10.1186/s13072-016-0051-y

Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis
Cited by: 51
Author(s): Takashi Urahama, Akihito Harada, Kazuhira Maehara, Naoki Horikoshi, Koichi Sato, Yuko Sato, Koji Shiraishi, Norihiro Sugino, Akihisa Osakabe, Hiroaki Tachiwana, Wataru Kagawa, Hiroshi Kimurâ, Yasuyuki Ohkawa, Hitoshi Kurumizaka
Software Mentions: 3
Published: over 10 years ago

10.1186/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/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/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: about 7 years ago

10.1038/s41598-020-77600-2

Genetic mapping and candidate gene analysis for melon resistance to Phytophthora capsici
Cited by: 4
Author(s): Pingyong Wang, Xiuhong Xu, Guangwei Zhao, Yue He, C. T. Hou, Weihu Kong, Jian Zhang, Shuimiao Liu, Yong Xu, Zhigao Xu
Software Mentions: 3
Published: over 5 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

10.3390/ijms21124378

Discovery of Isoplumbagin as a Novel NQO1 Substrate and Anti-Cancer Quinone
Cited by: 19
Author(s): Yen-Chi Tsao, Yu‐Jung Chang, Chun-Hsien Wang, Linyi Chen
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.28842

Cyclic di-GMP differentially tunes a bacterial flagellar motor through a novel class of CheY-like regulators
Cited by: 59
Author(s): Jutta Nesper, Isabelle Hug, Setsu Kato, Chee-Seng Hee, Judith Habazettl, Pablo Manfredi, Stephan Grzesiek, Tilman Schirmer, Thierry Emonet, Urs Jenal
Software Mentions: 3
Published: over 8 years ago

10.1107/S205225251700570X

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation
Cited by: 123
Author(s): José M. Martín-García, Chelsie E. Conrad, Garrett Nelson, Natasha Stander, Nadia A. Zatsepin, James Zook, Liya Zhu, James H. Geiger, Eugene Chun, David J. Kissick, Mark Hilgart, Craig M. Ogata, Andrii Ishchenko, Nirupa Nagaratnam, Shatabdi Roy-Chowdhury, Jesse Coe, Ganesh Subramanian, Alexander F. Schäffer, Daniel James, Gihan Ketwala, Nagarajan Venugopalan, Shenglan Xu, Stephen Corcoran, D.R. Ferguson, Uwe Weierstall, John C. H. Spence, Vadim Cherezov, Petra Fromme, Robert F. Fischetti, Wei Liu
Software Mentions: 3
Published: about 9 years ago

10.7554/eLife.58362

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

10.1371/journal.pbio.3001344

Structure of the human C9orf72-SMCR8 complex reveals a multivalent protein interaction architecture
Cited by: 6
Author(s): Julia Nörpel, Simone Cavadini, Andreas Schenk, Alexandra Graff-Meyer, Daniel Heß, Jan Seebacher, Jeffrey A. Chao, Varun Bhaskar
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.60552

Cryo-EM analysis of PIP2 regulation in mammalian GIRK channels
Cited by: 43
Author(s): Yiming Niu, Xiao Tao, Kouki K Touhara, Roderick MacKinnon
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.ppat.1008476

Past and ongoing adaptation of human cytomegalovirus to its host
Cited by: 18
Author(s): Alessandra Mozzi, Matteo Biolatti, Rachele Cagliani, Diego Forni, Valentina Dell’Oste, Chiara Pontremoli, Chiara Vantaggiato, Diego Forni, Mario Clerici, Santo Landolfo, Manuela Sironi
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-25346-3

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

10.1007/s11103-020-01052-5

Structural insights into Arabidopsis ethylene response factor 96 with an extended N-terminal binding to GCC box
Cited by: 12
Author(s): Chun‐Yen Chen, Pei‐Hsuan Lin, Kun-Hung Chen, Yi-Sheng Cheng
Software Mentions: 3
Published: almost 6 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: over 5 years ago

10.1016/j.jmb.2015.10.027

A Substrate Mimic Allows High-Throughput Assay of the FabA Protein and Consequently the Identification of a Novel Inhibitor of Pseudomonas aeruginosa FabA
Cited by: 6
Author(s): L. Moynié, Anthony G. Hope, Kara Finzel, J.W. Schmidberger, Stuart M. Leckie, Günter Schneider, Michael D. Burkart, Andrew D. Smith, David W. Gray, James H. Naismith
Software Mentions: 3
Published: over 10 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: almost 11 years ago

