Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: PyMOL

https://packages.ecosyste.ms/registries/pypi.org/packages/PyMOL


1 version
Latest release: over 1 year ago
5 dependent packages

Papers Mentioning PyMOL 8,266

10.1107/S2053230X17001376
Crystal structure of the type IV secretion system component CagX fromHelicobacter pylori
Cited by: 7
Author(s): Jin Zhang, Fan Fei, Yunmeng Zhao, Lifang Sun, Yadan Liu, Ronan Keegan, Michail N. Isupov, Yunkun Wu
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12900-015-0037-1
Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase
Cited by: 8
Author(s): Norbert Schormann, Surajit Banerjee, Robert P. Ricciardi, Debasish Chattopadhyay
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0050769
Using RosettaLigand for Small Molecule Docking into Comparative Models
Cited by: 38
Author(s): Kristian Kaufmann, Jens Meiler
Software Mentions: 2
Published: about 12 years ago
10.1107/S1399004714019725
Structural characterization of the virulence factor nuclease A from<i>Streptococcus agalactiae</i>
Cited by: 7
Author(s): A.F. Moon, Philippe Gaudu, Lars C. Pedersen
Software Mentions: 2
Published: over 10 years ago
10.1107/S2053230X20006172
Enhanced X-ray diffraction of <i>in vivo</i>-grown μNS crystals by viscous jets at XFELs
Cited by: 5
Author(s): Nirupa Nagaratnam, Yanyang Tang, Sabine Botha, Justin M. Saul, Chufeng Li, Hao Hu, Sahba Zaare, Mark S. Hunter, David Lowry, Uwe Weierstall, Nadia A. Zatsepin, John C. H. Spence, Ji Qiu, Joshua LaBaer, Petra Fromme, José M. Martín-García
Software Mentions: 2
Published: over 4 years ago
10.1186/1472-6807-10-34
Prediction and analysis of the modular structure of cytochrome P450 monooxygenases
Cited by: 94
Author(s): Demet Sirim, Michael Widmann, Florian Wagner, Jürgen Pleiss
Software Mentions: 2
Published: over 14 years ago
10.1371/journal.pone.0245358
Insights into structure and dynamics of extracellular domain of Toll-like receptor 5 in Cirrhinus mrigala (mrigala): A molecular dynamics simulation approach
Cited by: 8
Author(s): Ajaya Kumar Rout, Varsha Acharya, Diptimayee Maharana, Budheswar Dehury, Sheela Rani Udgata, Rajkumar Jena, Bhaskar Behera, Pranaya Kumar Parida, Bijay Kumar Behera
Software Mentions: 2
Published: about 4 years ago
10.1073/pnas.1901318116
Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing
Cited by: 53
Author(s): Guido A. Stoll, Shun-ichiro Oda, Zheng-Shan Chong, Myeong-Hee Yu, Stephen H. McLaughlin, Yorgo Modis
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0209420
Deciphering the ATP-binding mechanism(s) in NLRP-NACHT 3D models using structural bioinformatics approaches
Cited by: 22
Author(s): Jitendra Maharana, Debashis Panda, Sachinandan De
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0115409
Characterization of M. tuberculosis SerB2, an Essential HAD-Family Phosphatase, Reveals Novel Properties
Cited by: 12
Author(s): Gaya P. Yadav, Sonal Shree, Ruchi Maurya, Niyati Rai, Diwakar Singh, Kirti Srivastava, Ravishankar Ramachandran
Software Mentions: 2
Published: about 10 years ago
10.1186/s12900-016-0064-6
Conservation of the C-type lectin fold for accommodating massive sequence variation in archaeal diversity-generating retroelements
Cited by: 15
Author(s): Sumit Handa, Blair G. Paul, Jeffery F. Miller, David L. Valentine, Partho Ghosh
Software Mentions: 2
Published: over 8 years ago
10.1107/S2059798319009574
Biochemical and structural explorations of α-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction
Cited by: 4
Author(s): Hsien‐Wei Yeh, Kuan Hung Lin, S.Y. Lyu, Yi Shan Li, Chun Man Huang, Yung Lin Wang, Hao Wei Shih, N.S. Hsu, Chang Jer Wu, Tsung Lin Li
Software Mentions: 2
Published: over 5 years ago
10.1073/pnas.2014896117
The SERCA residue Glu340 mediates interdomain communication that guides Ca <sup>2+</sup> transport
Cited by: 11
