pypi: PyMOL | Projects | Ecosyste.ms: Papers

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

10.1371/journal.pone.0088229

Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts
Cited by: 29
Author(s): Dallas Thomas, Abdul G. Lone, L. Brent Selinger, Eduardo N. Taboada, Richard R. E. Uwiera, D. Wade Abbott, G. Douglas Inglis
Software Mentions: 3
Published: over 12 years ago

10.3389/fmicb.2017.00048

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

10.1074/jbc.M116.730382

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

10.7717/peerj.4728

Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain from <i>Mycobacterium tuberculosis</i>
Cited by: 5
Author(s): Mingjing Yu, Chao Dou, Yijun Gu, Wei Cheng
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-37699-w

The EZH2 SANT1 domain is a histone reader providing sensitivity to the modification state of the H4 tail
Cited by: 15
Author(s): Tyler Weaver, Jiachen Liu, Katelyn E. Connelly, Chris Coble, Katayoun Varzavand, Emily C. Dykhuizen, Catherine A. Musselman
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.50175

Ligand recognition and gating mechanism through three ligand-binding sites of human TRPM2 channel
Cited by: 64
Author(s): Yongyang Huang, Becca Roth, Wei Lü, Juan Du
Software Mentions: 3
Published: about 7 years ago

10.1074/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/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

10.1073/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

10.3390/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: almost 7 years ago

10.1016/j.str.2020.04.010

CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions
Cited by: 16
Author(s): Takashi Ochi, Valentina Quarantotti, Huawen Lin, Jérôme Jullien, Ivan Rosa e Silva, Francesco Boselli, Deepak D. Barnabas, Christopher M. Johnson, Stephen H. McLaughlin, Stefan Freund, Andrew N. Blackford, Yuu Kimata, Raymond E. Goldstein, Stephen Jackson, Tom L. Blundell, Susan K. Dutcher, Fanni Gergely, M. van Breugel
Software Mentions: 3
Published: over 6 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

10.3390/ijms22189833

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

10.3389/fgene.2021.620472

Case Report: Novel RPGRIP1L Gene Mutations Identified by Whole Exome Sequencing in a Patient With Multiple Primary Tumors
Cited by: 0
Author(s): Jianghong Guo, Yu Ye, Zhuqing Ji, Ming Yao, Xiaotian Xia, Xiaofeng Sha, Ming‐De Huang
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms221910493

Discovery and Validation of Lmj_04_BRCT Domain, a Novel Therapeutic Target: Identification of Candidate Drugs for Leishmaniasis
Cited by: 6
Author(s): José Peña-Guerrero, Celia Fernández-Rubio, Aroia Burguete-Mikeo, Rima El-Dirany, Alfonso T. García-Sosa, Paul A. Nguewa
Software Mentions: 3
Published: about 5 years ago

10.1016/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

10.7554/eLife.22086

Molecular architecture of the 90S small subunit pre-ribosome
Cited by: 116
Author(s): Qiaoyan Sun, Xing Zhu, Qiong Jia, Wenling An, Pengfei Lan, Dan Tan, Rongchang Chen, Bing Wang, Sanduo Zheng, Cheng Zhang, Xining Chen, Wei Zhang, Jing Chen, Meng‐Qiu Dong, Keqiong Ye
Software Mentions: 3
Published: over 9 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.2021.100700

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

10.3390/ijms20040884

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

10.3390/ijms20225734

A Single Synonymous Variant (c.354G>A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity
Cited by: 23
Author(s): Ryan Hunt, Gaya Hettiarachchi, Upendra Katneni, Nancy Hernandez, David D. Holcomb, Jacob Kames, Redab Alnifaidy, Brian C. Lin, Nobuko Hamasaki-Katagiri, Aaron Wesley, Tal Kafri, Christina Morris, Laura Bouché, Maria Panico, Tal Schiller, Juan C. Ibla, Haim Bar, Amra Ismail, Howard R. Morris, Anton A. Komar
Software Mentions: 3
Published: almost 7 years ago