10.3390/ijms20040884

Identification and Evaluation of Inhibitors of Lipase from Malassezia restricta using Virtual High-Throughput Screening and Molecular Dynamics Studies
Cited by: 67
Author(s): Shahid Ali, Faez Iqbal Khan, Taj Mohammad, Dongming Lan, Md. Imtaiyaz Hassan, Yonghua Wang
Software Mentions: 3
Published: over 7 years ago

10.1111/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: about 11 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: almost 15 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: about 7 years ago

10.3390/ijms20225574

Establishing Computational Approaches Towards Identifying Malarial Allosteric Modulators: A Case Study of Plasmodium falciparum Hsp70s
Cited by: 10
Author(s): Arnold Amusengeri, Lindy Astl, Kevin A. Lobb, Gennady M. Verkhivker, Özlem Tastan Bishop
Software Mentions: 3
Published: over 6 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: over 10 years ago

10.1371/journal.pone.0182016

An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins
Cited by: 20
Author(s): Marcin Michalik, Marcella Orwick‐Rydmark, Michael Habeck, Vikram Alva, Thomas C. Arnold, Dirk Linke
Software Mentions: 3
Published: almost 9 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: about 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: almost 11 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

10.1074/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: over 11 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

10.1371/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: almost 13 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.59018

Structural ordering of the Plasmodium berghei circumsporozoite protein repeats by inhibitory antibody 3D11
Cited by: 10
Author(s): Iga Kucharska, Elaine Thai, Ananya Srivastava, John L. Rubinstein, Régis Pomès, Jean-Philippe Julien
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms20225734

A Single Synonymous Variant (c.354G&gt;A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity
Cited by: 23
Author(s): Ryan Hunt, Gaya Hettiarachchi, Upendra Katneni, Nancy Hernandez, David D. Holcomb, Jacob Kames, Redab Alnifaidy, Brian C. Lin, Nobuko Hamasaki-Katagiri, Aaron Wesley, Tal Kafri, Christina Morris, Laura Bouché, Maria Panico, Tal Schiller, Juan C. Ibla, Haim Bar, Amra Ismail, Howard R. Morris, Anton A. Komar
Software Mentions: 3
Published: over 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: over 5 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: over 12 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: about 13 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: about 6 years ago

10.3390/ijms19113340

Physical Background of the Disordered Nature of “Mutual Synergetic Folding” Proteins
Cited by: 6
Author(s): Csaba Magyar, Anikó Mentes, Erzsébet Fichó, Miklós Cserző, István Simon
Software Mentions: 3
Published: over 7 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: about 10 years ago

10.1016/j.bpj.2018.09.002

Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR
Cited by: 3
Author(s): Graham M. Saunders, Hannah E. Bruce Macdonald, Jonathan W. Essex, Syma Khalid
Software Mentions: 3
Published: almost 8 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: almost 9 years ago

10.3390/molecules23112954

Molecular Modeling and In Vitro Studies of a Neutral Oxime as a Potential Reactivator for Acetylcholinesterase Inhibited by Paraoxon
Cited by: 15
Author(s): Reuel L. de Paula, Joyce S. F. D. de Almeida, Samir F. A. Cavalcante, Arlan da Silva Gonçalves, Alessandro B. C. Simas, Tanos C. C. França, Martin Vališ, Kamil Kuča, Eugenie Nepovimová, José Mauro Granjeiro
Software Mentions: 3
Published: over 7 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: over 6 years ago

10.1038/s41598-021-97871-7

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

10.1371/journal.ppat.1009016

Structural insights into loss of function of a pore forming toxin and its role in pneumococcal adaptation to an intracellular lifestyle
Cited by: 10
Author(s): Dilip Badgujar, Anjali Anil, Angharad E Green, Manalee Vishnu Surve, Shilpa Madhavan, Alison J. Beckett, Ian A. Prior, Barsa Kanchan Jyotshna Godsora, Sanket B. Patil, Prachi More, Shruti Guha Sarkar, Andrea M. Mitchell, Rinti Banerjee, Prashant S. Phale, Timothy J. Mitchell, Daniel R. Neill, Prasenjit Bhaumik, Anirban Banerjee
Software Mentions: 3
Published: over 5 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: over 5 years ago

10.1371/journal.pone.0032858

Molecular and Antigenic Characterization of Reassortant H3N2 Viruses from Turkeys with a Unique Constellation of Pandemic H1N1 Internal Genes
Cited by: 17
Author(s): Yohannes Berhane, Helen Kehler, Katherine Handel, Tamiko Hisanaga, Wanhong Xu, Davor Ojkić, John Pasick
Software Mentions: 3
Published: over 14 years ago