Author(s): Maxwell M. G. Geurts, Johannes Clausen, Bertrand Arnou, Cédric Montigny, Guillaume Lenoir, Robin A. Corey, Christine Jaxel, Jesper Møller, Poul Nissen, Jens Peter Andersen, Marc le Maire, Maike Bublitz
Software Mentions: 2
Published: about 4 years ago
10.1073/pnas.2021785118
Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein
Cited by: 179
Author(s): Thomas G Flower, Cosmo Z. Buffalo, Richard M. Hooy, Marc Allaire, Xuefeng Ren, James H. Hurley
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0122512
Crystal Structure of a Two-Subunit TrkA Octameric Gating Ring Assembly
Cited by: 2
Author(s): Marc C. Deller, Hope A. Johnson, Mitchell D. Miller, Glen Spraggon, Marc‐André Elsliger, Ian A. Wilson, Scott A. Lesley
Software Mentions: 2
Published: almost 10 years ago
10.1371/journal.pone.0052066
Structural and Functional Insights into (S)-Ureidoglycolate Dehydrogenase, a Metabolic Branch Point Enzyme in Nitrogen Utilization
Cited by: 4
Author(s): Myungil Kim, Inchul Shin, Suhee Cho, Jee Hyun Lee, Sangkee Rhee
Software Mentions: 2
Published: about 12 years ago
10.1007/s13238-017-0405-7
The binding of a monoclonal antibody to the apical region of SCARB2 blocks EV71 infection
Cited by: 17
Author(s): Xuyuan Zhang, Yang Pan, Nan Wang, Jialong Zhang, Jingyun Li, Hao Guo, Xiangyun Yin, Zihe Rao, Xiangxi Wang, Liguo Zhang
Software Mentions: 2
Published: almost 8 years ago
10.1007/s13238-018-0526-7
Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate
Cited by: 59
Author(s): Danni Zhou, Xing Zhu, Sanduo Zheng, Dan Tan, Meng‐Qiu Dong, Keqiong Ye
Software Mentions: 2
Published: almost 7 years ago
10.1107/S0907444913001479
Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data
Cited by: 79
Author(s): Qun Li, Qinglian Liu, Wayne A. Hendrickson
Software Mentions: 2
Published: over 11 years ago
10.1002/pro.2456
The crystal structure of NS5A domain 1 from genotype 1a reveals new clues to the mechanism of action for dimeric HCV inhibitors
Cited by: 91
Author(s): Sebastian Lambert, David R. Langley, James A. Garnett, Richard Angell, Katy Hedgethorne, Nicholas A. Meanwell, Stephen Matthews
Software Mentions: 2
Published: almost 11 years ago
10.1002/pro.3779
ConSurf‐DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins
Cited by: 74
Author(s): Adi Ben Chorin, Gal Masrati, Amit Kessel, Aya Narunsky, Josef Sprinzak, Shlomtzion Lahav, Haim Ashkenazy, Nir Ben‐Tal
Software Mentions: 2
Published: about 5 years ago
10.1002/pro.3732
Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations
Cited by: 17
Author(s): Ji Young Lee, James Krieger, Hongchun Li, İvet Bahar
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0097015
Structural Studies of an Anti-Inflammatory Lectin from Canavalia boliviana Seeds in Complex with Dimannosides
Cited by: 22
Author(s): G.A. Bezerra, Roland Viertlmayr, Tales Rocha de Moura, P. Delatorre, B.A.M. Rocha, Kyria S. Nascimento, Jozi Godoy Figueiredo, Ingrid Gonçalves Bezerra, C.S. Teixeira, Rafael Conceição Simões, Celso Shiniti Nagano, Nylane Maria Nunes de Alencar, Karl Gruber, Benildo S. Cavada
Software Mentions: 2
Published: over 10 years ago
10.1186/1472-6807-7-45
Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly
Cited by: 35
Author(s): Norbert Schormann, Alexei Grigorian, Alexandra B. Samal, Krishnan Raman, Lawrence J. DeLucas, Debasish Chattopadhyay
Software Mentions: 2
Published: over 17 years ago
10.1128/AAC.00123-20
Structure and Molecular Recognition Mechanism of IMP-13 Metallo-β-Lactamase
Cited by: 8
Author(s): Charlotte A Softley, Krzysztof Żak, Mark J. Bostock, Roberto Fino, Richard Xu Zhou, Marta Kolonko, Ramona Mejdi-Nitiu, Hannelore Meyer, Michael Sattler, Grzegorz M. Popowicz
Software Mentions: 2
Published: almost 5 years ago
10.1002/prot.26018
<scp>PDB‐tools</scp> web: A user‐friendly interface for the manipulation of <scp>PDB</scp> files
Cited by: 12
