10.1074/jbc.M113.534628

Crystal Structures of Leukotriene C4 Synthase in Complex with Product Analogs
Cited by: 22
Author(s): Damian Niegowski, Thea K. Kleinschmidt, Ulrika Olsson, Shabbir Ahmad, Agnes Rinaldo-Matthis, Jesper Z. Haeggström
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.ppat.1007979

The TIR-domain containing effectors BtpA and BtpB from Brucella abortus impact NAD metabolism
Cited by: 39
Author(s): Julia María Coronas-Serna, Arthur Louche, María Rodríguez-Escudero, Morgane Roussin, Paul R. C. Imbert, Isabel Rodríguez-Escudero, Laurent Terradot, Marı́a Molina, Jean‐Pierre Gorvel, Víctor J. Cid, Suzana P. Salcedo
Software Mentions: 2
Published: over 5 years ago

10.1128/mBio.02531-20

Structural Basis for a Neutralizing Antibody Response Elicited by a Recombinant Hantaan Virus Gn Immunogen
Cited by: 10
Author(s): Ilona Rissanen, Stefanie A. Krumm, Robert Stass, Annalis Whitaker, James E. Voss, Emily A. Bruce, Sylvia Rothenberger, Stefan Kunz, Dennis R. Burton, J.T. Huiskonen, Jason Botten, Thomas A. Bowden, Katie J. Doores
Software Mentions: 2
Published: about 4 years ago

10.1155/2020/2396569

Systematically Exploring the Antitumor Mechanisms of Core Chinese Herbs on Hepatocellular Carcinoma: A Computational Study
Cited by: 4
Author(s): Zhulin Wu, Li He, Lianan Wang, Lisheng Peng
Software Mentions: 2
Published: about 5 years ago

10.1155/2020/4863015

Uncovering the Mechanism of the Effects of <i>Pien-Tze-Huang</i> on Liver Cancer Using Network Pharmacology and Molecular Docking
Cited by: 5
Author(s): Shanghui Liu, Run Wang, Yan Lou, Jia Liu
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.ppat.1008652

A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization
Cited by: 38
Author(s): Andrea Sánchez‐Vallet, Hui Tian, Luis Rodríguez‐Moreno, D.J. Valkenburg, Raspudin Saleem-Batcha, Stephan Wawra, Anja Kombrink, Leonie Verhage, Ronnie de Jonge, H. Peter van Esse, Alga Zuccaro, Daniel Croll, J.R. Mesters, B.P.H.J. Thomma
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1008650

A Toxoplasma gondii patatin-like phospholipase contributes to host cell invasion
Cited by: 10
Author(s): Sarah K. Wilson, Justine Heckendorn, Bruno Martorelli Di Genova, Lindsey L. Koch, Peggy J. Rooney, Naomi S. Morrissette, Maryse Lebrun, Laura J. Knoll
Software Mentions: 2
Published: over 5 years ago

10.1007/s00018-019-03150-0

The PCNA interaction motifs revisited: thinking outside the PIP-box
Cited by: 69
Author(s): Andreas Prestel, Nanna Wichmann, João M. Martins, Riccardo Marabini, Noah Kassem, Sebastian S. Broendum, Marit Otterlei, Olaf Nielsen, Martin Willemoës, Michael Ploug, Wouter Boomsma
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1008794

Evolution-guided mutagenesis of the cytoplasmic incompatibility proteins: Identifying CifA’s complex functional repertoire and new essential regions in CifB
Cited by: 21
Author(s): J. Dylan Shropshire, Mahip Kalra, Seth R. Bordenstein
Software Mentions: 2
Published: about 5 years ago

10.1128/mSphere.00792-19

A Multifunctional Polysaccharide Utilization Gene Cluster in <i>Colwellia echini</i> Encodes Enzymes for the Complete Degradation of κ-Carrageenan, ι-Carrageenan, and Hybrid β/κ-Carrageenan
Cited by: 17
Author(s): Line Christiansen, Duleepa Pathiraja, Pernille Kjersgaard Bech, Mikkel Schultz‐Johansen, Rosanna C. Hennessy, David Tezé, In Geol Choi, Peter Stougaard
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0019510

Insight into the Interaction of Metal Ions with TroA from Streptococcus suis
Cited by: 52
Author(s): Beiwen Zheng, Qiangmin Zhang, Jia Gao, Haitao Han, Ming Li, Jing-Ren Zhang, Jianxun Qi, Jinghua Yan, George F. Gao
Software Mentions: 2
Published: over 14 years ago

10.1128/mSphere.00244-20

Tetanus Toxin <i>cis</i> -Loop Contributes to Light-Chain Translocation
Cited by: 9
Author(s): Madison Zuverink, Matthew S. Bluma, Joseph T. Barbieri
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1008871

