pypi: PyMOL | Projects | Ecosyste.ms: Papers

10.3390/ijms22115896

Serotonin Promotes Serum Albumin Interaction with the Monomeric Amyloid β Peptide
Cited by: 9
Author(s): Ekaterina A. Litus, Alexei S. Kazakov, Evgenia I. Deryusheva, Ekaterina L. Nemashkalova, Marina P. Shevelyova, Aliya A. Nazipova, Maria E. Permyakova, Elena V Raznikova, Vladimir N. Uversky, Sergei E. Permyakov
Software Mentions: 2
Published: about 5 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: about 5 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: about 5 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 5 years ago

10.1186/1472-6807-11-12

Human Nek6 is a monomeric mostly globular kinase with an unfolded short N-terminal domain
Cited by: 21
Author(s): Gabriela Vaz Meirelles, Júlio C. Silva, Yuri de A Mendonça, Carlos H.I. Ramos, Íris L. Torriani, Jörg Kobarg
Software Mentions: 2
Published: over 15 years ago

10.3390/ijms22020650

Comparative Analysis of Transcriptome and sRNAs Expression Patterns in the Brachypodium distachyon—Magnaporthe oryzae Pathosystems
Cited by: 15
Author(s): Silvia Zanini, Ena Šečić, Tobias Busche, Matteo Galli, Ying Zheng, Jörn Kalinowski, Karl‐Heinz Kogel
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22042040

Accumulation of the Auxin Precursor Indole-3-Acetamide Curtails Growth through the Repression of Ribosome-Biogenesis and Development-Related Transcriptional Networks
Cited by: 6
Author(s): Beatriz Sánchez-Parra, Marta‐Marina Pérez‐Alonso, Paloma Ortiz‐García, José Moya-Cuevas, Mathias Hentrich, Stephan Pollmann
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22063219

Crystal Structure of a Phospholipase D from the Plant-Associated Bacteria Serratia plymuthica Strain AS9 Reveals a Unique Arrangement of Catalytic Pocket
Cited by: 7
Author(s): Fanghua Wang, Siyu Liu, Xuejing Mao, Ruiguo Cui, Bo Yang, Yonghua Wang
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21249422

A Novel Amino Acid Substitution, Fibrinogen Bβp.Pro234Leu, Associated with Hypofibrinogenemia Causing Impairment of Fibrinogen Assembly and Secretion
Cited by: 1
Author(s): Takahiro Kaido, Masahiro Yoda, Tomu Kamijo, Shinpei Arai, Chiaki Taira, Yumiko Higuchi, Nobuo Okumura
Software Mentions: 2
Published: over 5 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: almost 6 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: over 5 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: almost 6 years ago

10.7554/eLife.68829

Analysis of the PcrA-RNA polymerase complex reveals a helicase interaction motif and a role for PcrA/UvrD helicase in the suppression of R-loops
Cited by: 15
Author(s): Íñigo Urrutia-Irazábal, James R. Ault, Frank Sobott, Nigel J. Savery, Mark S. Dillingham
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms21165915

Biochemical Characterization and Crystal Structure of a Novel NAD+-Dependent Isocitrate Dehydrogenase from Phaeodactylum tricornutum
Cited by: 5
Author(s): Shiping Huang, Luchun Zhou, Bin Wen, Peng Wang
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms22010270

Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling
Cited by: 10
Author(s): Hisham Dokainish, Yuji Sugita
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.32866

Mfn2 ubiquitination by PINK1/parkin gates the p97-dependent release of ER from mitochondria to drive mitophagy
Cited by: 243
Author(s): Gian‐Luca McLelland, Thomas Goiran, Wei Yi, Geneviève Dorval, Carol X Chen, Nadine Lauinger, Andrea I Krahn, Sepideh Valimehr, Aleksandar Raković, Isabelle Rouiller, Thomas M. Durcan, Jean‐François Trempe, Edward A. Fon
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.17983