Author(s): Brian Jiménez‐García, João M.C. Teixeira, Mikaël Trellet, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin
Software Mentions: 2
Published: over 4 years ago
10.1107/S2059798315021683
<i>In meso in situ</i>serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures
Cited by: 89
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Nicole Howe, Lutz Vogeley, Xiangyu Liu, Rangana Warshamanage, T. Weinert, Ezequiel Panepucci, Brian K. Kobilka, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 2
Published: about 9 years ago
10.1038/srep19501
Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase–an Essential Enzyme of the Polyamine Metabolism
Cited by: 17
Author(s): Sebastian Krossa, Annette Faust, Dietrich Ober, Axel J. Scheidig
Software Mentions: 2
Published: about 9 years ago
10.1107/S0907444911014302
Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain
Cited by: 7
Author(s): Gretchen Meinke, Paul J. Phelan, Amélie Fradet-Turcotte, Jacques Archambault, Peter A. Bullock
Software Mentions: 2
Published: almost 14 years ago
10.1038/srep19981
Structural and functional attributes of malaria parasite diadenosine tetraphosphate hydrolase
Cited by: 12
Author(s): Amit Sharma, Manickam Yogavel
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.pone.0041710
Predicting HLA Class I Non-Permissive Amino Acid Residues Substitutions
Cited by: 21
Author(s): T.A. Binkowski, Susana R. Marino, A. Joachimiak
Software Mentions: 2
Published: over 12 years ago
10.1186/s12900-014-0024-y
Structural insights into Escherichia coli polymyxin B resistance protein D with X-ray crystallography and small-angle X-ray scattering
Cited by: 9
Author(s): Hang-Hyun Jo, Eui Young Jeong, Jinseong Jeon, Changill Ban
Software Mentions: 2
Published: about 10 years ago
10.1089/ars.2017.7104
Inhibition of Diverse DsbA Enzymes in Multi-DsbA Encoding Pathogens
Cited by: 33
Author(s): Makrina Totsika, Dimitrios Vagenas, Jason J. Paxman, Geqing Wang, Rabeb Dhouib, Pooja Sharma, Jennifer L. Martin, M.J. Scanlon, Begoña Heras
Software Mentions: 2
Published: over 6 years ago
10.1186/s12900-014-0025-x
In vitro histone lysine methylation by NSD1, NSD2/MMSET/WHSC1 and NSD3/WHSC1L
Cited by: 33
Author(s): Masaki Morishita, Damiaan E. H. F. Mevius, Eric di Luccio
Software Mentions: 2
Published: about 10 years ago
10.3390/antiox10020152
Function and Regulation of Chloroplast Peroxiredoxin IIE
Cited by: 10
Author(s): Anna Dreyer, Patrick Treffon, Daniel Basiry, Anna Maria Józefowicz, Andrea Matros, Hans‐Peter Mock, Karl‐Josef Dietz
Software Mentions: 2
Published: about 4 years ago
10.1038/srep29097
Glycogen synthase kinase 3β suppresses polyglutamine aggregation by inhibiting Vaccinia-related kinase 2 activity
Cited by: 12
Author(s): Eun‐Ju Lee, Hye Guk Ryu, Sangjune Kim, Dohyun Lee, Young‐Hun Jeong, Kyong‐Tai Kim
Software Mentions: 2
Published: over 8 years ago
10.1107/S2059798316003065
A generic protocol for protein crystal dehydration using the HC1b humidity controller
Cited by: 14
Author(s): C.M.C. Lobley, James Sandy, Juan Sánchez-Weatherby, Marco Mazzorana, T. Krojer, Radosław P. Nowak, Thomas Sørensen
Software Mentions: 2
Published: almost 9 years ago
10.1186/1472-6807-7-34
The NMR structure of the murine DLC2 SAM domain reveals a variant fold that is similar to a four-helix bundle
Cited by: 17
Author(s): Janice Kwan, Logan W. Donaldson
Software Mentions: 2
Published: about 18 years ago
10.3390/antiox7120171
Crystal Structure of Chloroplastic Thioredoxin f2 from Chlamydomonas reinhardtii Reveals Distinct Surface Properties
Cited by: 16
Author(s): Stéphane D. Lemaire, Daniele Tedesco, Pierre Crozet, Laure Michelet, Simona Fermani, Mirko Zaffagnini, Julien Henri
Software Mentions: 2
Published: about 6 years ago
10.1186/1472-6807-14-17
Characterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3
Cited by: 36