10.1074/jbc.RA119.007709

Structure and interactions of the archaeal motility repression module ArnA–ArnB that modulates archaellum gene expression in Sulfolobus acidocaldarius
Cited by: 15
Author(s): Lena Hoffmann, Katrin Anders, Lisa Franziska Bischof, Xing Ye, Julia Reimann, Sunia Khadouma, Trong Khoa Pham, Chris van der Does, Phillip C. Wright, Lars‐Oliver Essen, Sonja‐Verena Albers
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.ppat.1009566

Characterization of changes in the hemagglutinin that accompanied the emergence of H3N2/1968 pandemic influenza viruses
Cited by: 4
Author(s): Johanna West, Juliane Röder, Tatyana Matrosovich, Jana Beicht, Jan Baumann, Nancy Mounogou Kouassi, Jennifer Doedt, Nicolai V. Bovin, Gianpiero Zamperin, Michele Gastaldelli, Annalisa Salviato, Francesco Bonfante, Sergei L. Kosakovsky Pond, Sander Herfst, Ron A. M. Fouchier, Jochen Wilhelm, Hans‐Dieter Klenk, Mikhail Matrosovich
Software Mentions: 3
Published: almost 5 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: about 5 years ago

10.1074/jbc.RA118.004469

Discovery of peptide ligands targeting a specific ubiquitin-like domain–binding site in the deubiquitinase USP11
Cited by: 24
Author(s): Anastasios Spiliotopoulos, Lia Blokpoel Ferreras, Ruth M Densham, Simon G. Caulton, Ben C. Maddison, Joanna R. Morris, James E. Dixon, Kevin C. Gough, Ingrid Dreveny
Software Mentions: 3
Published: over 7 years ago

10.1074/jbc.RA118.006045

Structural insights into non-covalent ubiquitin activation of the cIAP1-UbcH5B∼ubiquitin complex
Cited by: 12
Author(s): Amrita Patel, Gary Sibbet, Danny T. Huang
Software Mentions: 3
Published: over 7 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: about 5 years ago

10.1016/j.str.2017.01.002

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

10.1371/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

10.1074/jbc.M117.776476

Allosteric mechanism of action of the therapeutic anti-IgE antibody omalizumab
Cited by: 57
Author(s): Anna M. Davies, Elizabeth G. Allan, Anthony H. Keeble, Jean Delgado, Benjamin P. Cossins, A.N. Mitropoulou, M.O.Y. Pang, Tom Ceska, Andrew J. Beavil, Graham Craggs, Marta Westwood, Alistair J. Henry, James M. McDonnell, Brian J. Sutton
Software Mentions: 3
Published: about 9 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: over 11 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

10.1371/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

10.3389/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/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: almost 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: almost 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

10.1111/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: almost 6 years ago

10.1038/s41598-021-94019-5

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

10.1002/jmr.2696

The evolutionary characteristics and structural biology of <i>Gallus</i> toll-like receptor 21
Cited by: 6
Author(s): Hongping Wu, Hai Wang, Weibo Jiang, Zhengxing Lian
Software Mentions: 3
Published: over 8 years ago

10.1042/BSR20140088

Apo, Zn2+-bound and Mn2+-bound structures reveal ligand-binding properties of SitA from the pathogen <i>Staphylococcus pseudintermedius</i>
Cited by: 29
Author(s): Francesca Abate, E. Malito, Roberta Cozzi, Paola Lo Surdo, Domenico Maione, Matthew J. Bottomley
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-021-91494-8

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

10.1016/j.jmb.2018.05.019

Proteomic and Biochemical Comparison of the Cellular Interaction Partners of Human VPS33A and VPS33B
Cited by: 20
Author(s): Morag R. Hunter, Geoffrey G. Hesketh, Tomasz H. Benedyk, Anne‐Claude Gingras, Stephen C. Graham
Software Mentions: 3
Published: about 8 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: over 8 years ago

10.1016/j.jmb.2015.08.023

Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain
Cited by: 9
Author(s): Nora Cronin, Jing Yang, Ziguo Zhang, Kiran Kulkarni, Leifu Chang, Hiroyuki Yamano, David Barford
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-018-27051-7

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

10.1371/journal.ppat.1008848

Chaperone-tip adhesin complex is vital for synergistic activation of CFA/I fimbriae biogenesis
Cited by: 1
Author(s): Libang He, Hao Wang, Yang Liu, Mei Kang, Tao Li, Changcheng Li, Aiping Tong, Yuanfeng Zhu, Yingjie Song, Stephen J. Savarino, Michael G. Prouty, Di Xia, Rui Bao
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0169687

