pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.7554/eLife.09375

Mechanism of Na+-dependent citrate transport from the structure of an asymmetrical CitS dimer
Cited by: 53
Author(s): David Wöhlert, Maria J Grötzinger, Werner Kühlbrandt, Özkan Yıldız
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.53853

Structural insights into sodium transport by the oxaloacetate decarboxylase sodium pump
Cited by: 10
Author(s): Xin Xu, Huigang Shi, Xiaohua Gong, Pu Chen, Ying Gao, Xinzheng Zhang, Song Xiang
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0154046

Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics
Cited by: 2
Author(s): Gloria Ruiz-Gómez, John C. Hawkins, Patrick Jenny, Georg Künze, Robert Wodtke, Reik Löser, Karim Fahmy, M. Teresa Pisabarro
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-08303-4

Structural characterization of CAS SH3 domain selectivity and regulation reveals new CAS interaction partners
Cited by: 12
Author(s): Jakub Gemperle, R. Hexnerova, Martin Lepšı́k, Petr Těšina, Michal Dibus, Marián Novotný, Jan Brábek, Václav Veverka, Daniel Rösel
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.67336

Contingency and chance erase necessity in the experimental evolution of ancestral proteins
Cited by: 24
Author(s): Victoria Cochran Xie, Jinyue Pu, Brian P. H. Metzger, Joseph W. Thornton, Bryan C. Dickinson
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.55853

Cryo-EM structures and functional properties of CALHM channels of the human placenta
Cited by: 24
Author(s): Katarzyna Drożdżyk, Marta Sawicka, Maria-Isabel Bahamonde-Santos, Jonas Zaugg, Dawid Deneka, Christiane Albrecht, Raimund Dutzler
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.01739

FRET-based reporters for the direct visualization of abscisic acid concentration changes and distribution in Arabidopsis
Cited by: 198
Author(s): Rainer Waadt, Katsundo Hitomi, Noriyuki Nishimura, Chiharu Hitomi, Stephen Adams, Elizabeth D. Getzoff, Julian I. Schroeder
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-017-01705-4

Structural analysis of the regulatory mechanism of MarR protein Rv2887 in M. tuberculosis
Cited by: 16
Author(s): Yunrong Gao, Defeng Li, Joy Fleming, Ya‐Feng Zhou, Ying Liu, Jiao-Yu Deng, Lin Zhou, Jie Zhou, Guofeng Zhu, Xian-En Zhang, Dacheng Wang, Lijun Bi
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.21829

Structure of the transporter associated with antigen processing trapped by herpes simplex virus
Cited by: 80
Author(s): Michael L. Oldham, Nikolaus Grigorieff, Jue Chen
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.41848

An unexpected INAD PDZ tandem-mediated plcβ binding in Drosophila photo receptors
Cited by: 9
Author(s): Fei Ye, Yuguang Huang, J. Li, Yinfa Ma, Chensu Xie, Zexu Liu, Xiǎoyīng Dèng, Jun Wan, Tian Xue, Wei Liu, Mingjie Zhang
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.10034

Structural determinants of nuclear export signal orientation in binding to exportin CRM1
Cited by: 68
Author(s): Ho Yee Joyce Fung, Szu Chin Fu, Chad A. Brautigam, Yuh Min Chook
Software Mentions: 2
Published: about 9 years ago

10.3390/ijms21155277

Biophysical Characterization of Cancer-Related Carbonic Anhydrase IX
Cited by: 4
Author(s): Katarina Koruza, Akilah B. Murray, Brian P. Mahon, Jesse B. Hopkins, Wolfgang Knecht, Robert McKenna, S.Z. Fisher
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21197261

Atomistic Structure and Dynamics of the Ca2+-ATPase Bound to Phosphorylated Phospholamban
Cited by: 6
Author(s): Rodrigo Aguayo‐Ortiz, L. Michel Espinoza-Fonseca
Software Mentions: 2
Published: about 4 years ago

10.3390/ijms21218066

Alpha-Carbonic Anhydrases from Hydrothermal Vent Sources as Potential Carbon Dioxide Sequestration Agents: In Silico Sequence, Structure and Dynamics Analyses
Cited by: 6
Author(s): Colleen Varaidzo Manyumwa, Reza Zolfaghari Emameh, Özlem Tastan Bishop
Software Mentions: 2
Published: about 4 years ago