Structures of TorsinA and its disease-mutant complexed with an activator reveal the molecular basis for primary dystonia
Cited by: 53
Author(s): F. Esra Demircioglu, Brian A Sosa, Jessica R. Ingram, Hidde L. Ploegh, Thomas Schwartz
Software Mentions: 2
Published: almost 10 years ago

10.7554/eLife.48847

A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS
Cited by: 78
Author(s): Mary McMahon, Adrian Contreras, Mikael Holm, Tamayo Uechi, Craig M. Forester, Xiaming Pang, Cody B. Jackson, Meredith Calvert, Bin Chen, David A. Quigley, John M. Luk, R. K. Kelley, John D. Gordan, Ryan M. Gill, Scott C. Blanchard, Davide Ruggero
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.36340

Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2-d]pyrimidine non-nucleoside inhibitors
Cited by: 53
Author(s): Yang Yang, Dongwei Kang, Laura A. Nguyen, Z.B. Smithline, Christophe Pannecouque, Peng Zhan, Xinyong Liu, Thomas A. Steitz
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.32963

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima
Cited by: 31
Author(s): Ekaterina Morgunova, Yimeng Yin, Pratyush Kumar Das, Arttu Jolma, Fei Zhu, A. Popov, You Xu, Lennart Nilsson, Jussi Taipale
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0028218

Engineered Single-Domain Antibodies with High Protease Resistance and Thermal Stability
Cited by: 112
Author(s): Greg Hussack, Takashi Hirama, Wen Ding, Ross MacKenzie, Jamshid Tanha
Software Mentions: 2
Published: over 14 years ago

10.7554/eLife.03604

Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters
Cited by: 49
Author(s): Z.L. Johnson, Jun-Ho Lee, Kiyoun Lee, Minhee Lee, Deok-Ho Kwon, Jiyong Hong, Seok‐Yong Lee
Software Mentions: 2
Published: almost 12 years ago

10.7554/eLife.00482

Mechanism for priming DNA synthesis by yeast DNA Polymerase α
Cited by: 89
Author(s): Rajika L. Perera, Rubben Torella, Sebastian Klinge, M.L. Kilkenny, Joseph D. Maman, Luca Pellegrini
Software Mentions: 2
Published: over 13 years ago

10.7554/eLife.32893

IRS-1 acts as an endocytic regulator of IGF-I receptor to facilitate sustained IGF signaling
Cited by: 39
Author(s): Yoshimasa Yoneyama, Peter Lanzerstorfer, Hideaki Niwa, Takashi Umehara, Takashi Shibano, Shigeyuki Yokoyama, Kazuhiro Chida, Julian Weghuber, Fumihiko Hakuno, Shinichiro Takahashi
Software Mentions: 2
Published: about 8 years ago

10.3390/ijms22010370

Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types
Cited by: 8
Author(s): Joshua Yi Yeo, Darius Wen‐Shuo Koh, Ping Yap, Ghin-Ray Goh, Samuel Ken‐En Gan
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.3000277

Structural insights into histone chaperone Chz1-mediated H2A.Z recognition and histone replacement
Cited by: 17
Author(s): Yunyun Wang, Sheng Liu, Lu Sun, Ning Xu, Shan Shan, Fei Wu, Xiaoping Liang, Yingzi Huang, Ed Luk, Carl Wu, Zheng Zhou
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.38433

Structural relationship between the putative hair cell mechanotransduction channel TMC1 and TMEM16 proteins
Cited by: 80
Author(s): Ángela Ballesteros, Cristina Fenollar–Ferrer, Kenton J. Swartz
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.06547

ULK3 regulates cytokinetic abscission by phosphorylating ESCRT-III proteins
Cited by: 78
Author(s): Anna Caballe, Dawn M Wenzel, Monica Agromayor, Steven L. Alam, Jack J. Skalicky, Magdalena Kloc, Jeremy G. Carlton, Leticia Labrador, Wesley I. Sundquist, Juan Martín-Serrano
Software Mentions: 2
Published: about 11 years ago