Recessive coding and regulatory mutations in FBLIM1 underlie the pathogenesis of chronic recurrent multifocal osteomyelitis (CRMO)
Cited by: 59
Author(s): Allison Cox, Benjamin W. Darbro, Ronald M. Laxer, Gabriel Vélez, Xinyu Bing, Alexis L. Finer, Albert Erives, Vinit B. Mahajan, Alexander G. Bassuk, Polly J. Ferguson
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms19030916

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations
Cited by: 2
Author(s): Long‐Can Mei, Yanping Zhou, Lizhe Zhu, Changlin Liu, Zhuo Wu, Fangkui Wang, Ge‐Fei Hao, Di Yu, Hong Yuan, Yanfang Cui
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0241513

Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX
Cited by: 12
Author(s): Linda Yingqi Lin, Sawyer McCarthy, Barrett M. Powell, Yanti Manurung, Irene M. Xiang, William L. Dean, Brad Chaires, Liliya A. Yatsunyk
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms21082764

Structural Characterization of Carbonic Anhydrase VIII and Effects of Missense Single Nucleotide Variations to Protein Structure and Function
Cited by: 11
Author(s): Taremekedzwa Allan Sanyanga, Özlem Tastan Bishop
Software Mentions: 3
Published: about 6 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: about 5 years ago

10.3389/fmolb.2021.643728

Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction
Cited by: 1
Author(s): Ennys Gheyouche, Matthias Bagueneau, Gervaise Loirand, Bernard Offmann, Stéphane Téletchéa
Software Mentions: 3
Published: about 5 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: over 9 years ago

10.3389/fmicb.2016.00901

Reconstruction of the High-Osmolarity Glycerol (HOG) Signaling Pathway from the Halophilic Fungus Wallemia ichthyophaga in Saccharomyces cerevisiae
Cited by: 8
Author(s): Tilen Konte, Ulrich Terpitz, Ana Plemenitaš
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0145053

Synergistic Interactions of Eugenol-tosylate and Its Congeners with Fluconazole against Candida albicans
Cited by: 57
Author(s): Aijaz Ahmad, Mohmmad Younus Wani, Amber Khan, Nikhat Manzoor, Julitha Molepo
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2018.03192

Predictable Molecular Adaptation of Coevolving Enterococcus faecium and Lytic Phage EfV12-phi1
Cited by: 29
Author(s): Stephen Wandro, Andrew Oliver, Tara Gallagher, Claudia Weihe, Whitney England, Jennifer B. H. Martiny, Katrine Whiteson
Software Mentions: 3
Published: over 7 years ago

10.1016/j.bpj.2018.03.040

Evaluating Anti-CD32b F(ab) Conformation Using Molecular Dynamics and Small-Angle X-Ray Scattering
Cited by: 3
Author(s): Emma J. Sutton, Richard T. Bradshaw, Christian M. Orr, Björn Frendéus, Gunilla Larsson, Ingrid Teige, Mark S. Cragg, Ivo Tews, Jonathan W. Essex
Software Mentions: 3
Published: about 8 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: over 10 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

10.12688/f1000research.12301.2

In silico analysis of natural compounds targeting structural and nonstructural proteins of chikungunya virus
Cited by: 16
Author(s): Jaspreet Jain, Anchala Kumari, Pallavi Somvanshi, Abhinav Grover, S. Somnath Pai, Sujatha Sunil
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0243429

A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations
Cited by: 2
Author(s): Dimitrios A. Mitsikas, Nicholas M. Glykos
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-017-10085-8

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

10.1038/s41598-018-19991-x

Thermal stabilization of the deglycating enzyme Amadoriase I by rational design
Cited by: 18
Author(s): Federica Rigoldi, Stefano Donini, Francesca Giacomina, Federico Sorana, Alberto Redaelli, Tiziano Bandiera, Emilio Parisini, Alfonso Gautieri
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-24775-4

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

10.1371/journal.pone.0022201

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

10.1016/j.jmb.2013.10.039

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

10.7554/eLife.70560

Processing of the ribosomal ubiquitin-like fusion protein FUBI-eS30/FAU is required for 40S maturation and depends on USP36
Cited by: 5
Author(s): Jasmin van den Heuvel, Caroline Ashiono, Ludovic Gillet, Kerstin Dörner, Emanuel Wyler, Ivo Zemp, Ulrike Kutay
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.22693

The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels
Cited by: 77
Author(s): A. J. Miles, Stephen P. Burr, GL Grice, James A. Nathan
Software Mentions: 3
Published: over 9 years ago

10.1186/1754-6834-7-18

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

10.1371/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: over 5 years ago

10.1371/journal.pone.0182972

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