10.3390/ijms21249701

Origin and Evolution of the Human Bcl2-Associated Athanogene-1 (BAG-1)
Cited by: 4
Author(s): Peter Q. Nguyen, Kyle Hess, Larissa Smulders, Dat Le, Carolina Briseno, Christina M Chavez, Nikolas Nikolaidis
Software Mentions: 2
Published: almost 4 years ago

10.1042/BCJ20160791

Structure and lipid-binding properties of the kindlin-3 pleckstrin homology domain
Cited by: 39
Author(s): Ni Tien, Antreas C. Kalli, Fiona B. Naughton, Luke A. Yates, Omar Naneh, Mirijam Kozorog, Gregor Anderluh, Mark S. P. Sansom, Robert J.C. Gilbert
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms22115895

In-Silico Evaluation of Genetic Alterations in Ovarian Carcinoma and Therapeutic Efficacy of NSC777201, as a Novel Multi-Target Agent for TTK, NEK2, and CDK1
Cited by: 8
Author(s): Harshita Khedkar, Yu-Chi Wang, Vijesh Kumar Yadav, Prateeti Srivastava, Bashir Lawal, Ntlotlang Mokgautsi, Maryam Rachmawati Sumitra, Alexander T.H. Wu, Hsu-Shan Huang
Software Mentions: 2
Published: over 3 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 13 years ago

10.3390/ijms22116063

Mutations in bdcA and valS Correlate with Quinolone Resistance in Wastewater Escherichia coli
Cited by: 2
Author(s): Negin Malekian, Ali Al-Fatlawi, Thomas U. Berendonk, Michael Schroeder
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms22136910

Mutagenic Analysis of the Putative ABCC6 Substrate-Binding Cavity Using a New Homology Model
Cited by: 8
Author(s): Flóra Szeri, Valentina Corradi, Fatemeh Niaziorimi, Sylvia Donnelly, Gwenaëlle Conseil, Susan P. C. Cole, D. Peter Tieleman, Koen van de Wetering
Software Mentions: 2
Published: over 3 years ago

10.1038/s42003-018-0123-6

In situ serial crystallography for rapid de novo membrane protein structure determination
Cited by: 26
Author(s): Chia-Ying Huang, V. Oliéric, Nicole Howe, Rangana Warshamanage, T. Weinert, Ezequiel Panepucci, Lutz Vogeley, Shibom Basu, Kay Diederichs, Martin Caffrey, Meitian Wang
Software Mentions: 2
Published: about 6 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 13 years ago

10.1038/s41598-017-06278-w

Mechanisms and Specificity of Phenazine Biosynthesis Protein PhzF
Cited by: 11
Author(s): Christina Diederich, Mario Leypold, Martin Culka, Hansjörg Weber, Rolf Breinbauer, G. Matthias Ullmann, Wulf Blankenfeldt
Software Mentions: 2
Published: over 7 years ago

10.1080/21655979.2017.1342911

Genome mining, <i>in silico</i> validation and phase selection of a novel aldo-keto reductase from <i>Candida glabrata</i> for biotransformation
Cited by: 3
Author(s): Souvik Basak, Nanda Gopal Sahoo, Angayar K. Pavanasam
Software Mentions: 2
Published: over 7 years ago

10.1038/s42003-020-01640-7

Molecular basis of IRGB10 oligomerization and membrane association for pathogen membrane disruption
Cited by: 8
Author(s): Hyekyung Ha, Hye Lin Chun, So Yeon Lee, Jin Ho Jeong, Yeon-Gil Kim, Hyun Ho Park
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pcbi.1003995

Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation
Cited by: 8
Author(s): Michael Graf, Zhihua Lin, Urban Bren, Dietmar Haltrich, W. F. van Gunsteren, Chris Oostenbrink
Software Mentions: 2
Published: almost 10 years ago