Evidence that immunization with TP0751, a bipartite Treponema pallidum lipoprotein with an intrinsically disordered region and lipocalin fold, fails to protect in the rabbit model of experimental syphilis
Cited by: 15
Author(s): Amit Luthra, Jairo M. Montezuma-Rusca, Carson J. La Vake, Morgan LeDoyt, Kristina N. Delgado, Timothy C. Davenport, Mary Fiel-Gan, Melissa J. Caimano, Justin D. Radolf, Kelly L. Hawley
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0151412

Monitoring Solution Structures of Peroxisome Proliferator-Activated Receptor β/δ upon Ligand Binding
Cited by: 13
Author(s): Rico Schwarz, Dirk Tänzler, Christian Ihling, Andrea Sinz
Software Mentions: 2
Published: over 9 years ago

10.1007/s00018-019-03211-4

Discovering the chloride pathway in the CFTR channel
Cited by: 14
Author(s): Bianka Farkas, Hedvig Tordai, Rita Padányi, Attila Tordai, János Gera, Gábor Paragi, Tamás Hegedüs
Software Mentions: 2
Published: over 6 years ago

10.1128/mSphere.00108-21

Cryptic β-Lactamase Evolution Is Driven by Low β-Lactam Concentrations
Cited by: 16
Author(s): Christopher Fröhlich, João Alves Gama, Klaus Harms, Viivi H. A. Hirvonen, Bjarte Aarmo Lund, Marc W. van der Kamp, Pål Jarle Johnsen, Ørjan Samuelsen, Hanna‐Kirsti S. Leiros
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0252786

DNAH11 compound heterozygous variants cause heterotaxy and congenital heart disease
Cited by: 5
Author(s): Xia Hong, Xiangjun Huang, Sheng Deng, Hongbo Xu, Yan Yang, Xin Liu, Lamei Yuan, Hao Deng
Software Mentions: 2
Published: over 4 years ago

10.1155/2013/487158

Metabonomics Combined with UPLC-MS Chemical Profile for Discovery of Antidepressant Ingredients of a Traditional Chinese Medicines Formula, Chaihu-Shu-Gan-San
Cited by: 10
Author(s): Hongmei Jia, Zhiheng Su, Wei Long, Yuetao Liu, Xing Chang, Hongwu Zhang, Gang Ding, Yun Feng, Duan Cai, Zhong‐Mei Zou
Software Mentions: 2
Published: almost 13 years ago

10.1128/mSystems.00650-19

Horizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen <i>Pectobacterium brasiliense</i>
Cited by: 10
Author(s): Daniel Bellieny-Rabelo, Ntombikayise Precious Nkomo, Divine Yufetar Shyntum, Lucy N. Moleleki
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0061327

Prospecting for Novel Plant-Derived Molecules of Rauvolfia serpentina as Inhibitors of Aldose Reductase, a Potent Drug Target for Diabetes and Its Complications
Cited by: 46
Author(s): Shivalika Pathania, Vinay Randhawa, Ganesh Bagler
Software Mentions: 2
Published: over 12 years ago

10.1128/mSystems.00232-20

Integrating CRISPR-Enabled Trackable Genome Engineering and Transcriptomic Analysis of Global Regulators for Antibiotic Resistance Selection and Identification in Escherichia coli
Cited by: 8
Author(s): Cong Chen, Alaksh Choudhury, Shuanghong Zhang, Andrew D. Garst, Xin Song, Xunli Liu, Tao Chen, Ryan T. Gill, Zhiwen Wang
Software Mentions: 2
Published: over 5 years ago

10.1186/1743-422X-10-269

Chikungunya virus capsid protein contains nuclear import and export signals
Cited by: 37
Author(s): Saijo Thomas, Jagdish Rai, Lijo John, Stephan Schaefer, Brigitte M. Pützer, Ottmar Herchenröder
Software Mentions: 2
Published: about 12 years ago

10.1128/mSystems.00053-21

Genomic Determinants Encode the Reactivity and Regioselectivity of Flavin-Dependent Halogenases in Bacterial Genomes and Metagenomes
Cited by: 3
Author(s): Jehyun Jeon, Jaehee Lee, Se Min Jung, Jae Hong Shin, Woon Ju Song, Mina Rho
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0020864

Identification of the Allosteric Regulatory Site of Insulysin
Cited by: 36
Author(s): Nicholas Noinaj, Sonia K. Bhasin, Eun Suk Song, Kirsten E. Scoggin, María A. Juliano, Luiz Juliano, Louis B. Hersh, David W. Rodgers
Software Mentions: 2
Published: over 14 years ago

10.3390/v11060504

Transcriptional Control and mRNA Capping by the GDP Polyribonucleotidyltransferase Domain of the Rabies Virus Large Protein
Cited by: 15
Author(s): Tomoaki Ogino, Todd Green
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1009393