10.7554/eLife.65903

The crystal structure of bromide-bound GtACR1 reveals a pre-activated state in the transmembrane anion tunnel
Cited by: 10
Author(s): Hai Li, Chia‐Ying Huang, Elena G. Govorunova, Oleg A. Sineshchekov, Adrian Yi, Kenneth J. Rothschild, Meitian Wang, Lei Zheng, John L. Spudich
Software Mentions: 2
Published: about 5 years ago

10.1007/s00894-016-2982-4

Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis
Cited by: 17
Author(s): Tomasz Makarewicz, Rajmund Kaźmierkiewicz
Software Mentions: 2
Published: about 10 years ago

10.1016/j.jmb.2009.10.010

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

10.1007/s00894-012-1563-4

Principal component and clustering analysis on molecular dynamics data of the ribosomal L11·23S subdomain
Cited by: 94
Author(s): Antje Wolf, Karl N. Kirschner
Software Mentions: 2
Published: almost 14 years ago

10.7554/eLife.56451

Characterization of the kinetic cycle of an ABC transporter by single-molecule and cryo-EM analyses
Cited by: 47
Author(s): Ling Wang, Z.L. Johnson, Mark Wasserman, Jesper Levring, Jue Chen, Shixin Liu
Software Mentions: 2
Published: about 6 years ago

10.1016/j.jmb.2013.10.024

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

10.1016/j.str.2019.10.012

Cryo-EM Structure of Nucleotide-Bound Tel1ATM Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations
Cited by: 27
Author(s): Luke A. Yates, Rhys M. Williams, Sarem Hailemariam, Rafael Ayala, Peter M. Burgers, Xiaodong Zhang
Software Mentions: 2
Published: over 6 years ago

10.1016/j.jmb.2013.03.019

Structure of the Tubulin/FtsZ-Like Protein TubZ from Pseudomonas Bacteriophage ΦKZ
Cited by: 30
Author(s): C.H.S. Aylett, Thierry Izoré, Linda Amos, Jan Löwe
Software Mentions: 2
Published: about 13 years ago

10.1016/j.str.2016.10.005

Functional Annotation of Ion Channel Structures by Molecular Simulation
Cited by: 60
Author(s): Jemma L. Trick, Sivapalan Chelvaniththilan, Gianni Klesse, Prafulla Aryal, E. Jayne Wallace, Stephen J. Tucker, Mark S. P. Sansom
Software Mentions: 2
Published: over 9 years ago

10.1016/j.str.2012.02.011

Structure of the Discoidin Domain Receptor 1 Extracellular Region Bound to an Inhibitory Fab Fragment Reveals Features Important for Signaling
Cited by: 78
Author(s): Federico Carafoli, Marie Cathrin Mayer, Kazushige Shiraishi, Mira Anguelova Pecheva, Lai Yi Chan, Ruodan Nan, Birgit Leitinger, Erhard Hohenester
Software Mentions: 2
Published: over 14 years ago

10.1016/j.str.2018.05.001

Structural Basis of Phosphatidic Acid Sensing by APH in Apicomplexan Parasites
Cited by: 22
Author(s): Nick Darvill, David Jean Dubois, Sarah L. Rouse, Pierre‐Mehdi Hammoudi, Thomas C. A. Blake, Stefi Benjamin, Bing Liu, Dominique Soldati‐Favre, Steve Matthews
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.jmb.2013.05.024

Characterization of 14-3-3-ζ Interactions with Integrin Tails
Cited by: 29
Author(s): Roman Bonet, Ioannis Vakonakis, Iain D. Campbell
Software Mentions: 2
Published: almost 13 years ago

10.7554/eLife.21600

Crenactin forms actin-like double helical filaments regulated by arcadin-2
Cited by: 31
Author(s): Thierry Izoré, Danguole Kureisaite-Ciziene, Stephen H. McLaughlin, Jan Löwe
Software Mentions: 2
Published: over 9 years ago