10.1038/s42003-021-01650-z

Comparative multi-omics analyses reveal differential expression of key genes relevant for parasitism between non-encapsulated and encapsulated Trichinella
Cited by: 3
Author(s): Xiaolei Liu, Yue Feng, Xue Bai, Xuelin Wang, Rui Qin, Bin Tang, Xinxin Yu, Yong Yang, Mingyuan Liu, Fei Gao
Software Mentions: 2
Published: almost 4 years ago

10.1186/1745-6150-1-25

The signaling helix: a common functional theme in diverse signaling proteins
Cited by: 124
Author(s): Vivek Anantharaman, S. Balaji, L. Aravind
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pcbi.1005441

Peptide probes derived from pertuzumab by molecular dynamics modeling for HER2 positive tumor imaging
Cited by: 14
Author(s): Xiaoliang Yang, Zihua Wang, Zhichu Xiang, Dan Li, Zhiyuan Hu, Wei Cui, Li Geng, Qiaojun Fang
Software Mentions: 2
Published: over 7 years ago

10.3390/md17080479

Characterization of an Alkaline GH49 Dextranase from Marine Bacterium Arthrobacter oxydans KQ11 and Its Application in the Preparation of Isomalto-Oligosaccharide
Cited by: 14
Author(s): Hongfei Liu, Wei Ren, Mingsheng Ly, Haifeng Li, Shujun Wang
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-018-0262-9

Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters
Cited by: 19
Author(s): Yong Wei, Zi Jian Xiong, Jun Li, Chunxia Zou, Christopher W. Cairo, John S. Klassen, Gilbert G. Privé
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-017-06575-4

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene
Cited by: 70
Author(s): Tikam Chand Dakal, Deepak Kala, Gourav Dhiman, Vinod Kumar Yadav, A. Krokhotin, Nikolay V. Dokholyan
Software Mentions: 2
Published: over 7 years ago

10.1038/s42003-018-0236-y

The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release
Cited by: 19
Author(s): Heidi B. Cao, Mu Gao, Hongyi Zhou, Jeffrey Skolnick
Software Mentions: 2
Published: almost 6 years ago

10.3390/md17050295

A New Tyrosinase Inhibitor from the Red Alga Symphyocladia latiuscula (Harvey) Yamada (Rhodomelaceae)
Cited by: 23
Author(s): Pradeep Paudel, Aditi Wagle, Su Hui Seong, Hye Jin Park, Hyun Ah Jung, Jae Sue Choi
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-019-0562-8

Identification of an amphipathic peptide sensor of the Bacillus subtilis fluid membrane microdomains
Cited by: 5
Author(s): Yiping Jiang, Xin Dai, Mingming Qin, Zhihong Guo
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-017-08834-w

Structural analysis of Wss1 protein from saccharomyces cerevisiae
Cited by: 9
Author(s): Xiaoyun Yang, Yanhua Li, Zengqiang Gao, Zongqiang Li, Jianhua Xu, Wenjia Wang, Yuhui Dong
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-05268-2

Structural and Functional Analysis of Latex Clearing Protein (Lcp) Provides Insight into the Enzymatic Cleavage of Rubber
Cited by: 25
Author(s): Lorena Ilcu, Wolf Röther, Jakob Birke, Anton Brausemann, Oliver Einsle, Dieter Jendrossek
Software Mentions: 2
Published: over 7 years ago

10.1016/j.bcp.2016.12.013

High affinity binding of the peptide agonist TIP-39 to the parathyroid hormone 2 (PTH 2 ) receptor requires the hydroxyl group of Tyr-318 on transmembrane helix 5
Cited by: 7
Author(s): Richard E. Weaver, Juan Carlos Mobarec, Mark Wigglesworth, Christopher A. Reynolds, Daniel P. Donnelly
Software Mentions: 2
Published: over 7 years ago

10.1186/s13062-019-0232-2

Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions
Cited by: 24
Author(s): S Jayashree, Pavalam Murugavel, Ramanathan Sowdhamini, Narayanaswamy Srinivasan
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-017-05509-4

Structure of polyhydroxyalkanoate (PHA) synthase PhaC from Chromobacterium sp. USM2, producing biodegradable plastics
Cited by: 69
Author(s): Min Fey Chek, Sunyong Kim, Tomoyuki Mori, Hasni Arsad, Mohammed Razip Samian, Kumar Sudesh, Toshio Hakoshima
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-06612-2