ADAM17 is an essential attachment factor for classical swine fever virus
Cited by: 10
Author(s): Fei Yuan, Dandan Li, Changyao Li, Yanan Zhang, Hao Song, Suhua Li, Hongkui Deng, George F. Gao, Ai Zheng
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0160165

Insight on Mutation-Induced Resistance from Molecular Dynamics Simulations of the Native and Mutated CSF-1R and KIT
Cited by: 8
Author(s): Priscila da Silva Figueiredo Celestino Gomes, Isaure Chauvot de Beauchêne, Nicolas Panel, Sophie Lopez, Paulo De Sepulveda, Pedro Geraldo Pascutti, Éric Solary, Luba Tchertanov
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0030305

Virtual Screening, Identification and In Vitro Testing of Novel Inhibitors of O-Acetyl-L-Serine Sulfhydrylase of Entamoeba histolytica
Cited by: 62
Author(s): Isha Nagpal, Isha Raj, Naidu Subbarao, S. Gourinath
Software Mentions: 2
Published: over 13 years ago

10.3390/toxins11110625

The Sequence and a Three-Dimensional Structural Analysis Reveal Substrate Specificity among Snake Venom Phosphodiesterases
Cited by: 14
Author(s): Atta Ullah, Kifayat Ullah, Hamid Ali, Christian Betzel, Shafiq Ur Rehman
Software Mentions: 2
Published: about 6 years ago

10.1242/jcs.226852

Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing
Cited by: 36
Author(s): Tiina Viita, Salla Kyheröinen, Bina Prajapati, Jori Virtanen, Mikko J. Frilander, Markku Varjosalo, Maria K. Vartiainen
Software Mentions: 2
Published: almost 7 years ago

10.1242/jcs.258399

Maintenance of complex I and its supercomplexes by NDUF-11 is essential for mitochondrial structure, function and health
Cited by: 13
Author(s): Amber Knapp-Wilson, Gonçalo C. Pereira, Emma Buzzard, Holly C Ford, A. Richardson, Robin A. Corey, Chris Neal, Paul Verkade, Andrew P. Halestrap, Vicki A. M. Gold, Patricia E. Kuwabara, Ian Collinson
Software Mentions: 2
Published: over 4 years ago

10.1093/braincomms/fcab063

Dominant <i>ACO2</i> mutations are a frequent cause of isolated optic atrophy
Cited by: 12
Author(s): Majida Charif, Naïg Guéguen, Marc Ferré, Zouhair Elkarhat, Salim Khiati, Morgane LeMao, Arnaud Chevrollier, Valérie Desquiret-Dumas, David Goudenège, Céline Bris, Selma Kane, Jennifer Alban, Stéphanie Chupin, Céline Wetterwald, Leonardo Caporali, Fabrizio Tagliavini, Chiara LaMorgia, Michele Carbonelli, Neringa Jurkutė, Abdelhamid Barakat, Philippe Gohier, Christophe Verny, Magalie Barth, Vincent Procaccio, Dominique Bonneau, Xavier Zanlonghi, Isabelle Meunier, Nicole Weisschuh, Simone Schimpf-Linzenbold, Felix Tonagel, Ulrich Kellner, Patrick Yu‐Wai‐Man, Valerio Carelli, Bernd Wissinger, Patrizia Amati‐Bonneau, Pascal Reynier, Guy Lenaers
Software Mentions: 2
Published: over 4 years ago

10.1021/acs.jctc.0c01281

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties
Cited by: 29
Author(s): Kara K. Grotz, Sergio Cruz-León, Nadine Schwierz
Software Mentions: 2
Published: over 4 years ago

10.3390/toxins13050319

Mechanistic Insight into the Peptide Binding Modes to Two M. tb MazF Toxins
Cited by: 2
Author(s): Ran Chen, Jie Zhou, Wei Xie
Software Mentions: 2
Published: over 4 years ago

10.1186/1758-2946-4-17

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
Cited by: 5,518
Author(s): Marcus D. Hanwell, Donald Curtis, David Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey Hutchison
Software Mentions: 2
Published: over 13 years ago

10.1111/tra.12283

Recruitment of <scp>VPS33A</scp> to <scp>HOPS</scp> by <scp>VPS16</scp> Is Required for Lysosome Fusion with Endosomes and Autophagosomes
Cited by: 111
Author(s): Lena Wartosch, Ufuk Günesdogan, Stephen C. Graham, J. Paul Luzio
Software Mentions: 2
Published: over 10 years ago

10.1111/tra.12457

Cellular and viral peptides bind multiple sites on the N-terminal domain of clathrin
Cited by: 29
Author(s): Julia Muenzner, Linton M. Traub, Bernard T. Kelly, Stephen C. Graham
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41398-018-0168-9

Carbamoylated erythropoietin modulates cognitive outcomes of social defeat and differentially regulates gene expression in the dorsal and ventral hippocampus
Cited by: 18
Author(s): Monica Sathyanesan, Michael J. Watt, Jacob M Haiar, Jamie L. Scholl, Shaydel R. Davies, Riley T. Paulsen, Jayme Wiederin, Paweł Ciborowski, Samuel S. Newton
Software Mentions: 2
Published: over 7 years ago