10.1016/j.str.2013.02.014

Structure of the Catalytic Region of DNA Ligase IV in Complex with an Artemis Fragment Sheds Light on Double-Strand Break Repair
Cited by: 58
Author(s): Takashi Ochi, Xiaorong Gu, Tom L. Blundell
Software Mentions: 2
Published: over 13 years ago

10.1063/1.4974176

Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites
Cited by: 21
Author(s): Nicholas M. Pearce, A.R. Bradley, T. Krojer, Brian D. Marsden, Charlotte M. Deane, Frank von Delft
Software Mentions: 2
Published: over 9 years ago

10.1016/j.str.2013.04.008

Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region
Cited by: 30
Author(s): James Stephenson, Haitao Li, Julia C. Kenyon, Martyn F. Symmons, David Klenerman, Andrew M. L. Lever
Software Mentions: 2
Published: about 13 years ago

10.1126/scisignal.abe1202

High-resolution structures of the SARS-CoV-2 2′- <i>O</i> -methyltransferase reveal strategies for structure-based inhibitor design
Cited by: 132
Author(s): Mónica Rosas‐Lemus, G. Minasov, L. Shuvalova, Nicole L. Inniss, O. Kiryukhina, J.S. Brunzelle, K.J.F. Satchell
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-96217-7

A multiscale approach for bridging the gap between potency, efficacy, and safety of small molecules directed at membrane proteins
Cited by: 7
Author(s): Rodrigo Aguayo‐Ortiz, Jeffery Creech, Eric N. Jiménez-Vázquez, Guadalupe Guerrero-Serna, Nulang Wang, A.M. Rocha, Todd J. Herron, L. Michel Espinoza-Fonseca
Software Mentions: 2
Published: almost 5 years ago

10.1155/2019/8605743

GC/MS Analysis of Fatty Acids on <i>Pliek U</i> Oil and Its Pharmacological Study by Molecular Docking to Filaggrin as a Drug Candidate in Atopic Dermatitis Treatment
Cited by: 33
Author(s): Nanda Earlia, Muslem, Rivansyah Suhendra, Mohamad Amin, Crs Prakoeswa, Khairan, Rinaldi Idroes
Software Mentions: 2
Published: over 6 years ago

10.1016/j.str.2013.05.001

Crystal Structures of Malonyl-Coenzyme A Decarboxylase Provide Insights into Its Catalytic Mechanism and Disease-Causing Mutations
Cited by: 18
Author(s): D. Sean Froese, F. Forouhar, Timothy H. Tran, M. Vollmar, Yi Seul Kim, Scott Lew, H. Neely, J. Seetharaman, Yang Shen, Rong Xiao, Thomas Acton, J.K. Everett, Giuseppe Cannone, Sriharsha Puranik, P. Savitsky, T. Krojer, Ewa S. Pilka, W. Kiyani, Wen‐Hwa Lee, Brian D. Marsden, Frank von Delft, C.K. Allerston, Laura Spagnolo, O. Gileadi, Gaetano T. Montelione, U. Oppermann, Wyatt W. Yue, Liang Tong
Software Mentions: 2
Published: about 13 years ago

10.1038/s41598-021-91765-4

BING, a novel antimicrobial peptide isolated from Japanese medaka plasma, targets bacterial envelope stress response by suppressing cpxR expression
Cited by: 4
Author(s): Mingdong Dong, Shu Hin Kwok, Joseph L. Humble, Yimin Liang, Sze Wing Tang, Kin Hung Tang, Man Kit Tse, Josh Haipeng Lei, R. Rajkumar, Mohamad Koohi‐Moghadam, Doris Wai Ting Au, Hongyan Sun, Yun Wah Lam
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-88920-2

Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants
Cited by: 4
Author(s): Wojciech Witek, Joanna Śliwiak, M. Ruszkowski
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-89556-y

ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer
Cited by: 1
Author(s): Bárbara Abreu, Carlos Cruz, A. Sofia F. Oliveira, Cláudio M. Soares
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0236538