Author(s): Catherine Leettola, Mary Jane Knight, Duilio Cascio, Sigrid Hoffman, James U. Bowie
Software Mentions: 2
Published: over 10 years ago
10.3390/antiox8080240
Phlorotannins with Potential Anti-tyrosinase and Antioxidant Activity Isolated from the Marine Seaweed Ecklonia stolonifera
Cited by: 55
Author(s): Bandana Manandhar, Aditi Wagle, Su Hui Seong, Pradeep Paudel, Hyeung‐Rak Kim, Hyun Ah Jung, Jae Sue Choi
Software Mentions: 2
Published: over 5 years ago
10.1038/srep32481
On the saliva proteome of the Eastern European house mouse (Mus musculus musculus) focusing on sexual signalling and immunity
Cited by: 28
Author(s): Pavel Stopka, Barbora Kuntová, Petr Klempt, Leona Havrdová, Martina Černá, Romana Stopková
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0069833
An Activating Mutation Reveals a Second Binding Mode of the Integrin α2 I Domain to the GFOGER Motif in Collagens
Cited by: 29
Author(s): Federico Carafoli, Samir Hamaia, Dominique Bihan, Erhard Hohenester, Richard W. Farndale
Software Mentions: 2
Published: over 11 years ago
10.1186/1472-6807-7-10
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1
Cited by: 70
Author(s): D.J. Ferraro, Eric N. Brown, Chung Huang Yu, Rebecca E. Parales, David T. Gibson, S. Ramaswamy
Software Mentions: 2
Published: almost 18 years ago
10.3390/antiox9020180
Pharmacological Targets of Kaempferol Within Inflammatory Pathways—A Hint Towards the Central Role of Tryptophan Metabolism
Cited by: 15
Author(s): Stefanie Hofer, Simon Geisler, Rebecca Lisandrelli, Huu Tung Nguyen, Markus Ganzera, Harald Schennach, Dietmar Fuchs, Julian E. Fuchs, Johanna M. Gostner, Katharina Kurz
Software Mentions: 2
Published: almost 5 years ago
10.1107/S2053230X18012992
Crystal structures and kinetics of<i>N</i>-acetylneuraminate lyase from<i>Fusobacterium nucleatum</i>
Cited by: 5
Author(s): J. Kumar, Harshvardhan Rao, Vinod Nayak, S. Ramaswamy
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0017624
Structure and Function of the First Full-Length Murein Peptide Ligase (Mpl) Cell Wall Recycling Protein
Cited by: 24
Author(s): Debanu Das, Mireille Hervé, Julie Feuerhelm, Carol L. Farr, Hsiu‐Ju Chiu, Marc‐André Elsliger, Mark W. Knuth, Heath E. Klock, Mitchell D. Miller, Adam Godzik, Scott A. Lesley, Ashley M. Deacon, Dominique Mengin‐Lecreulx, Ian A. Wilson
Software Mentions: 2
Published: almost 14 years ago
10.1038/srep37284
Genetic Epidemiology of Glucose-6-Phosphate Dehydrogenase Deficiency in the Arab World
Cited by: 51
Author(s): George Priya Doss C, Dima R. Alasmar, Reem I. Bux, P. Sneha, Fadheela Dad Bakhsh, Iman K. Al-Azwani, Rajaa El Bekay, Hatem Zayed
Software Mentions: 2
Published: over 8 years ago
10.1186/1472-6807-7-38
Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate dehydrogenase Gnd1
Cited by: 32
Author(s): Weiwei He, Yi Wang, Wei Liu, Cong‐Zhao Zhou
Software Mentions: 2
Published: over 17 years ago
10.1038/srep38137
Engineering of a thermostable esterase Est816 to improve its quorum-quenching activity and the underlying structural basis
Cited by: 11
Author(s): Xiwen Liu, Liping Cao, Xiaoran Fan, Yuhuan Liu, Wei Xie
Software Mentions: 2
Published: about 8 years ago
10.1107/S2053230X14017725
The structure of alanine racemase from<i>Acinetobacter baumannii</i>
Cited by: 4
Author(s): Emily Davis, Emma Rose Scaletti, Helen K. Opel-Reading, Yoshio Nakatani, Kurt L. Krause
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0196642
Structure of frequency-interacting RNA helicase from Neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance
Cited by: 9
Author(s): Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean Johnson
Software Mentions: 2
Published: almost 7 years ago
10.3390/antiox8010010
Structural and Biochemical Insights into the Reactivity of Thioredoxin h1 from Chlamydomonas reinhardtii
Cited by: 14