Evaluation of Sofosbuvir (β-D-2′-deoxy-2′-α-fluoro-2′-β-C-methyluridine) as an inhibitor of Dengue virus replication #
Cited by: 51
Author(s): Hongtao Xu, Susan P. Colby-Germinario, Said Hassounah, Clare Fogarty, Nathan Osman, Navaneethan Palanisamy, Ying-Shan Han, Maureen Oliveira, Yudong Quan, Mark A. Wainberg
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-03220-y

Bacterial protease uses distinct thermodynamic signatures for substrate recognition
Cited by: 13
Author(s): G.A. Bezerra, Yuko Ohara‐Nemoto, Irina Cornaciu, Sofiya Fedosyuk, Guillaume Hoffmann, Adam Round, José Antonio Márquez, Takayuki Nemoto, Kristina Djinović-Carugo
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-02803-z

Construction of novel repeat proteins with rigid and predictable structures using a shared helix method
Cited by: 22
Author(s): Suk-Jun Youn, Nayoung Kwon, Ji Hyun Lee, Jin Hong Kim, Jin‐Woo Choi, Hayyoung Lee, Jie‐Oh Lee
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-03664-2

Antibacterial and detoxifying activity of NZ17074 analogues with multi-layers of selective antimicrobial actions against Escherichia coli and Salmonella enteritidis
Cited by: 48
Author(s): Na Yang, Xuehui Liu, Da Teng, Zhanzhan Li, Xiumin Wang, Ruoyu Mao, Xiao Wang, Ya Hao, Jianhua Wang
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-06023-3

Search for non-lactam inhibitors of mtb β-lactamase led to its open shape in apo state: new concept for antibiotic design
Cited by: 10
Author(s): Amin Sagar, Nazia Haleem, Yaawar Mir Bashir, . Ashish
Software Mentions: 2
Published: over 7 years ago

10.3390/md19040191

Characterization of a New Biofunctional, Exolytic Alginate Lyase from Tamlana sp. s12 with High Catalytic Activity and Cold-Adapted Features
Cited by: 14
Author(s): Rui Yin, Yan-Jun Yi, Zhuo Chen, Baoxun Wang, Xue-Han Li, Yanxia Zhou
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-08742-z

Identification and Characterization of a Bacterial Homolog of Chloride Intracellular Channel (CLIC) Protein
Cited by: 18
Author(s): Shubha Gururaja Rao, Devasena Ponnalagu, Sowmya Sukur, Harkewal Singh, Shridhar Sanghvi, Yixiao Mei, Ding Jun Jin, Harpreet Singh
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-36839-6

Search for efficient inhibitors of myotoxic activity induced by ophidian phospholipase A2-like proteins using functional, structural and bioinformatics approaches
Cited by: 23
Author(s): Daniela P. Marchi-Salvador, Filomena Cardoso, Antoniel Augusto Severo Gomes, Walter Luís Garrido Cavalcante, Márcia Gallacci, Marcos R.M. Fontes
Software Mentions: 2
Published: almost 6 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 6 years ago

10.3390/ijms22042211

Identification of Active Site Residues of the Siderophore Synthesis Enzyme PvdF and Evidence for Interaction of PvdF with a Substrate-Providing Enzyme
Cited by: 3
Author(s): Priya Philem, Torsten Kleffmann, Sinan Gai, Bill C. Hawkins, Sigurd M. Wilbanks, Iain L. Lamont
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-00147-2

PRL3 phosphatase active site is required for binding the putative magnesium transporter CNNM3
Cited by: 41
Author(s): Huizhi Zhang, Guennadi Kozlov, Xinlu Li, Howie Wu, Irina Gulerez, Kalle Gehring
Software Mentions: 2
Published: over 7 years ago

10.1038/srep45224

Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics
Cited by: 10
Author(s): Hannah A. Davies, Daniel J. Rigden, Marie M. Phelan, Jillian Madine
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-01186-5

Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine
Cited by: 12
Author(s): Cha San Koh, Rohini Madireddy, Timothy J. Beane, Phillip D. Zamore, А.A. Коростелев
Software Mentions: 2
Published: over 7 years ago