Sites of vulnerability on ricin B chain revealed through epitope mapping of toxin-neutralizing monoclonal antibodies
Cited by: 3
Author(s): David J. Vance, Amanda Y. Poon, Nicholas J. Mantis
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-018-25361-4

NADH/NADPH bi-cofactor-utilizing and thermoactive ketol-acid reductoisomerase from Sulfolobus acidocaldarius
Cited by: 12
Author(s): Chin‐Yu Chen, Tzu‐Ping Ko, Kuan-Fu Lin, Bo‐Lin Lin, Chun‐Hsiang Huang, Cheng‐Hung Chiang, Jia‐Cherng Horng
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-27175-w

An Evolutionarily Conserved Structural Platform for PRC2 Inhibition by a Class of Ezh2 Inhibitors
Cited by: 26
Author(s): Matthew Bratkowski, Xin Yang, Xin Liu
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-021-92687-x

Polyimide mesh-based sample holder with irregular crystal mounting holes for fixed-target serial crystallography
Cited by: 15
Author(s): Ki Hyun Nam, Jihan Kim, Yunje Cho
Software Mentions: 2
Published: about 5 years ago

10.1016/j.str.2014.04.015

Structure of the LdcB LD-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition
Cited by: 31
Author(s): C.N. Hoyland, Christine Aldridge, Robert M. Cleverley, Marie Clémence Duchêne, G. Minasov, O. Onopriyenko, Karzan R. Sidiq, P.J. Stogios, W.F. Anderson, Richard A. Daniel, Alexei Savchenko, Waldemar Vollmer, Richard J. Lewis
Software Mentions: 2
Published: about 12 years ago

10.7554/eLife.02217

Structural basis for the assembly of the mitotic motor Kinesin-5 into bipolar tetramers
Cited by: 62
Author(s): Jonathan M. Scholey, Stanley Nithianantham, Jonathan M. Scholey, Jawdat Al-Bassam
Software Mentions: 2
Published: about 12 years ago

10.1038/s41598-018-22883-9

Analysis of mutations in pncA reveals non-overlapping patterns among various lineages of Mycobacterium tuberculosis
Cited by: 3
Author(s): Ramani Baddam, Narender Kumar, Lothar H. Wieler, Aditya Kumar Lankapalli, Niyaz Ahmed, Sharon J. Peacock, Torsten Semmler
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-21357-2

Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function
Cited by: 23
Author(s): Viveca Lindahl, Pontus Gourdon, Magnus Andersson, Berk Hess
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-24124-5

Exploration of the effect of sequence variations located inside the binding pocket of HIV-1 and HIV-2 proteases
Cited by: 6
Author(s): Dhoha Triki, Telli Billot, Benoît Visseaux, Diane Descamps, Delphine Flatters, Anne-Claude Camproux, Leslie Regad
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-19530-8

APLP1 is endoproteolytically cleaved by γ-secretase without previous ectodomain shedding
Cited by: 22
Author(s): Linda Schauenburg, Filip Liebsch, Murat Eravci, Magnus C. Mayer, Christoph Weise, Gerhard Multhaup
Software Mentions: 2
Published: over 8 years ago

10.1016/j.molcel.2021.03.020

Non-canonical autophagy drives alternative ATG8 conjugation to phosphatidylserine
Cited by: 84
Author(s): Joanne Durgan, Alf Håkon Lystad, Katherine E. Sloan, Sven R. Carlsson, Michael Wilson, Elena Marcassa, Rachel Ulferts, Judith Webster, Andrea F. Lopez-Clavijo, Michael J.O. Wakelam, Rupert Beale, Anne Simonsen, David Oxley, Oliver Florey
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-017-16846-9

Combined genetic approaches yield a 48% diagnostic rate in a large cohort of French hearing-impaired patients
Cited by: 55
Author(s): David Baux, Christel Vaché, Christophe Blanchet, Marjolaine Willems, Claude Baudoin, Mélodie Moclyn, Valérie Faugère, Renaud Touraine, Bertrand Isidor, Delphine Dupin-Deguine, Mathilde Nizon, Marie‐Françoise Vincent, Sandra Mercier, C. Calais, Gema García‐García, Z. Azher, Linda M. Lambert, Yaumara Perdomo-Trujillo, Fabienne Giuliano, Mireille Claustres, M. Kœnig, M. Mondain, Anne‐Françoise Roux
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-20557-0