Author(s): Christophe Marchand, Simona Fermani, Jacopo Rossi, Libero Gurrieri, Daniele Tedesco, Julien Henri, Francesca Sparla, Paolo Bernardo Trost, Stéphane D. Lemaire, Mirko Zaffagnini
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0140984
Improving the pH-stability of Versatile Peroxidase by Comparative Structural Analysis with a Naturally-Stable Manganese Peroxidase
Cited by: 40
Author(s): Verónica Sáez-Jiménez, Elena Fernández‐Fueyo, F.J. Medrano, Antonio Romero, Ángel T. Martínez, Francisco J. Ruíz-Dueñas
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0103099
In Silico Modeling of Human α2C-Adrenoreceptor Interaction with Filamin-2
Cited by: 11
Author(s): Marcin Pawłowski, Saras Saraswathi, Hanaa K. B. Motawea, Maqsood A. Chotani, Andrzej Kloczkowski
Software Mentions: 2
Published: over 10 years ago
10.1016/j.cell.2020.01.010
Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody
Cited by: 89
Author(s): Philipp Schommers, Henning Gruell, Morgan E. Abernathy, My-Kim Tran, Adam S. Dingens, Harry B. Gristick, Christopher O. Barnes, Till Schoofs, Maike Schlotz, Kanika Vanshylla, Christoph Kreer, Daniela Weiland, Udo Holtick, Christof Scheid, Markus M. Valter, Marit J. van Gils, Rogier W. Sanders, Jörg Janne Vehreschild, Oliver A. Cornely, Clara Lehmann, Gerd Fätkenheuer, Michael S. Seaman, Jesse D Bloom, Pamela J. Björkman, Florian Klein
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0235990
Drug targeting CYP2E1 for the treatment of early-stage alcoholic steatohepatitis
Cited by: 18
Author(s): Torsten Diesinger, Vyacheslav Buko, Alfred Lautwein, Radovan Dvorský, Elena Belonovskaya, Oksana Lukivskaya, Elena Naruta, Siarhei Kirko, В. П. Андреев, Dominik Buckert, Sebastian Bergler, Christian Renz, Edith Schneider, Florian Kuchenbauer, Mukesh Kumar, Çagatay Güneş, Berthold Büchele, Thomas Simmet, Dieter Müller‐Enoch, Thomas Wirth, Thomas Haehner
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0042473
Crystal Structures of the Network-Forming Short-Arm Tips of the Laminin β1 and γ1 Chains
Cited by: 51
Author(s): Federico Carafoli, Sadaf-Ahmahni Hussain, Erhard Hohenester
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0130888
Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies
Cited by: 16
Author(s): Shannon E. Hill, Rebecca K. Donegan, Elaine Nguyen, Tanay M. Desai, Raquel L. Lieberman
Software Mentions: 2
Published: over 9 years ago
10.1186/1472-6807-12-7
Crystal structure of a new benzoic acid inhibitor of influenza neuraminidase bound with a new tilt induced by overpacking subsite C6
Cited by: 10
Author(s): Lalitha Venkatramani, Eric S. Johnson, Gundurao Kolavi, Gillian M. Air, Wayne J. Brouillette, Blaine H. M. Mooers
Software Mentions: 2
Published: almost 13 years ago
10.3390/antiox10071112
Activation of Adenosine A1 Receptor in Ischemic Stroke: Neuroprotection by Tetrahydroxy Stilbene Glycoside as an Agonist
Cited by: 10
Author(s): Ling-Yu Ruan, Guanghui Li, Wenlong Zhao, Huihui Meng, Qi Zheng, Junsong Wang
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-018-33366-2
Increasing the distance between two monomers of topoisomerase IIβ under the action of antitumor agent 4β-sulfur-(benzimidazole) 4′-demethylepipodophyllotoxin
Cited by: 2
Author(s): Lin-Yang Sun, Liwen Zhu, Ya‐Jie Tang
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0201556
Deciphering the targets of retroviral protease inhibitors in Plasmodium berghei
Cited by: 16
Author(s): Noah Machuki Onchieku, Reagan M. Mogire, Loise Ndung’u, Peter Mwitari, Francis Kimani, Damaris Matoke-Muhia, Daniel Kiboi, Gabriel Magoma
Software Mentions: 2
Published: over 6 years ago
10.1107/S0907444911007888
Structure of HLA-A*0301 in complex with a peptide of proteolipid protein: insights into the role of HLA-A alleles in susceptibility to multiple sclerosis
Cited by: 27
Author(s): Róisín M. McMahon, Lone Smidstrup Friis, Christian Siebold, Manuel A. Friese, Lars Fugger, E Y Jones