10.1038/srep41212

Two strategies to engineer flexible loops for improved enzyme thermostability
Cited by: 111
Author(s): Haoran Yu, Yihan Yan, Cheng Zhang, Paul A. Dalby
Software Mentions: 2
Published: almost 8 years ago

10.1038/s42003-019-0427-1

Structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase reveals mechanism of substrate binding and metal catalysis
Cited by: 20
Author(s): K. Grave, M.D. Bennett, Martin Högbom
Software Mentions: 2
Published: over 5 years ago

10.1038/srep39024

Comparative Proteomics Reveals that Phosphorylation of β Carbonic Anhydrase 1 Might be Important for Adaptation to Drought Stress in Brassica napus
Cited by: 31
Author(s): Limin Wang, Xiang Jin, Qingbin Li, Xuchu Wang, Zaiyun Li, Xiaoming Wu
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep42711

Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage ΦAB6 tailspike protein
Cited by: 37
Author(s): I‐Ming Lee, I-Fan Tu, Yang Fu, Tzu‐Ping Ko, Jiahn-Haur Liao, Ning Lin, Chung‐Yi Wu, Chien‐Tai Ren, Andrew H.‐J. Wang, Ching-Ming Chang, Kai‐Fa Huang, Shih‐Hsiung Wu
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-017-00917-y

A bacterial ABC transporter enables import of mammalian host glycosaminoglycans
Cited by: 21
Author(s): Shigetoshi Oiki, Bunzo Mikami, Yukie Maruyama, Kousaku Murata, Wataru Hashimoto
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1008383

Crystal structure of Mokola virus glycoprotein in its post-fusion conformation
Cited by: 15
Author(s): Laura Belot, Malika Ouldali, Stéphane Roche, Pierre Legrand, Yves Gaudin, Aurélie A. Albertini
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0204026

Etersalate prevents the formations of 6Aβ16-22 oligomer: An in silico study
Cited by: 11
Author(s): Son Tung Ngo, Xuan-Cuong Luu, Nguyen Thanh Nguyen, Van V. Vu, Huong Thi Thu Phung
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.ppat.1008317

Phosphoinositide-binding proteins mark, shape and functionally modulate highly-diverged endocytic compartments in the parasitic protist Giardia lamblia
Cited by: 11
Author(s): Lenka Černíková, Carmen Faso, Adrian Hehl
Software Mentions: 2
Published: over 4 years ago

10.3390/vaccines9080818

Towards an Ensemble Vaccine against the Pegivirus Using Computational Modelling Approaches and Its Validation through In Silico Cloning and Immune Simulation
Cited by: 8
Author(s): Bowen Zheng, Muhammad Suleman, Zonara Zafar, Syed Shujait Ali, Syed Nouman Nasir, Namra, Zahid Hussain, Muhammad Waseem, Abbas Khan, Fakhrul Hassan, Yanjing Wang, Dong‐Qing Wei
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1000357

Amyloidogenesis Abolished by Proline Substitutions but Enhanced by Lipid Binding
Cited by: 39
Author(s): Ping Jiang, Wei Xu, Yuguang Mu
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.ppat.1007476

Structural basis of Toxoplasma gondii perforin-like protein 1 membrane interaction and activity during egress
Cited by: 10
Author(s): Alfredo J. Guerra, Ou Zhang, Constance M. Bahr, My Hang Huynh, James Delproposto, William Clay Brown, Z. Wawrzak, Nicole M. Koropatkin, Vern B. Carruthers
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.1007944

Alternative conformations of a major antigenic site on RSV F
Cited by: 25
Author(s): Harrison G. Jones, Michael B. Battles, Chun-Chi Lin, Siro Bianchi, Davide Corti, Jason S. McLellan
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1008323

Structural basis of Fusarium myosin I inhibition by phenamacril
Cited by: 17
Author(s): Yuxin Zhou, Xuemei Zhou, Yuanping Gong, Yuanye Zhu, Xiaoman Cao, J.S. Brunzelle, H. Eric Xu, Mingguo Zhou, Karsten Melcher, Feng Zhang
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21197081