ATP-dependent conformational change in ABC-ATPase RecF serves as a switch in DNA repair
Cited by: 15
Author(s): Qun Tang, Yan-Ping Liu, Hai-Huan Shan, Lu Tian, Jie-Zhong Zhang, Xiaozhi Yan
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-14101-9

Structure determination and activity manipulation of the turfgrass ABA receptor FePYR1
Cited by: 14
Author(s): Zhizhong Ren, Zhen Wang, Xin Zhou, Huazhong Shi, Yechun Hong, Min‐Jie Cao, Zhulong Chan, Lixin Xue, H. Eric Xu, Jian‐Kang Zhu
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-14008-5

Computational Analysis of the Molecular Mechanism of RamR Mutations Contributing to Antimicrobial Resistance in Salmonella enterica
Cited by: 6
Author(s): Yen‐Yi Liu, Chih-Chieh Chen
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-15715-9

Crystal structure of the N-terminal domain of human CDC73 and its implications for the hyperparathyroidism-jaw tumor (HPT-JT) syndrome
Cited by: 19
Author(s): Wei Sun, Xiaolin Kuang, Yan-Ping Liu, Lu Tian, Xiaozhi Yan, Wenqing Xu
Software Mentions: 2
Published: over 8 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: almost 7 years ago

10.1371/journal.ppat.1007024

Glycoengineering HIV-1 Env creates ‘supercharged’ and ‘hybrid’ glycans to increase neutralizing antibody potency, breadth and saturation
Cited by: 19
Author(s): Ema T. Crooks, Samantha L. Grimley, Michelle D. Cully, Keiko Osawa, Gillian Dekkers, Kevin O. Saunders, Sebastian Rämisch, Sergey Menis, William R. Schief, Nicole A. Doria‐Rose, Barton F. Haynes, Ben Murrell, Evan M. Cale, Amarendra Pegu, John R. Mascola, Gestur Vidarsson, James Μ. Binley
Software Mentions: 2
Published: about 8 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 6 years ago

10.1038/s41598-017-16427-w

Allosteric inhibitor remotely modulates the conformation of the orthestric pockets in mutant IDH2/R140Q
Cited by: 18
Author(s): Jiao Chen, Jie Yang, Xianqiang Sun, Zhongming Wang, Xiaolan Cheng, Wei Lü, Xueting Cai, Chunping Hu, Xu Shen, Peng Cao
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-24276-4

Tau Antibody Structure Reveals a Molecular Switch Defining a Pathological Conformation of the Tau Protein
Cited by: 19
Author(s): Jessica E. Chukwu, Jan T. Pedersen, Lars Østergaard Pedersen, Christiane Volbracht, Einar M. Sigurdsson, Xiang‐Peng Kong
Software Mentions: 2
Published: about 8 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 9 years ago

10.1371/journal.ppat.1005362

Structural Based Analyses of the JC Virus T-Antigen F258L Mutant Provides Evidence for DNA Dependent Conformational Changes in the C-Termini of Polyomavirus Origin Binding Domains
Cited by: 6
Author(s): Gretchen Meinke, Paul J. Phelan, Jong Shin, David Gagnon, Jacques Archambault, Andrew Bohm, Peter A. Bullock
Software Mentions: 2
Published: over 10 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 9 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: over 10 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: about 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 8 years ago

10.1371/journal.ppat.1007080

Neisseria gonorrhoeae employs two protein inhibitors to evade killing by human lysozyme
Cited by: 20
Author(s): Stephanie A. Ragland, María Victoria Humbert, Myron Christodoulides, Alison K. Criss
Software Mentions: 2
Published: about 8 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 6 years ago