Software Mentions: 2
Published: almost 14 years ago
10.1371/journal.pone.0024227
Get Phases from Arsenic Anomalous Scattering: de novo SAD Phasing of Two Protein Structures Crystallized in Cacodylate Buffer
Cited by: 22
Author(s): Xiang Liu, Heng Zhang, Wang Xiao-jun, Lanfen Li, Xiao‐Dong Su
Software Mentions: 2
Published: over 13 years ago
10.1038/s41598-018-36589-5
Kinetic and thermodynamic effects of phosphorylation on p53 binding to MDM2
Cited by: 23
Author(s): Shilpa Yadahalli, José L. Neira, Christopher M. Johnson, Yaw Sing Tan, Pamela J. E. Rowling, Anasuya Chattopadhyay, Chandra Verma, Laura S. Itzhaki
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0237999
Spectrum of clinical features and genetic variants in mevalonate kinase (MVK) gene of South Indian families suffering from Hyperimmunoglobulin D Syndrome
Cited by: 11
Author(s): Geeta Govindaraj, Abhinav Jain, Geetha Peethambaran, Rahul C. Bhoyar, Shamsudheen Karuthedath Vellarikkal, Arvind Ganapati, Pulukool Sandhya, Athulya Edavazhippurath, Dhananjayan Dhanasooraj, Jayakrishnan Machinary Puthenpurayil, Krishnan Chakkiyar, Anushree Mishra, Arushi Batra, Anu Punnen, Sathish Kumar, Sridhar Sivasubbu
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-018-37806-x
Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis
Cited by: 8
Author(s): Noriyuki Ogawa, Takehide Kimura, Fumi Umehara, Yuki Katayama, Go Nagai, Keiko Suzuki, Kazuo Aisaka, Yukie Maruyama, Takafumi Itoh, Wataru Hashimoto, Kousaku Murata, Michio Ichimura
Software Mentions: 2
Published: about 6 years ago
10.1186/1472-6750-11-85
Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis)
Cited by: 36
Author(s): Gustavo R. Oliveira, Maria C. M. Silva, Wagner Alexandre Lucena, Erich Yukio Tempel Nakasu, Alexandre Augusto Pereira Firmino, Magda Aparecida Beneventi, Djair S.L. Souza, José Erick Galindo Gomes, José Dijair Antonino, Daniel J. Rigden, H. B. Ramos, Carlos Ricardo Soccol, Maria Fátima Grossi‐de‐Sá
Software Mentions: 2
Published: over 13 years ago
10.1038/s41598-018-36950-8
Web-based display of protein surface and pH-dependent properties for assessing the developability of biotherapeutics
Cited by: 59
Author(s): Max Hebditch, Jim Warwicker
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0215555
Heavy-atom labeling of RNA by PLOR for de novo crystallographic phasing
Cited by: 6
Author(s): Jason R. Stagno, Ping Yü, Marcin Dyba, Yun‐Xing Wang, Yu Liu
Software Mentions: 2
Published: almost 6 years ago
10.1186/1472-6807-7-24
A previously unobserved conformation for the human Pex5p receptor suggests roles for intrinsic flexibility and rigid domain motions in ligand binding
Cited by: 24
Author(s): Will A. Stanley, Niko V. Pursiainen, Elspeth F. Garman, André H. Juffer, Matthias Wilmanns, Petri Kursula
Software Mentions: 2
Published: almost 18 years ago
10.1371/journal.pone.0052642
Specificity and Versatility of Substrate Binding Sites in Four Catalytic Domains of Human N-Terminal Acetyltransferases
Cited by: 6
Author(s): Cédric Grauffel, Angèle Abboud, Glen Liszczak, Ronen Marmorstein, Thomas Arnesen, Nathalie Reuter
Software Mentions: 2
Published: about 12 years ago
10.1186/s12918-017-0427-z
A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance
Cited by: 17
Author(s): Deepanwita Banerjee, Dharmeshkumar Parmar, Nivedita Bhattacharya, Avinash D. Ghanate, Venkateswarlu Panchagnula, Anu Raghunathan
Software Mentions: 2
Published: almost 8 years ago
10.1186/s13628-018-0048-y
Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments
Cited by: 6
Author(s): Aslı Yıldırım, Nathalie Brenner, Robert Sutherland, Michael Feig
Software Mentions: 2
Published: about 6 years ago
10.1186/s12917-019-2161-9
Bioinformatics analysis of capsid protein of different subtypes rabbit hemorrhagic disease virus
Cited by: 1