10.3390/molecules26040837

Exploring the Distinct Binding and Activation Mechanisms for Different CagA Oncoproteins and SHP2 by Molecular Dynamics Simulations
Cited by: 3
Author(s): Quan Wang, Wencheng Zhao, Xueqi Fu, Qing‐Chuan Zheng
Software Mentions: 2
Published: almost 5 years ago

10.3389/fnmol.2014.00051

In silico, in vitro and cellular analysis with a kinome-wide inhibitor panel correlates cellular LRRK2 dephosphorylation to inhibitor activity on LRRK2
Cited by: 46
Author(s): Renée Vancraenenbroeck, Joren De Raeymaecker, Evy Lobbestael, Fangye Gao, Marc De Maeyer, Arnout Voet, Veerle Baekelandt, Jean-Marc Taymans
Software Mentions: 2
Published: over 11 years ago

10.1101/2020.03.22.002386

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
Cited by: 210
Author(s): David E. Gordon, Gwendolyn Μ. Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Jeffrey Z. Guo, Danielle L. Swaney, Tia A. Tummino, Ruth Hüttenhain, Robyn M. Kaake, Alicia Richards, Beril Tutuncuoglu, Helene Foussard, Jyoti Batra, Kelsey M. Haas, Maya Modak, Minkyu Kim, Paige Haas, Benjamin J. Polacco, Hannes Braberg, Jacqueline M. Fabius, Manon Eckhardt, Margaret Soucheray, M. J. Bennett, Merve Çakır, Michael McGregor, Qiongyu Li, Zun Zar Chi Naing, Yuan Zhou, Shiming Peng, Ilsa T Kirby, James E. Melnyk, John S. Chorba, Kevin Lou, Shizhong Dai, Wenqi Shen, Ying Shi, Ziyang Zhang, Iñigo Barrio-Hernandez, Danish Memon, Claudia Hernández-Armenta, Christopher J.P. Mathy, Tina Perica, Kala Bharath Pilla, Sai J. Ganesan, Daniel J. Saltzberg, Rakesh Ramachandran, Xi Liu, Sara Brin Rosenthal, Lorenzo Calviello, Srivats Venkataramanan, José Liboy-Lugo, Yizhu Lin, Stephanie A. Wankowicz, Markus-Frederik Bohn, Phillip P. Sharp, Raphael Trenker, Janet M. Young, Devin A. Cavero, Joseph Hiatt, Theo Roth, Ujjwal Rathore, Advait Subramanian, Julia Noack, Mathieu Hubert, Ferdinand Roesch, Thomas Vallet, Björn Meyer, Kris M. White, Lisa Miorin, Oren S. Rosenberg, Kliment A. Verba, David A. Agard, Mélanie Ott, Michael Emerman, Davide Ruggero, Adolfo Garc iacute-Sastre, Natalia Jura, Mark von Zastrow, Jack Taunton, Alan Ashworth, Olivier Schwartz, Marco Vignuzzi, Shaeri Mukherjee, Matthew P. Jacobson, Harmit S. Malik, Danica Galonić Fujimori, Trey Ideker, Charles S. Craik, Stephen N. Floor, James S. Fraser, John D. Gross, Andrej Šali, Tanja Kortemme, Pedro Beltrão, Kevan M. Shokat, Brian K. Shoichet, Nevan J. Krogan
Software Mentions: 2
Published: over 5 years ago

10.1186/s13321-019-0390-3

Identifying new topoisomerase II poison scaffolds by combining publicly available toxicity data and 2D/3D-based virtual screening
Cited by: 5
Author(s): Anna Lovrics, Veronika F.S. Pape, Dániel Szisz, Adrián Kalászi, Petra Heffeter, Csaba Magyar, Gergely Szakács
Software Mentions: 2
Published: about 6 years ago

10.1186/s13321-020-00460-5

Molecular representations in AI-driven drug discovery: a review and practical guide
Cited by: 176
Author(s): Laurianne David, Amol Thakkar, Rocío Mercado, Ola Engkvist
Software Mentions: 2
Published: about 5 years ago

10.1101/2021.04.23.441209

Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants that merit monitoring
Cited by: 5
Author(s): Sofiya K Garushyants, Igor B. Rogozin, Eugene V. Koonin
Software Mentions: 2
Published: over 4 years ago

10.3389/fnmol.2018.00113

The LILI Motif of M3-S2 Linkers Is a Component of the NMDA Receptor Channel Gate
Cited by: 24
Author(s): Marek Ladislav, Jiří Černý, Jan Krůšek, Martin Hořák, Aleš Balík, Ladislav Vyklicky
Software Mentions: 2
Published: over 7 years ago