10.1016/j.jmb.2016.12.004

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures
Cited by: 307
Author(s): Harry Jubb, Alícia P. Higueruelo, Bernardo Ochoa‐Montaño, William R. Pitt, David B. Ascher, Tom L. Blundell
Software Mentions: 3
Published: over 9 years ago

10.1093/database/bau102

PolyprOnline: polyproline helix II and secondary structure assignment database
Cited by: 35
Author(s): Romain Chebrek, Sylvain Léonard, Alexandre G. de Brevern, Jean‐Christophe Gelly
Software Mentions: 3
Published: almost 12 years ago

10.3389/fgene.2021.713224

Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress
Cited by: 18
Author(s): Ahmed H. El-Sappah, Rania G. Elbaiomy, Ahmed S. Elrys, Yu Wang, Yumin Zhu, Qiulan Huang, Yan Ke, Xingbo Zhao, Yun Li, Khaled A. El‐Tarabily, Jia Li
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-40892-0

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

10.1038/s41598-018-34508-2

“Infostery” analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations
Cited by: 16
Author(s): Yasaman Karami, Tristan Bitard‐Feildel, Élodie Laine, Alessandra Carbone
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-019-40432-w

Reactive centre loop dynamics and serpin specificity
Cited by: 28
Author(s): Emilia M. Marijanovic, James Fodor, Blake T. Riley, Benjamin T. Porebski, Maurício G. S. Costa, Itamar Kass, David E. Hoke, Sheena McGowan, Ashley M. Buckle
Software Mentions: 3
Published: over 7 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

10.1107/S205225252000072X

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals
Cited by: 31
Author(s): Alexander M. Wolff, I.D. Young, Raymond G. Sierra, Aaron S. Brewster, Michael W. Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, J.T. Biel, Sergio Carbajo, Aina E. Cohen, S.V. Cortez, Ana González, Tsuneo Hino, Dohyun Im, Jake Koralek, Minoru Kubo, Tomas S. Lazarou, Takashi Nomura, Shigeki Owada, Avi J. Samelson, Tomoyuki Tanaka, R. Tanaka, Erin Thompson, H. van den Bedem, R.A. Woldeyes, Fumiaki Yumoto, Zhao Wei, Kensuke Tono, Sébastien Boutet, So Iwata, Tamir Gonen, Nicholas K. Sauter, James S. Fraser, Michael C. Thompson
Software Mentions: 3
Published: over 6 years ago

10.1371/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

10.1038/s42003-020-01639-0

Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization
Cited by: 14
Author(s): Jonathan R. Macey, Stephan Pabinger, Charles G. Barbieri, Ella S. Buring, Vanessa L. González, Daniel G. Mulcahy, Dustin DeMeo, Lara Urban, Paul M Hime, Stefan Prost, Aaron N. Elliott, Neil J. Gemmell
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.42426

TRIM28 promotes HIV-1 latency by SUMOylating CDK9 and inhibiting P-TEFb
Cited by: 61
Author(s): Xiancai Ma, Tao Yang, Yong Luo, Liyang Wu, Yawen Jiang, Sifa Zheng, Ting Pan, Bingfeng Liu, Guangyan Liu, Jun Li, Fei Yu, Zhangping He, Wanying Zhang, Jinyu Yang, Liting Liang, Yuanjun Guan, Xu Zhang, Linghua Li, Weiping Cai, Xiaoping Tang, Song Gao, Kai Deng, Hui Zhang
Software Mentions: 3
Published: almost 8 years ago

10.3390/ijms22168631

The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales
Cited by: 5
Author(s): Marie-Caroline Müller, T. Wagner
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.ppat.1009723