10.1371/journal.ppat.1008465

Structure of the protective nematode protease complex H-gal-GP and its conservation across roundworm parasites
Cited by: 13
Author(s): Charlotte A. Scarff, Rebecca Thompson, G. F. J. Newlands, A.H. Jamson, Christopher K. Kennaway, V.J. da Silva, Élida Mara Leite Rabelo, Chun Song, John Trinick, W.D. Smith, Stephen P. Muench
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-017-11508-2

Computational Cell Cycle Profiling of Cancer Cells for Prioritizing FDA-Approved Drugs with Repurposing Potential
Cited by: 25
Author(s): Yu‐Chen Lo, Silvia Senese, Bryan France, Ankur A. Gholkar, Robert Damoiseaux, Jorge Z. Torres
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0025369

Insights into the Membrane Interactions of the Saposin-Like Proteins Na-SLP-1 and Ac-SLP-1 from Human and Dog Hookworm
Cited by: 14
Author(s): Charlene Willis, Conan K. Wang, Asiah Osman, Anne Simon, Darren Pickering, Jason Mulvenna, Alan Riboldi-Tunicliffe, Malcolm K. Jones, Alex Loukas, Andreas Hofmann
Software Mentions: 2
Published: almost 15 years ago

10.1038/s41598-017-14953-1

Fragment-based screening identifies novel targets for inhibitors of conjugative transfer of antimicrobial resistance by plasmid pKM101
Cited by: 19
Author(s): Bastien Casu, T. Arya, Benoit Bessette, Christian Baron
Software Mentions: 2
Published: over 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: over 10 years ago

10.1038/s41598-017-16853-w

Kaempferide Prevents Titanium Particle Induced Osteolysis by Suppressing JNK Activation during Osteoclast Formation
Cited by: 31
Author(s): Zhipeng Jiao, Weifeng Xu, Jun Zheng, Pei Shen, An Qin, Sam Zhang, Yang Chen
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-17600-x

Development of Erasin: a chromone-based STAT3 inhibitor which induces apoptosis in Erlotinib-resistant lung cancer cells
Cited by: 18
Author(s): Christian Lis, Stefan Rubner, Martin Roatsch, Angela Berg, Tyler Gilcrest, Darwin Y. Fu, Elizabeth Dong Nguyen, Annemarie Schmidt, Harald Krautscheid, Jens Meiler, Thorsten Berg
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-19526-4

Blocking Zika virus vertical transmission
Cited by: 51
Author(s): Pinar Mesci, Angela Mácia, Spencer M. Moore, Sergey A. Shiryaev, Antonella Pinto, Chun-Teng Huang, Leon Tejwani, Isabella Rodrigues Fernandes, Nicole A. Suarez, Matthew J. Kolar, Sandro Montefusco, Scott Rosenberg, Roberto H. Herai, Fernanda R. Cugola, Fabiele Baldino Russo, Nicholas Sheets, Alan Saghatelian, Sujan Shresta, Jeremiah D. Momper, Jair L. Siqueira-Neto, K.D. Corbett, Patrícia Cristina Baleeiro Beltrão-Braga, Alexey V. Terskikh, Alysson R. Muotri
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-20899-9

Supersaturation-controlled microcrystallization and visualization analysis for serial femtosecond crystallography
Cited by: 5
Author(s): Dan Bi Lee, Jong Min Kim, Jong Hyeon Seok, Ji Hye Lee, Jae Deok Jo, Ji Young Mun, Chelsie E. Conrad, Jesse Coe, Gerrett Nelson, Brenda G. Hogue, Thomas A. White, Nadia A. Zatsepin, Uwe Weierstall, Anton Barty, Henry N. Chapman, Petra Fromme, John C. H. Spence, Mi Sook Chung, Chang Hyun Oh, Kyung Hyun Kim
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-21218-y

The Extracellular Domain of Pollen Receptor Kinase 3 is structurally similar to the SERK family of co-receptors
Cited by: 11
Author(s): Sayan Chakraborty, Haiyun Pan, Qingyu Tang, Colin Woolard, Gang Xu
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-21614-4