10.3389/fnmol.2018.00330

Molecular Details of Retinal Guanylyl Cyclase 1/GCAP-2 Interaction
Cited by: 9
Author(s): Anne Rehkamp, Dirk Tänzler, Claudio Iacobucci, Ralph Golbik, Christian Ihling, Andrea Sinz
Software Mentions: 2
Published: about 7 years ago

10.1172/JCI142823

An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection
Cited by: 16
Author(s): Cory A. Brennick, Mariam M. George, Marmar Moussa, Adam T. Hagymasi, Sahar Al Seesi, Tatiana Shcheglova, Ryan P Englander, Grant L.J. Keller, Jeremy L. Balsbaugh, Brian M. Baker, Andrea Schietinger, Ion Măndoiu, Pramod K. Srivastava
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.1006959

Ten quick tips for using a Raspberry Pi
Cited by: 10
Author(s): Anthony C. Fletcher, Cameron Mura
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1004620

NMR Methods to Study Dynamic Allostery
Cited by: 58
Author(s): Sarina Grutsch, Sven Brüschweiler, Martin Tollinger
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0172217

Rational design of DKK3 structure-based small peptides as antagonists of Wnt signaling pathway and in silico evaluation of their efficiency
Cited by: 16
Author(s): Mansour Poorebrahim, Sedigheh Sadeghi, Hamzeh Rahimi, Morteza Karimipoor, Kayhan Azadmanesh, Mohammad Ali Mazlomi, Ladan Teimoori‐Toolabi
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0100263

Insight into PreImplantation Factor (PIF*) Mechanism for Embryo Protection and Development: Target Oxidative Stress and Protein Misfolding (PDI and HSP) through Essential RIPK Binding Site
Cited by: 30
Author(s): Eytan R. Barnea, David M. Lubman, Yan Hui Liu, V. Absalon-Medina, Soren Hayrabedyan, Krassimira Todorova, R.O. Gilbert, Joy Guingab, Timothy J. Barder
Software Mentions: 2
Published: over 11 years ago

10.1128/mBio.00254-17

A Polymerization-Associated Structural Switch in FtsZ That Enables Treadmilling of Model Filaments
Cited by: 81
Author(s): Jane L. Wagstaff, M. Tsim, M.A. Oliva, Alba García-Sanchez, Danguole Kureisaite-Ciziene, José Manuel Andreu, Jan Löwe
Software Mentions: 2
Published: over 8 years ago

10.1007/s10822-020-00277-2

Conformational analysis of macrocycles: comparing general and specialized methods
Cited by: 16
Author(s): Gustav Olanders, Hiba Alogheli, Peter Brandt, Anders Karlén
Software Mentions: 2
Published: almost 6 years ago

10.1007/s10822-020-00301-5

A Taxicab geometry quantification system to evaluate the performance of in silico methods: a case study on adenosine receptors ligands
Cited by: 0
Author(s): Kamil Kuder, Ilona Michalik, Katarzyna Kieć‐Kononowicz, Peter Kolb
Software Mentions: 2
Published: over 5 years ago

10.1128/mBio.01564-17

An <i>Alphavirus</i> E2 Membrane-Proximal Domain Promotes Envelope Protein Lateral Interactions and Virus Budding
Cited by: 20
Author(s): Emily A. Byrd, Margaret Kielian
Software Mentions: 2
Published: almost 8 years ago

10.1007/s10822-015-9839-2

Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding
Cited by: 8
Author(s): Barbara Kalinowska, Piotr Fabian, Katarzyna Stąpor, Irena Roterman
Software Mentions: 2
Published: over 10 years ago

10.1128/mBio.02146-17

A Phosphorylation Switch on Lon Protease Regulates Bacterial Type III Secretion System in Host
Cited by: 23
Author(s): Xiaofeng Zhou, Doron Teper, Maxuel O. Andrade, Tong Zhang, Sixue Chen, Wenlei Song, Nian Wang
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1000306

Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis
Cited by: 66
Author(s): Wolfram Stacklies, M. Cristina Vega, Matthias Wilmanns, Frauke Gräter
Software Mentions: 2
Published: over 16 years ago

10.1002/jcc.26559

<scp> <i>MonteCarbo</i> </scp> : A software to generate and dock multifunctionalized ring molecules
Cited by: 0
Author(s): Santiago Alonso-Gil
Software Mentions: 2
Published: over 4 years ago

10.1186/1754-6834-7-2

Ligninolytic peroxidase genes in the oyster mushroom genome: heterologous expression, molecular structure, catalytic and stability properties, and lignin-degrading ability
Cited by: 99
Author(s): Elena Fernández‐Fueyo, Francisco J. Ruíz-Dueñas, Marı́a Jesús Martı́nez, Antonio Romero, Kenneth E. Hammel, Francisco J. Medrano, Ángel T. Martı́nez
Software Mentions: 2
Published: almost 12 years ago