ACE2-lentiviral transduction enables mouse SARS-CoV-2 infection and mapping of receptor interactions
Cited by: 17
Author(s): Daniel J. Rawle, Thuy T. Le, Troy Dumenil, Kexin Yan, Bing Tang, Wilson Nguyen, Daniel Watterson, Naphak Modhiran, Jody Hobson‐Peters, Cameron Bishop, Andreas Suhrbier
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.22964

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

10.1371/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

10.1128/mBio.01569-16

The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment
Cited by: 24
Author(s): Leo Hanke, Kevin E. Knockenhauer, R. Camille Brewer, Eline van Diest, Florian I. Schmidt, Thomas Schwartz, Hidde L. Ploegh
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-019-40323-0

Molecular cloning, GTP recognition mechanism and tissue-specific expression profiling of myxovirus resistance (Mx) protein in Labeo rohita (Hamilton) after Poly I:C induction
Cited by: 14
Author(s): Basanta Kumar Das, Pragyan Roy, Ajaya Kumar Rout, Deepak Ranjan Sahoo, Soumya Prasad Panda, Sushmita Pattanaik, Budheswar Dehury, Bijay Kumar Behera, Sudhansu Sekhar Mishra
Software Mentions: 3
Published: over 7 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

10.7554/eLife.56889

An ER translocon for multi-pass membrane protein biogenesis
Cited by: 68
Author(s): Philip T. McGilvray, S. Anghel, Arunkumar Sundaram, Frank Zhong, Michael J. Trnka, James R. Fuller, Hong Yu Hu, Alma L. Burlingame, Robert J. Keenan
Software Mentions: 3
Published: about 6 years ago

10.1016/j.dib.2016.01.016

Molecular determinants and interaction data of cyclic peptide inhibitor with the extracellular domain of TrkB receptor
Cited by: 5
Author(s): Nitin Chitranshi, Vivek Kumar Gupta, Yogita Dheer, Veer Bala Gupta, Roshana Vander Wall, Stuart L. Graham
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-018-29865-x

EPO does not promote interaction between the erythropoietin and beta-common receptors
Cited by: 18
Author(s): Karen S. Cheung Tung Shing, Sophie E. Broughton, Tracy L. Nero, Kevin R. Gillinder, Melissa Ilsley, Hayley S. Ramshaw, Angel F. Lopez, Michael D. W. Griffin, Michael W. Parker, Andrew C. Perkins, Urmi Dhagat
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-33068-9

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

10.3389/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

10.1038/s41598-018-33193-5

Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas
Cited by: 10
Author(s): Hong‐Hsiang Guan, Yin-Cheng Hsieh, Po‐Chun Lin, Yen‐Chieh Huang, Masato Yoshimura, Liying Chen, Shao-Kang Chen, Phimonphan Chuankhayan, Chien-Chih Lin, Nai-Chi Chen, Atsushi Nakagawa, Sunney I. Chan, Chun‐Jung Chen
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-32040-x

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

10.1038/s41598-019-39641-0

Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H
Cited by: 13
Author(s): Chang Woo Lee, Sun Ha Park, Chang-Sung Jeong, Sun Mi Shin, Hyun Park, Jun Hyuck Lee
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-36267-6

The reduced activity of PP-1α under redox stress condition is a consequence of GSH-mediated transient disulfide formation
Cited by: 7
Author(s): Simranjit Singh, Simon Lämmle, Heiko Giese, Susanne Kämmerer, Stefanie Meyer-Roxlau, Ezzaldin Ahmed Alfar, Hassan Dihazi, Kaomei Guan, Ali El‐Armouche, Florian Richter
Software Mentions: 3
Published: almost 8 years ago

10.1002/ctm2.296

Ursodesoxycholic acid alleviates liver fibrosis via proregeneration by activation of the ID1‐WNT2/HGF signaling pathway
Cited by: 8
Author(s): Dong Xi, Yun Luo, Shan Lu, Han Ma, Wenchao Zhang, Yue Zhu, Guibo Sun, Xiaobo Sun
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-39984-8