A multitarget approach to drug discovery inhibiting Mycobacterium tuberculosis PyrG and PanK
Cited by: 33
Author(s): Laurent R. Chiarelli, Giorgia Mori, Béatrice Silvia Orena, Marta Esposito, Thomas R. Lane, Ana Luisa de Jesus Lopes Ribeiro, Giulia Degiacomi, Júlia Zemanová, Sára Szádocka, Stanislav Huszár, Zuzana Palčeková, Marcello Manfredi, Fabio Gosetti, Joël Lelièvre, Lluís Ballell, Elena Kazakova, Vadim Makarov, Emílio Marengo, Katarı́na Mikušová, Stewart T. Cole, Giovanna Riccardi, Sean Ekins, Maria Rosalia Pasca
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-22382-x

High-affinity ligands of the colchicine domain in tubulin based on a structure-guided design
Cited by: 35
Author(s): Oskía Bueno, Juan Estévez-Gallego, Solange Martins, A.E. Prota, Federico Gago, Asier Gómez-SanJuan, María‐José Camarasa, Isabel Barasoaín, Michel O. Steinmetz, J. Fernando Díaz, María‐Jesús Pérez‐Pérez, Sandra Liekens, Eva-Marı́a Priego
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-24457-1

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources
Cited by: 22
Author(s): Liang-Chin Huang, Karen Ross, Timothy R. Baffi, Harold J. Drabkin, Krys J. Kochut, Zheng Ruan, Peter D’Eustachio, Daniel McSkimming, Cecilia N. Arighi, Chuming Chen, Darren A. Natale, Cynthia L. Smith, Pascale Gaudet, Alexandra C. Newton, Cathy H. Wu, Natarajan Kannan
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-25571-w

Propyl-5-hydroxy-3-methyl-1-phenyl-1H-pyrazole-4-carbodithioate (HMPC): a new bacteriostatic agent against methicillin—resistant Staphylococcus aureus
Cited by: 6
Author(s): Tatiana Johnston, Daria Van Tyne, Roy Fangxing Chen, Nicolas L. Fawzi, Bumsup Kwon, Michael J. Kelso, Michael S. Gilmore, Eleftherios Mylonakis
Software Mentions: 2
Published: about 8 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: about 9 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: over 12 years ago

10.3390/biom11081218

Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars
Cited by: 3
Author(s): Atieh Moradi, Shuaijian Dai, Emily Oi Ying Wong, Guang Zhu, Fengchao Yu, Hon‐Ming Lam, Zhiyong Wang, A. L. Burlingame, Lin Chen, Alireza Afsharifar, Weichuan Yu, Tingliang Wang, Ning Li
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-021-89450-7

Structural genomics approach to investigate deleterious impact of nsSNPs in conserved telomere maintenance component 1
Cited by: 17
Author(s): Arunabh Choudhury, Taj Mohammad, Nikhil Samarth, Afzal Hussain, Tabish Rehman, Asimul Islam, Mohamed F. Alajmi, Shailza Singh, Md. Imtaiyaz Hassan
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-91069-7

Combination of consensus and ensemble docking strategies for the discovery of human dihydroorotate dehydrogenase inhibitors
Cited by: 8
Author(s): Garri Chilingaryan, Narek Abelyan, A. A. Sargsyan, Karen Nazaryan, Andre Serobian, Hovakim Zakaryan
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-90287-3

Molecular insight into isoform specific inhibition of PI3K-α and PKC-η with dietary agents through an ensemble pharmacophore and docking studies
Cited by: 4
Author(s): Baki Vijaya Bhaskar, Aluru Rammohan, Tirumalasetty Munichandra Babu, Gui Yu Zheng, Weibin Chen, Wudayagiri Rajendra, Grigory V. Zyryanov, Wei Gu
Software Mentions: 2
Published: about 5 years ago

Projects: pypi: PyMOL

Science Score: 90/100

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Papers Mentioning PyMOL 8,266