10.3390/molecules23071688

Theoretical Model of EphA2-Ephrin A1 Inhibition
Cited by: 4
Author(s): Wiktoria Jedwabny, Alessio Lodola, Edyta Dyguda-Kazimierowicz
Software Mentions: 2
Published: over 7 years ago

10.1128/mBio.01137-19

Identification of Extracellular DNA-Binding Proteins in the Biofilm Matrix
Cited by: 89
Author(s): J.S. Kavanaugh, Caralyn E. Flack, Jessica Lister, Erica B. Ricker, Carolyn B. Ibberson, Christian Jenul, Derek E. Moormeier, Elizabeth Delmain, Kenneth W. Bayles, Alexander R. Horswill
Software Mentions: 2
Published: over 6 years ago

10.1210/js.2019-00260

Using Structural Analysis In Silico to Assess the Impact of Missense Variants in MEN1
Cited by: 14
Author(s): Richard Caswell, Martina Owens, Adam C. Gunning, Sian Ellard, Caroline F. Wright
Software Mentions: 2
Published: about 6 years ago

10.1128/mBio.02660-18

Targeting Mannitol Metabolism as an Alternative Antimicrobial Strategy Based on the Structure-Function Study of Mannitol-1-Phosphate Dehydrogenase in Staphylococcus aureus
Cited by: 16
Author(s): Thanh H. Nguyen, Truc Kim, Hai Minh Ta, Won Sik Yeo, Joon‐Hwan Choi, Pushpak Mizar, Seung Seo Lee, Taeok Bae, Akhilesh Kumar Chaurasia, Kyeong Kyu Kim
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0145142

How Intrinsic Molecular Dynamics Control Intramolecular Communication in Signal Transducers and Activators of Transcription Factor STAT5
Cited by: 7
Author(s): Florent Langenfeld, Yann Guarracino, Michel Arock, Alain Trouvé, Luba Tchertanov
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0021267

Expression of Enzymatically Inactive Wasp Venom Phospholipase A1 in Pichia pastoris
Cited by: 13
Author(s): Irina Borodina, Bettina M. Jensen, Tim Wagner, Maher Abou Hachem, Ib Søndergaard, Lars K. Poulsen
Software Mentions: 2
Published: over 14 years ago

10.1128/mBio.02272-19

Mycobacterial OtsA Structures Unveil Substrate Preference Mechanism and Allosteric Regulation by 2-Oxoglutarate and 2-Phosphoglycerate
Cited by: 5
Author(s): V. Mendes, Marta Acebrón-García-de-Eulate, Nandini Verma, M. Błaszczyk, M.V.B. Dias, Tom L. Blundell
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0071835

Functional Mapping of Human Dynamin-1-Like GTPase Domain Based on X-ray Structure Analyses
Cited by: 60
Author(s): Julia Wenger, Eva Klinglmayr, Chris Fröhlich, Clarissa Eibl, Ana Gimeno, Manuel Hessenberger, Sandra Puehringer, Oliver Daumke, Peter Goettig
Software Mentions: 2
Published: about 12 years ago

10.1111/j.1365-2958.2006.05332.x

Structure and reactivity of <i>Trypanosoma brucei</i> pteridine reductase: inhibition by the archetypal antifolate methotrexate
Cited by: 57
Author(s): Alice Dawson, Federica Gibellini, Natasha Sienkiewicz, L.B. Tulloch, Paul K. Fyfe, Karen McLuskey, Alan H. Fairlamb, William N. Hunter
Software Mentions: 2
Published: over 19 years ago

10.1371/journal.pone.0179155

Molecular and functional characterization of two isoforms of chalcone synthase and their expression analysis in relation to flavonoid constituents in Grewia asiatica L
Cited by: 24
Author(s): Tareq A. Wani, Shahzad A. Pandith, Ajai Prakash Gupta, Suresh Chandra, Namrata Sharma, Surrinder K. Lattoo
Software Mentions: 2
Published: over 8 years ago

10.1080/14756366.2017.1370584

Characterization of human S-adenosyl-homocysteine hydrolase <i>in vitro</i> and identification of its potential inhibitors
Cited by: 2
Author(s): Weiwei Hao, Yanhua Li, Qiuli Shan, Ting Han, Wencheng Li, Sheng He, Kongkai Zhu, Yumei Li, Xiaojun Tan, Jinsong Gu
Software Mentions: 2
Published: almost 9 years ago

10.1128/mBio.00172-20

Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors
Cited by: 14
Author(s): Ashley N. Matthew, J. Zephyr, Desaboini Nageswara Rao, M. Henes, Wasih Kamran, K. Kosovrasti, Adam K. Hedger, G.J. Lockbaum, Jennifer Timm, Akbar Ali, Neşe Kurt Yilmaz, Celia A. Schiffer
Software Mentions: 2
Published: over 5 years ago