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

10.1016/j.str.2021.04.004

Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein
Cited by: 8
Author(s): Patryk Ludzia, E.D. Lowe, Gabriele Marcianò, Shabaz Mohammed, Christina Redfield, Bungo Akiyoshi
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-40762-9

Meta-analysis suggests evidence of novel stress-related pathway components in Orsay virus - Caenorhabditis elegans viral model
Cited by: 3
Author(s): Prachi Mishra, Jessica Ngo, Jahanshah Ashkani, Frédéric Pio
Software Mentions: 3
Published: over 7 years ago

10.1128/mBio.02858-18

Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket
Cited by: 13
Author(s): Pierrick Craveur, A.T. Gres, Karen A. Kirby, Dandan Liu, John A. Hammond, Yisong Deng, Stefano Forli, David S. Goodsell, James R. Williamson, Stefan G. Sarafianos, Arthur J. Olson
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2019.00466

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

10.1038/s41598-019-39588-2

The IKK-binding domain of NEMO is an irregular coiled coil with a dynamic binding interface
Cited by: 18
Author(s): Adam H. Barczewski, Michael J. Ragusa, Dale F. Mierke, Maria Pellegrini
Software Mentions: 3
Published: over 7 years ago

10.3389/frobt.2018.00133

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

10.1111/cea.12230

Human <scp>I</scp> g <scp>E</scp> against the major allergen <scp>B</scp> et v 1 – defining an epitope with limited cross‐reactivity between different <scp>PR</scp> ‐10 family proteins
Cited by: 20
Author(s): Mattias Levin, Anna M. Davies, Maria Liljekvist, Fredrika Carlsson, Hannah J. Gould, Brian J. Sutton, Mats Ohlin
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.ppat.1008848

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

10.1016/j.jbc.2021.101061

A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase
Cited by: 7
Author(s): Emily Chen, Krystle Reiss, Dilip Shah, R Manjula, Brandon Allen, Eva Murphy, James W. Murphy, Víctor S. Batista, Vineet Bhandari, Elias Lolis, George P. Lisi
Software Mentions: 3
Published: about 5 years ago

10.1128/mBio.03066-19

How Bacterial Chemoreceptors Evolve Novel Ligand Specificities
Cited by: 45
Author(s): José A. Gavira, Vadim M. Gumerov, Míriam Rico-Jiménez, Marharyta Petukh, Amit A. Upadhyay, Álvaro Ortega, Miguel A. Matilla, Igor B. Zhulin, Tino Krell
Software Mentions: 3
Published: over 6 years ago

10.1038/s42003-021-02532-0

Modulation of Toll-like receptor 1 intracellular domain structure and activity by Zn2+ ions
Cited by: 7
Author(s): Владислав А. Лушпа, Marina V. Goncharuk, Cong Lin, Arthur O. Zalevsky, Irina A. Talyzina, Aleksandra Luginina, Daniil Vakhrameev, M.B. Shevtsov, Sergey A. Goncharuk, Alexander S. Arseniev, Valentin Borshchevskiy, Xiaohui Wang, K.S. Mineev
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

10.1038/s42003-020-01123-9

Structure and function of a malaria transmission blocking vaccine targeting Pfs230 and Pfs230-Pfs48/45 proteins
Cited by: 34
Author(s): Kavita Singh, Martin Burkhardt, Sofia Nakuchima, Raúl Herrera, Olga Muratova, Apostolos G. Gittis, Emily Kelnhofer, Karine Reiter, Margery Smelkinson, Daniel Veltri, Bruce J. Swihart, Richard L. Shimp, Vu Nguyen, Baoshan Zhang, Nicholas J. MacDonald, Patrick E. Duffy, David N. Garboczi, David L. Narum
Software Mentions: 3
Published: about 6 years ago