Author(s): Ruibin Qi, Jie Zhu, Qiuhong Miao, Aoxing Tang, De-Li Dong, Xiaoxue Wang, Guangqing Liu
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0224753
Streptococcal phosphotransferase system imports unsaturated hyaluronan disaccharide derived from host extracellular matrices
Cited by: 8
Author(s): Shigetoshi Oiki, Yusuke Nakamichi, Yukie Maruyama, Bunzo Mikami, Kousaku Murata, Wataru Hashimoto
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0216979
Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis
Cited by: 2
Author(s): Ke Shi, Chong-Min Kyung, Kelly G. Aukema, Thomas Lee, Asim K. Bera, Jennifer L. Seffernick, Lawrence P. Wackett, Hideki Aihara
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0018413
Co-Crystal Structures of PKG Iβ (92–227) with cGMP and cAMP Reveal the Molecular Details of Cyclic-Nucleotide Binding
Cited by: 51
Author(s): Jeong Joo Kim, Darren E. Casteel, Gary B. Huang, Tai Hun Kwon, Ronnie Kuo Ren, Peter H. Zwart, Jeffrey J. Headd, Nicholas G. Brown, Dar Chone Chow, Timothy Palzkill, Choel Kim
Software Mentions: 2
Published: almost 14 years ago
10.1371/journal.pone.0195355
Solution scattering study of the Bacillus subtilis PgdS enzyme involved in poly-γ-glutamic acids degradation
Cited by: 1
Author(s): Jumei Zeng, Yipeng Jin, Zhongchuan Liu
Software Mentions: 2
Published: almost 7 years ago
10.1128/AEM.00390-19
Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese Peroxidase <i>In Vitro</i>
Cited by: 18
Author(s): Peter L. Herzog, Leander Sützl, Beate Eisenhut, Daniel Maresch, Dietmar Haltrich, Christian Obinger, Clemens K. Peterbauer
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-019-39214-1
Deferiprone: Pan-selective Histone Lysine Demethylase Inhibition Activity and Structure Activity Relationship Study
Cited by: 20
Author(s): Verjine Khodaverdian, Subhasish Tapadar, Ian A. Macdonald, Yuan Xu, Po Y. Ho, Allison Bridges, Pragya Rajpurohit, Bhakti A. Sanghani, Yuhong Fan, Muthusamy Thangaraju, Nathaniel A. Hathaway, Adegboyega K. Oyelere
Software Mentions: 2
Published: almost 6 years ago
10.1186/2046-1682-6-10
Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies
Cited by: 8
Author(s): Anke Steinbach, Christine K. Maurer, Elisabeth Weidel, Claudia Henn, Christian Brengel, Rolf W. Hartmann, Matthias Negri
Software Mentions: 2
Published: over 11 years ago
10.1038/s41598-019-41300-3
An engineered GH1 β-glucosidase displays enhanced glucose tolerance and increased sugar release from lignocellulosic materials
Cited by: 33
Author(s): Clelton A. Santos, M.A.B. Morais, Oliver M. Terrett, Jan J. Lyczakowski, L.M. Zanphorlin, Jaire A. Ferreira-Filho, C.C.C. Tonoli, Mário Tyago Murakami, Paul Dupree, Anete Pereira de Souza
Software Mentions: 2
Published: almost 6 years ago
10.1107/S2053230X16007263
Crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from<i>Arabidopsis thaliana</i>
Cited by: 7
Author(s): Youhong Song, Hua Pu, Tianyue Jiang, Lixin Zhang, Ming Ouyang
Software Mentions: 2
Published: over 8 years ago
10.1038/s41598-019-42104-1
Identification of a Novel Anti-cancer Protein, FIP-bbo, from Botryobasidium botryosum and Protein Structure Analysis using Molecular Dynamic Simulation
Cited by: 9
Author(s): Ying Wang, Ying Gao, Rui Bai, Hong Yu Chen, Ying Wu, Jun Jun Shang, Da Peng Bao
Software Mentions: 2
Published: almost 6 years ago
10.1186/2046-1682-5-7
Arbitrary protein−protein docking targets biologically relevant interfaces
Cited by: 37
Author(s): Juliette Martin, Richard Lavery
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0203079
Fungicidal action of geraniol against Candida albicans is potentiated by abrogated CaCdr1p drug efflux and fluconazole synergism
Cited by: 53
Author(s): Shweta Singh, Zeeshan Fatima, Kamal Ahmad, Saif Hameed
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0077558
Isozyme-Specific Ligands for O-acetylserine sulfhydrylase, a Novel Antibiotic Target