10.1111/j.1365-2958.2007.05785.x

An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS
Cited by: 32
Author(s): James S. Fraser, John P. Merlie, Nathaniel Echols, Shellie R. Weisfield, Tâm Mignot, David E. Wemmer, David R. Zusman, Tom Alber
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pone.0092249

Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6
Cited by: 20
Author(s): Keisuke Sugimoto, Masuo Senda, Daisuke Kasai, Masao Fukuda, Eiji Masai, Toshiya Senda
Software Mentions: 2
Published: over 11 years ago

10.1016/j.jmb.2013.03.019

Structure of the Tubulin/FtsZ-Like Protein TubZ from Pseudomonas Bacteriophage ΦKZ
Cited by: 30
Author(s): C.H.S. Aylett, Thierry Izoré, Linda Amos, Jan Löwe
Software Mentions: 2
Published: over 12 years ago

10.1016/j.jmb.2013.09.016

Plug-and-Play Pairing via Defined Divalent Streptavidins
Cited by: 86
Author(s): M. Fairhead, Denis Krndija, E.D. Lowe, Mark Howarth
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0020950

Conformational Changes of rBTI from Buckwheat upon Binding to Trypsin: Implications for the Role of the P8′ Residue in the Potato Inhibitor I Family
Cited by: 13
Author(s): Long Wang, Fei Zhao, Mei Li, Hongmei Zhang, Yu Gao, Peng Cao, Xiaowei Pan, Zhuanhua Wang, Wenrui Chang
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pcbi.1007749

Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel
Cited by: 4
Author(s): Luca Ponzoni, Nga H. Nguyen, İvet Bahar, Jeffrey L. Brodsky
Software Mentions: 2
Published: over 5 years ago

10.1016/j.jmb.2011.11.007

Structure and Kinetic Stability of the p63 Tetramerization Domain
Cited by: 26
Author(s): Eviatar Natan, A.C. Joerger
Software Mentions: 2
Published: almost 14 years ago

10.1016/j.jmb.2013.10.024

Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY
Cited by: 63
Author(s): Lukas S. Stelzl, Philip W. Fowler, Mark S. P. Sansom, Oliver Beckstein
Software Mentions: 2
Published: almost 12 years ago

10.1016/j.jmb.2013.05.024

Characterization of 14-3-3-ζ Interactions with Integrin Tails
Cited by: 29
Author(s): Roman Bonet, Ioannis Vakonakis, Iain D. Campbell
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pcbi.1002170

Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity
Cited by: 58
Author(s): Nir London, Corissa L. Lamphear, James L. Hougland, Carol A. Fierke, Ora Schueler‐Furman
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pcbi.1004130

Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts
Cited by: 62
Author(s): Juan Manuel Palacios‐Moreno, Lauren Foltz, Ailan Guo, Matthew P. Stokes, Emily D. Kuehn, Lynn George, Michael J. Comb, Mark L. Grimes
Software Mentions: 2
Published: over 10 years ago

10.1016/j.jmb.2015.07.014

Structures of the Ultra-High-Affinity Protein–Protein Complexes of Pyocins S2 and AP41 and Their Cognate Immunity Proteins from Pseudomonas aeruginosa
Cited by: 25
Author(s): Amar Joshi, Rhys Grinter, Inokentijs Josts, Sabrina Chen, Justyna Aleksandra Wojdyla, E.D. Lowe, Renata Kaminska, Connor Sharp, Laura C. McCaughey, A.W. Roszak, Richard J. Cogdell, Olwyn Byron, Daniel Walker, Colin Kleanthous
Software Mentions: 2
Published: over 10 years ago

10.3389/fonc.2021.606820

Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level
Cited by: 3
Author(s): Michael T. Zimmermann, Angela Mathison, Tim Stodola, Douglas B. Evans, Jenica Abrudan, Wendy Demos, Michael Tschannen, Mohammed Aldakkak, Jennifer L. Geurts, Gwen Lomberk, Susan Tsai, Raúl Urrutia
Software Mentions: 2
Published: over 4 years ago

10.1186/s13068-017-1006-7

Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum
Cited by: 23
Author(s): Anna S. Borisova, Elena V. Eneyskaya, Suvamay Jana, Silke Flindt Badino, Jeppe Kari, Antonella Amore, Magnus Karlsson, Henrik Hansson, Mats Sandgren, Michael E. Himmel, Peter Westh, Christina M. Payne, Anna A. Kulminskaya, Jerry Ståhlberg
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pcbi.1002326

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding
Cited by: 59
Author(s): Tianyun Liu, Russ B. Altman
Software Mentions: 2
Published: almost 14 years ago

10.1080/14756366.2020.1837123

Crystal structure-guided design of berberine-based novel chitinase inhibitors
Cited by: 13
Author(s): Lei Chen, Ling Zhu, Jinli Chen, Wei Chen, Xuhong Qian, Qing Yang
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.jmb.2010.01.035