Impact of HLA-DR Antigen Binding Cleft Rigidity on T Cell Recognition
Cited by: 5
Author(s): Christopher Szeto, Joseph Bloom, Hannah Sloane, Christian A. Lobos, James Fodor, Dhilshan Jayasinghe, D.S.M. Chatzileontiadou, Emma J. Grant, Ashley M. Buckle, Stéphanie Gras
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-017-01057-z

Structural investigations on orotate phosphoribosyltransferase from Mycobacterium tuberculosis, a key enzyme of the de novo pyrimidine biosynthesis
Cited by: 22
Author(s): Stefano Donini, Davide M. Ferraris, Riccardo Miggiano, Alberto Massarotti, Menico Rizzi
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1006400

Structural insights into reptarenavirus cap-snatching machinery
Cited by: 27
Author(s): Maria Rosenthal, Nadja Gogrefe, Dominik Vogel, Juan Reguera, Bianka Rauschenberger, Stephen Cusack, Stephan Günther, Sophia Reindl
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1006244

Lactoferrin binding protein B – a bi-functional bacterial receptor protein
Cited by: 25
Author(s): Nicholas Ostan, Rong-hua Yu, Dixon Ng, Christine Chieh-Lin Lai, Anastassia K. Pogoutse, Vladimir Sarpe, Morgan Hepburn, Joey Sheff, Shaunak Raval, David C. Schriemer, Trevor F. Moraes, Anthony B. Schryvers
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.50722

A polyomavirus peptide binds to the capsid VP1 pore and has potent antiviral activity against BK and JC polyomaviruses
Cited by: 4
Author(s): Jason M. Kane, Susan Fong, Jacob Shaul, Alexandra Frommlet, Andreas Frank, Mark Knapp, Dirksen E. Bussiere, Peter Kim, Elizabeth Ornelas, Carlos Cuellar, Anastasia Hyrina, Johanna R. Abend, Charles Wartchow
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.ppat.1006552

Structural analysis of P. falciparum KAHRP and PfEMP1 complexes with host erythrocyte spectrin suggests a model for cytoadherent knob protrusions
Cited by: 27
Author(s): Erin E. Cutts, Niklas Laasch, Dirk M. Reiter, Raphael Trenker, Leanne M. Slater, Phillip J. Stansfeld, Ioannis Vakonakis
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1006098

Receptor Activation of HIV-1 Env Leads to Asymmetric Exposure of the gp41 Trimer
Cited by: 31
Author(s): Mukta D. Khasnis, Konstantine Halkidis, Anshul Bhardwaj, Michael J. Root
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.1005248

An O-Methyltransferase Is Required for Infection of Tick Cells by Anaplasma phagocytophilum
Cited by: 31
Author(s): Adela S. Oliva Chávez, J.W. Fairman, Roderick F. Felsheim, Curtis M. Nelson, Michael J. Herron, Lee Ann Higgins, Nicole Y. Burkhardt, Jonathan D. Oliver, Todd W. Markowski, Timothy J. Kurtti, Thomas E. Edwards, Ulrike G. Munderloh
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.ppat.1006231

Structure of a pentameric virion-associated fiber with a potential role in Orsay virus entry to host cells
Cited by: 10
Author(s): Yingying Fan, Yusong R. Guo, Yuan Wang, Ying Zhou, Matthew V. Holt, Tao Wang, Borries Demeler, Nicolas L. Young, Weiwei Zhong, Yizhi Jane Tao
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1006714

A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase
Cited by: 15
Author(s): Isabelle Jupin, Maya Ayach, Lucile Jomat, Sonia Fieulaine, Stéphane Bressanelli
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.ppat.1004334

P. aeruginosa SGNH Hydrolase-Like Proteins AlgJ and AlgX Have Similar Topology but Separate and Distinct Roles in Alginate Acetylation
Cited by: 52
Author(s): Perrin Baker, Tyler Ricer, Patrick J. Moynihan, Elena N. Kitova, Marthe T. C. Walvoort, Dustin J. Little, John C. Whitney, Karen Dawson, Joel T. Weadge, Howard Robinson, Dennis E. Ohman, Jeroen D. C. Codée, John S. Klassen, Anthony J. Clarke, P. Lynne Howell
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.ppat.1003966