10.1038/s42003-018-0063-1

Transient antibody-antigen interactions mediate the strain-specific recognition of a conserved malaria epitope
Cited by: 6
Author(s): Bankala Krishnarjuna, Toshihiko Sugiki, Rodrigo Morales, Jeffrey Seow, Toshimichi Fujiwara, Karyn L. Wilde, Raymond S. Norton, Christopher A. MacRaild
Software Mentions: 3
Published: over 8 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

10.1101/2021.02.21.432184

High-Throughput, Single-Copy Sequencing Reveals SARS-CoV-2 Spike Variants Coincident with Mounting Humoral Immunity during Acute COVID-19
Cited by: 4
Author(s): Sung Hee Ko, Elham Bayat Mokhtari, Prakriti Mudvari, Sydney Stein, Christopher D. Stringham, Danielle A. Wagner, Sabrina Ramelli, Marcos J. Ramos‐Benitez, Jeffrey R Strich, Richard T. Davey, Tongqing Zhou, John Misasi, Peter D. Kwong, Daniel S. Chertow, Nancy J. Sullivan, Eli Boritz
Software Mentions: 3
Published: over 5 years ago

10.3389/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

10.7554/eLife.27829

Structure-based analysis of CysZ-mediated cellular uptake of sulfate
Cited by: 9
Author(s): Zahra Assur Sanghai, Qun Liu, Oliver B Clarke, Meagan Belcher Dufrisne, Pattama Wiriyasermkul, Maria Giese, Edgar Leal-Pinto, Brian Kloss, Shantelle Tabuso, J. Love, Marco Punta, Surajit Banerjee, Kanagalaghatta R. Rajashankar, Burkhard Rost, Diomedes E. Logothetis, Matthias Quick, Wayne A. Hendrickson, Filippo Mancia
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.57861

Profiling of myristoylation in Toxoplasma gondii reveals an N-myristoylated protein important for host cell penetration
Cited by: 19
Author(s): Malgorzata Broncel, Caia Dominicus, Luis Vigetti, Stephanie D. Nofal, Edward Bartlett, Bastien Touquet, Alex Hunt, Bethan A. Wallbank, Stefania Federico, Stephen Matthews, J. M. Young, Edward W. Tate, Isabelle Tardieux, Moritz Treeck
Software Mentions: 3
Published: over 6 years ago

10.1016/j.csbj.2018.10.008

Quantitative comparison of ABC membrane protein type I exporter structures in a standardized way
Cited by: 4
Author(s): Georgina Csizmadia, Bianka Farkas, Zoltán Spagina, Hedvig Tordai, Tamás Hegedüs
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.46497

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

10.7554/eLife.60481

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

10.3390/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

10.7554/eLife.46754

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

10.7554/eLife.65339

Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein
Cited by: 12
Author(s): Xiangrong Chen, Yusuf Ali, Charlotte E L Fisher, Raquel Arribas-Bosacoma, Mohan B. Rajasekaran, Gareth Williams, Sarah Walker, Jessica R Booth, Jessica J. R. Hudson, S. Mark Roe, Laurence H. Pearl, Simon E. Ward, Frances M. G. Pearl, Antony W. Oliver
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms19030916

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

10.3390/ijms19113340

Physical Background of the Disordered Nature of “Mutual Synergetic Folding” Proteins
Cited by: 6
Author(s): Csaba Magyar, Anikó Mentes, Erzsébet Fichó, Miklós Cserző, István Simon
Software Mentions: 3
Published: almost 8 years ago

10.3390/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

10.3390/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: over 6 years ago

10.1074/jbc.RA119.010697

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

10.7554/eLife.41741

Crystal structure of a natural light-gated anion channelrhodopsin
Cited by: 30
Author(s): Hai Li, Chia‐Ying Huang, Elena G. Govorunova, Christopher T. Schafer, Oleg A. Sineshchekov, Meitian Wang, Lei Zheng, John L. Spudich
Software Mentions: 3
Published: almost 8 years ago