Structural Basis of Substrate Binding in WsaF, a Rhamnosyltransferase from Geobacillus stearothermophilus
Cited by: 22
Author(s): Kerstin Steiner, Gregor Hagelueken, Paul Messner, Christina Schäffer, James H. Naismith
Software Mentions: 2
Published: over 15 years ago

10.3390/biom11081083

The Right-Handed Parallel β-Helix Topology of Erwinia chrysanthemi Pectin Methylesterase Is Intimately Associated with Both Sequential Folding and Resistance to High Pressure
Cited by: 3
Author(s): Jessica Guillerm, Jean‐Marie Frère, Filip Meersman, André Matagne
Software Mentions: 2
Published: over 4 years ago

10.3389/fonc.2019.01294

p38α Mitogen-Activated Protein Kinase Is a Druggable Target in Pancreatic Adenocarcinoma
Cited by: 19
Author(s): Ling Yang, Xiaoting Sun, Ying Ye, Yongtian Lu, Jiane Zuo, Wen Li, Adrian H. Elcock, Shun Zhu
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1002404

Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex
Cited by: 54
Author(s): Cyril Reboul, Grischa R. Meyer, Benjamin T. Porebski, Natalie A. Borg, Ashley M. Buckle
Software Mentions: 2
Published: over 13 years ago

10.1016/j.jmb.2009.10.010

The Central Portion of Factor H (Modules 10–15) Is Compact and Contains a Structurally Deviant CCP Module
Cited by: 50
Author(s): Christoph Q. Schmidt, Andrew P. Herbert, Haydyn D. T. Mertens, Mara Guariento, Dinesh C. Soares, Dušan Uhrı́n, Arthur J. Rowe, Dmitri I. Svergun, Paul N. Barlow
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0254929

Norcycloartocarpin targets Akt and suppresses Akt-dependent survival and epithelial-mesenchymal transition in lung cancer cells
Cited by: 4
Author(s): Nongyao Nonpanya, Kittipong Sanookpan, Keerati Joyjamras, Duangdao Wichadakul, Boonchoo Sritularak, Chatchai Chaotham, Pithi Chanvorachote
Software Mentions: 2
Published: over 4 years ago

10.3389/fped.2019.00343

Biallelic Missense Mutation in the ECEL1 Underlies Distal Arthrogryposis Type 5 (DA5D)
Cited by: 14
Author(s): Muhammad Umair, Amjad Khan, Amir Hayat, Safdar Abbas, Abdulaziz Asiri, Muhammad Younus, Wajid Amin, Shoaib Nawaz, Shazia Khan, Erum Malik, Majid Alfadhel, Farooq Ahmad
Software Mentions: 2
Published: about 6 years ago

10.1016/j.jmb.2011.03.047

Interaction of the p53 DNA-Binding Domain with Its N-Terminal Extension Modulates the Stability of the p53 Tetramer
Cited by: 79
Author(s): Eviatar Natan, Çetin Baloğlu, Kevin Pagel, Stefan Freund, Nina Morgner, Carol V. Robinson, Alan R. Fersht, A.C. Joerger
Software Mentions: 2
Published: over 14 years ago

10.1016/j.jmb.2009.07.026

Crystal Structures of Wzb of Escherichia coli and CpsB of Streptococcus pneumoniae, Representatives of Two Families of Tyrosine Phosphatases that Regulate Capsule Assembly
Cited by: 69
Author(s): Gregor Hagelueken, Hexian Huang, Iain L. Mainprize, Chris Whitfield, James H. Naismith
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0206709

The three dimensional structure of Bovine Salivary Protein 30b (BSP30b) and its interaction with specific rumen bacteria
Cited by: 1
Author(s): Heng Zhang, Judith Burrows, G.L. Card, Graeme T. Attwood, Tom T. Wheeler, Vickery L. Arcus
Software Mentions: 2
Published: over 6 years ago

10.3389/fphar.2020.00526

Kaempferol, a Major Flavonoid in Ginkgo Folium, Potentiates Angiogenic Functions in Cultured Endothelial Cells by Binding to Vascular Endothelial Growth Factor
Cited by: 26
Author(s): Weihui Hu, Huaiyou Wang, Yiteng Xia, Diana Dai, Qingping Xiong, Tina Tingxia Dong, Ran Duan, Gallant Kar-Lun Chan, Qi Qin, Karl Wah-Keung Tsim
Software Mentions: 2
Published: over 5 years ago

10.1016/j.jmb.2010.03.043

Solution Structure and Characterisation of the Human Pyruvate Dehydrogenase Complex Core Assembly
Cited by: 51
Author(s): Swetha Víjayakríshnan, Sharon M. Kelly, Robert J.C. Gilbert, Philip Callow, David Bhella, V. Trevor Forsyth, J. Gordon Lindsay, Olwyn Byron
Software Mentions: 2
Published: over 15 years ago