Insights into the Initiation of JC Virus DNA Replication Derived from the Crystal Structure of the T-Antigen Origin Binding Domain
Cited by: 12
Author(s): Gretchen Meinke, Paul J. Phelan, Radha L. Kalekar, Jong Shin, Jacques Archambault, Andrew Bohm, Peter A. Bullock
Software Mentions: 2
Published: almost 11 years ago

10.7554/eLife.07485

The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helix
Cited by: 105
Author(s): David Barneda, Joan Planas-Iglesias, María L. Gaspar, Dariush Mohammadyani, Sunil Prasannan, Dirk Dormann, Gil‐Soo Han, Stephen A. Jesch, George M. Carman, Valerian E. Kagan, Malcolm G. Parker, Nicholas T. Ktistakis, Judith Klein‐Seetharaman, Ann M. Dixon, Susan A. Henry, Mark Christian
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.ppat.1004835

Conserved Streptococcus pneumoniae Spirosomes Suggest a Single Type of Transformation Pilus in Competence
Cited by: 26
Author(s): Raphaël Laurenceau, Petya V. Krasteva, Amy Diallo, Sahra Ouarti, Magalie Duchateau, Christian Malosse, Julia Chamot‐Rooke, Rémi Fronzes
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.ppat.1003624

The Crystal Structure and RNA-Binding of an Orthomyxovirus Nucleoprotein
Cited by: 36
Author(s): Wei Zheng, John S. Olson, Vikram N. Vakharia, Yizhi Jane Tao
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.ppat.1003549

Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5 Reveals a Conserved Methyltransferase-Polymerase Interface
Cited by: 187
Author(s): Guangquan Lu, Peng Gong
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1003673

Crystal Structure of the Gamma-2 Herpesvirus LANA DNA Binding Domain Identifies Charged Surface Residues Which Impact Viral Latency
Cited by: 29
Author(s): Bruno E. Correia, Sofia Cerqueira, Chantal Beauchemin, Marta Pires de Miranda, Shijun Li, Rajesh Ponnusamy, Lénia Rodrigues, Thomas R. Schneider, Maria Arménia Carrondo, Kenneth M. Kaye, J. Pedro Simas, Colin E. McVey
Software Mentions: 2
Published: about 11 years ago

10.3390/biology2041296

Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust
Cited by: 3
Author(s): Allen Holder, Jacqueline C. Simon, Jonathon Strauser, Jonathan Taylor, Yosi Shibberu
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.ppat.1005104

Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity
Cited by: 22
Author(s): Michael H. C. Buch, A. Manuel Liaci, Samantha D. O’Hara, Robert L. Garcea, Ursula Neu, Thilo Stehle
Software Mentions: 2
Published: about 9 years ago

10.3390/md15120366

Computer-Aided Drug Design Applied to Marine Drug Discovery: Meridianins as Alzheimer’s Disease Therapeutic Agents
Cited by: 39
Author(s): Laura Llorach-Parés, Alfons Nonell-Canals, Melchor Sánchez-Martínez, Conxita Àvila
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pcbi.1003007

Cleavage Entropy as Quantitative Measure of Protease Specificity
Cited by: 50
Author(s): Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Michael A. Margreiter, Gudrun M. Spitzer, Hannes G. Wallnoefer, Klaus R. Liedl
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1006935

Structural basis for recognition of the central conserved region of RSV G by neutralizing human antibodies
Cited by: 45
Author(s): Harrison G. Jones, Tina Ritschel, Gabriel Pascual, Just P. J. Brakenhoff, Elissa Keogh, Polina Furmanova-Hollenstein, Ellen Lanckacker, Jehangir S. Wadia, M.S.A. Gilman, R. Anthony Williamson, Dirk Roymans, Angélique B. van ’t Wout, Johannes P. M. Langedijk, Jason S. McLellan
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-017-01989-6

Structural studies of the periplasmic portion of the diguanylate cyclase CdgH from Vibrio cholerae
Cited by: 8
Author(s): Min Xu, Yizhi Wang, Xiu‐An Yang, Tao Jiang, Wei Xie
Software Mentions: 2
Published: over 7 years ago