10.1534/g3.119.400224

Contraction of the ROS Scavenging Enzyme Glutathione<i>S</i>-Transferase Gene Family in Cetaceans
Cited by: 11
Author(s): Ran Tian, Inge Seim, Wenhua Ren, Shixia Xu
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

10.1038/s41598-018-29058-6

Structural determinants of specificity and regulation of activity in the allosteric loop network of human KLK8/neuropsin
Cited by: 7
Author(s): Mekdes Debela, Viktor Magdolen, Wolfgang Skala, Brigitta Elsässer, Eric L. Schneider, Charles S. Craik, Martin L. Biniossek, Oliver Schilling, Wolfram Bode, Hans Brandstetter, Peter Goettig
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-37506-6

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

10.1038/s41598-019-46094-y

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

10.1155/2014/697532

In SilicoAntitubercular Activity Analysis of Benzofuran and Naphthofuran Derivatives
Cited by: 5
Author(s): Prashantha Karunakar, C. R. Girija, Venkatappa Krishnamurthy, V. Krishna, K. V. Shivakumar
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-019-40564-z

Decline of transmissible gastroenteritis virus and its complex evolutionary relationship with porcine respiratory coronavirus in the United States
Cited by: 38
Author(s): Fangzhou Chen, Todd P. Knutson, Stephanie Rossow, Linda J. Saif, Douglas Marthaler
Software Mentions: 3
Published: over 7 years ago

10.1155/2014/162150

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

10.3389/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

10.1038/s42003-021-02518-y

14-3-3 proteins inactivate DAPK2 by promoting its dimerization and protecting key regulatory phosphosites
Cited by: 18
Author(s): Matej Horvath, Olívia Petrvalská, Petr Heřman, Veronika Obšilová, Tomáš Obšil
Software Mentions: 3
Published: about 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: almost 6 years ago

10.7554/eLife.59753

Structures of diverse poxin cGAMP nucleases reveal a widespread role for cGAS-STING evasion in host–pathogen conflict
Cited by: 29
Author(s): J.B. Eaglesham, Kacie McCarty, Philip J. Kranzusch
Software Mentions: 3
Published: almost 6 years ago

10.1038/s42003-020-01401-6

Structure-based dynamic analysis of the glycine cleavage system suggests key residues for control of a key reaction step
Cited by: 13
Author(s): Han Zhang, Yuchen Li, Jinglei Nie, Jie Ren, An‐Ping Zeng
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0233689

The crystal structures of Thermus thermophilus CMP kinase complexed with a phosphoryl group acceptor and donor
Cited by: 3
Author(s): Ryosuke Mega, Noriko Nakagawa, Seiki Kuramitsu, Ryoji Masui
Software Mentions: 3
Published: over 6 years ago

10.3390/genes12050784

Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress
Cited by: 48
Author(s): Zahra Musavizadeh, Hamid Najafi-Zarrini, Seyed Kamal Kazemitabar, Seyyed Hamidreza Hashemi, Sahar Faraji, Gianni Barcaccia, Parviz Heidari
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.97018

Fine epitope signature of antibody neutralization breadth at the HIV-1 envelope CD4-binding site
Cited by: 16
Author(s): Hao Cheng, Sebastian K. Grimm, M.S.A. Gilman, Luc Christian Gwom, Devin Sok, Christopher Sundling, G. Donofrio, Gunilla B. Karlsson Hedestam, Mattia Bonsignori, Barton F. Haynes, Timothy Lahey, Isaac Maro, C. Fordham von Reyn, Miroslaw K. Gorny, Susan Zolla‐Pazner, Bruce D. Walker, Galit Alter, Dennis R. Burton, Merlin L. Robb, Shelly J. Krebs, Michael S. Seaman, Chris Bailey‐Kellogg, Margaret E. Ackerman
Software Mentions: 3
Published: over 8 years ago

10.1371/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

Projects: pypi: PyMOL

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Papers Mentioning PyMOL 8,266