Cited by: 44
Author(s): Francesca Spyrakis, Ratna Singh, Pietro Cozzini, Barbara Campanini, Enea Salsi, Paolo Felici, Samanta Raboni, Paolo Benedetti, Gabriele Cruciani, Glen E. Kellogg, Paul F. Cook, Andrea Mozzarelli
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0092996
Modular Hyperthermostable Bacterial Endo-β-1,4-Mannanase: Molecular Shape, Flexibility and Temperature-Dependent Conformational Changes
Cited by: 11
Author(s): Viviam M. da Silva, Francieli Colussi, Mário de Oliveira Neto, Antônio Sérgio Kimus Braz, Fábio M. Squina, Cristiano L. P. Oliveira, Wânius Garcia
Software Mentions: 2
Published: almost 11 years ago
10.1016/j.bbrep.2016.03.004
Molecular docking, a tool to determine interaction of CuO and TiO 2 nanoparticles with human serum albumin
Cited by: 18
Author(s): Sandesh Chibber, Irshad Ahmad
Software Mentions: 2
Published: over 8 years ago
10.1038/s41598-020-69637-0
Crystal structure of the Rab33B/Atg16L1 effector complex
Cited by: 8
Author(s): Janina Metje-Sprink, Johannes Groffmann, Piotr Neumann, Brigitte Barg-Kues, Ralf Ficner, Karin Kühnel, Amanda M. Schalk, Beyenech Binotti
Software Mentions: 2
Published: over 4 years ago
10.1016/j.bbrep.2021.100982
Repurposing of approved drugs with potential to interact with SARS-CoV-2 receptor
Cited by: 5
Author(s): Tamim Ahsan, Abu Ashfaqur Sajib
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-020-70680-0
Antibody-protein binding and conformational changes: identifying allosteric signalling pathways to engineer a better effector response
Cited by: 25
Author(s): Mohammed M. Al Qaraghuli, Karina Kubiak-Ossowska, Valerie A. Ferro, Paul A. Mulheran
Software Mentions: 2
Published: over 4 years ago
10.1107/S2059798319006831
Structural and functional characterization of CMP-<i>N</i>-acetylneuraminate synthetase from<i>Vibrio cholerae</i>
Cited by: 1
Author(s): Sucharita Bose, Debayan Purkait, Deepthi Joseph, Vinod Nayak, Ramaswamy Subramanian
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-020-72102-7
Automated AFM analysis of DNA bending reveals initial lesion sensing strategies of DNA glycosylases
Cited by: 7
Author(s): Disha Mohan Bangalore, Hannah S. Heil, Christian F. Mehringer, Lisa Hirsch, Katherina Hemmen, Katrin G. Heinze, Ingrid Teßmer
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-020-73483-5
Molecular dynamics of the histamine H3 membrane receptor reveals different mechanisms of GPCR signal transduction
Cited by: 3
Author(s): Leonardo David Herrera-Zúñiga, Liliana M. Moreno‐Vargas, Luck Ballaud, José Correa‐Basurto, Diego Prada‐Gracia, David Pastré, Patrick A. Curmi, Jean‐Michel Arrang, Rachid C. Maroun
Software Mentions: 2
Published: over 4 years ago
10.1042/BCJ20160806
<i>Neisseria meningitidis</i> factor H-binding protein bound to monoclonal antibody JAR5: implications for antibody synergy
Cited by: 18
Author(s): E. Malito, Paola Lo Surdo, Daniele Veggi, Laura Santini, Heather Stefek, Brunella Brunelli, Enrico Luzzi, Matthew J. Bottomley, Peter T. Beernink, María Scarselli
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0219436
Identification of lysine methylation in the core GTPase domain by GoMADScan
Cited by: 6
Author(s): Hirofumi Yoshino, Guowei Yin, Risa Karakida Kawaguchi, Konstantin Popov, Brenda Temple, Mika Sasaki, Satoshi Kofuji, Kara Wolfe, Kaori Kofuji, Kōichi Okumura, Jaskirat Randhawa, Akshiv Malhotra, Nazanin Majd, Yoshiki Ikeda, Hiroko Shimada, Emily Rose Kahoud, Sasson Haviv, Shigeki Iwase, John M. Asara, Sharon L. Campbell, Atsuo T. Sasaki
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0154190
X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1) Reveals Features of Its Chitin Binding Domain
Cited by: 32
Author(s): Firas Fadel, Yuguang Zhao, A. Cousido-Siah, Francesc Xavier Ruiz, A. Mitschler, A. Podjarny
Software Mentions: 2
Published: almost 9 years ago