10.3390/life10070109

Optimization of Molecular Dynamics Simulations of c-MYC1-88—An Intrinsically Disordered System
Cited by: 8
Author(s): Sandra S. Sullivan, Robert O. J. Weinzierl
Software Mentions: 2
Published: over 4 years ago

10.3390/vaccines8020288

Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach
Cited by: 50
Author(s): Muhammad Tahir ul Qamar, Zeeshan Shokat, Iqra Muneer, Usman Ali Ashfaq, Hamna Javed, Farooq Anwar, Amna Bari, Barira Zahid, Nazamid Saari
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.ppat.1003078

The GM2 Glycan Serves as a Functional Coreceptor for Serotype 1 Reovirus
Cited by: 95
Author(s): Kerstin Reiß, Jennifer Stencel, Yan Liu, Bärbel S. Blaum, Dirk M. Reiter, Ten Feizi, Terence S. Dermody, Thilo Stehle
Software Mentions: 2
Published: almost 12 years ago

10.1093/ve/veab061

Adaptation of the endemic coronaviruses HCoV-OC43 and HCoV-229E to the human host
Cited by: 10
Author(s): Diego Forni, Rachele Cagliani, Federica Arrigoni, Martino Benvenuti, Alessandra Mozzi, Diego Forni, Mario Clerici, Luca De Gioia, Manuela Sironi
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.ppat.1002832

The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors
Cited by: 179
Author(s): Keith P. Romano, Akbar Ali, Cihan Aydın, Djadé I. Soumana, Ayşegül Özen, Laura M. Deveau, C. N. Silver, Hong Cao, Alicia Newton, Christos J. Petropoulos, Wei Huang, Celia A. Schiffer
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.ppat.1002112

A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors
Cited by: 78
Author(s): Tasia M. Pyburn, Barbara A. Bensing, Yan Q. Xiong, Bruce J. Melancon, Thomas Tomasiak, Nicholas J Ward, Victoria Yankovskaya, Kevin Michael Oliver, Gary Cecchini, Gary A. Sulikowski, Matthew J. Tyska, Paul M. Sullam, T.M. Iverson
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.ppat.1002859

Structural Bases of Coronavirus Attachment to Host Aminopeptidase N and Its Inhibition by Neutralizing Antibodies
Cited by: 156
Author(s): Juan Reguera, César Santiago, Gaurav Mudgal, Desiderio Ordoño, Luis Enjuanes, José M. Casasnovas
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.ppat.1003202

A gp41 MPER-specific Llama VHH Requires a Hydrophobic CDR3 for Neutralization but not for Antigen Recognition
Cited by: 62
Author(s): D. Lutje Hulsik, Yingying Lin, Nika M. Strokappe, Simone Battella, Mohamed El Khattabi, Laura E. McCoy, C. Sabin, Andreas Hinz, M. Benjamin Hock, Pauline Machebœuf, Alexandre M. J. J. Bonvin, Johannes P. M. Langedijk, David A. Davis, Anna Forsman Quigley, Marlén M. I. Aasa-Chapman, Michael S. Seaman, Alejandra Ramos, Pascal Poignard, Adrien Favier, Jean-Pierre Simorre, Robin A. Weiss, C. Theo Verrips, Winfríed Weissenhorn, Lucy Rutten
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1000147

The Cysteine-Rich Interdomain Region from the Highly Variable Plasmodium falciparum Erythrocyte Membrane Protein-1 Exhibits a Conserved Structure
Cited by: 50
Author(s): Max M. Klein, Apostolos G. Gittis, Hua-Poo Su, Morris O. Makobongo, Jaime M. Moore, Sanjay Singh, Louis H. Miller, David N. Garboczi
Software Mentions: 2
Published: about 16 years ago

10.1016/j.bbabio.2015.07.002

Calcium-induced conformational changes in the regulatory domain of the human mitochondrial ATP-Mg/Pi carrier
Cited by: 34
Author(s): Steven P. D. Harborne, Jonathan J. Ruprecht, Edmund R. S. Kunji
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pcbi.1003022

Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure
Cited by: 11
Author(s): Xin Wan, Yue Ma, Christopher L. McClendon, Lily Huang, Niu Huang
Software Mentions: 2
Published: over 11 years ago

Projects: pypi: PyMOL

Papers Mentioning PyMOL 8,266