by Automated Water Placement
Cited by: 17
Author(s): Miguel Steiner, Tanja Holzknecht, Michael Schauperl, Maren Podewitz
Software Mentions: 3
Published: over 5 years ago

10.1186/1754-6834-7-18

Close relationship of a novel Flavobacteriaceaeα-amylase with archaeal α-amylases and good potentials for industrial applications
Cited by: 28
Author(s): Chunfang Li, Miaofen Du, Bin Cheng, Lushan Wang, Xinqiang Liu, Cuiqing Ma, Chunyu Yang, Ping Xu
Software Mentions: 3
Published: over 12 years ago

10.1186/s13068-017-0944-4

Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity
Cited by: 29
Author(s): Bruno Luan Mello, Anna Alessi, Diego Mauricio Riaño‐Pachón, Eduardo R. deAzevedo, Francisco Eduardo Gontijo Guimarães, Melissa C. Espirito Santo, Simon J. McQueen‐Mason, Neil C. Bruce, Igor Polikarpov
Software Mentions: 3
Published: almost 9 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

10.1074/jbc.M117.806893

Negatively charged residues in the first extracellular loop of the L-type CaV1.2 channel anchor the interaction with the CaVα2δ1 auxiliary subunit
Cited by: 16
Author(s): Benoîte Bourdin, Julie Briot, Marie-Philippe Tétreault, Rémy Sauvé, Lucie Parent
Software Mentions: 3
Published: about 9 years ago

10.1074/jbc.M114.621789

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

10.3389/fchem.2020.597495

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

10.1155/2020/2758640

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

10.3389/fcimb.2021.730288

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

10.1007/s10822-018-0148-4

Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3
Cited by: 19
Author(s): Panagiotis I. Koukos, Xue Li, Alexandre M. J. J. Bonvin
Software Mentions: 3
Published: about 8 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

10.3390/biom11070929

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

10.3390/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

10.1038/s41598-018-29664-4

Structural basis for selective inhibition of immunoglobulin E-receptor interactions by an anti-IgE antibody
Cited by: 20
Author(s): Jiun-Bo Chen, Faruk Ramadani, M.O.Y. Pang, Rebecca L. Beavil, Mary D. Holdom, A.N. Mitropoulou, Andrew J. Beavil, Hannah J. Gould, Tse Wen Chang, Brian J. Sutton, James M. McDonnell, Anna M. Davies
Software Mentions: 3
Published: about 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

10.1038/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

10.3390/biom10040509

The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II
Cited by: 7
Author(s): Steffen Glöckner, K. Ngo, Björn Wagner, A. Heine, G. Klebe
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pbio.1001669

An RNA-Binding Complex Involved in Ribosome Biogenesis Contains a Protein with Homology to tRNA CCA-Adding Enzyme
Cited by: 32
Author(s): Jinzhong Lin, Jing Lü, Yingang Feng, Mengyi Sun, Keqiong Ye
Software Mentions: 3
Published: about 13 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

10.1371/journal.pbio.3001057

The dominantly expressed class II molecule from a resistant MHC haplotype presents only a few Marek’s disease virus peptides by using an unprecedented binding motif
Cited by: 11
Author(s): Samer Halabi, Michael Ghosh, Stefan Stevanović, Hans‐Georg Rammensee, Luca D. Bertzbach, Benedikt B. Kaufer, Martin C. Moncrieffe, Bernd Kaspers, Sonja Härtle, Jim Kaufman
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0004978

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

10.1371/journal.pntd.0007868

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

10.7554/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

10.1371/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.pone.0078059

Perturbation Centrality and Turbine: A Novel Centrality Measure Obtained Using a Versatile Network Dynamics Tool
Cited by: 25
Author(s): Kristóf Z. Szalay, Péter Csermely
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0172743

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

10.3390/md18070349

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