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: cran: vmd
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/vmd
Variational Mode Decomposition
1 version
Latest release: about 7 years ago
1 dependent package
0 downloads
Papers Mentioning vmd 24
10.1111/acel.12296
Proteins in aggregates functionally impact multiple neurodegenerative disease models by forming proteasome‐blocking complexesCited by: 51
Author(s): Srinivas Ayyadevara, Meenakshisundaram Balasubramaniam, Yuan Gao, Li‐Rong Yu, Ramani Alla, Robert Shmookler Reis
Software Mentions: 5
Published: almost 10 years ago
10.1002/2211-5463.12491
Crystal structure of the retroviral protease‐like domain of a protozoal <scp>DNA</scp> damage‐inducible 1 proteinCited by: 9
Author(s): Sushant Kumar, K. Suguna
Software Mentions: 5
Published: over 6 years ago
10.1016/j.jbc.2021.101129
In silico and in vitro analysis of an Aspergillus niger chitin deacetylase to decipher its subsite sugar preferencesCited by: 7
Author(s): Martin Bonin, Lisanne Hameleers, Lea Hembach, Thomas Roret, Stefan Cord‐Landwehr, Gurvan Michel, Bruno M. Moerschbacher
Software Mentions: 5
Published: about 3 years ago
10.1186/1471-2105-8-232
TMM@: a web application for the analysis of transmembrane helix mobilityCited by: 2
Author(s): Lars Skjærven, Inge Jonassen, Nathalie Reuter
Software Mentions: 4
Published: over 17 years ago
10.1016/j.dib.2019.104460
Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane dockingCited by: 2
Author(s): Astrid F. Brandner, Dario De Vecchis, Marc Baaden, Mickaël M. Cohen, Antoine Taly
Software Mentions: 4
Published: about 5 years ago
10.1111/j.1742-4658.2011.08320.x
Crystal structure of Onconase at 1.1 Å resolution – insights into substrate binding and collective motionCited by: 13
Author(s): Daniel E. Holloway, Umesh Singh, Kuslima Shogen, K. Ravi Acharya
Software Mentions: 3
Published: about 13 years ago
10.1111/acel.12772
Metformin directly targets the H3K27me3 demethylase KDM6A/UTXCited by: 56
Author(s): Elisabet Cuyàs, Sara Verdura, Laura Llorach-Parés, Salvador Fernández-Arroyo, Fedra Luciano-Mateo, Noemí Cabré, Jan Štursa, Lukáš Werner, Begoña Martín-Castillo, Benoı̂t Viollet, Jiřı́ Neužil, Jorge Joven, Alfons Nonell-Canals, Melchor Sánchez-Martínez, Javier A. Menendez
Software Mentions: 3
Published: over 6 years ago
10.3762/bjnano.8.77
First examples of organosilica-based ionogels: synthesis and electrochemical behaviorCited by: 10
Author(s): Andreas Taubert, Ruben Löbbicke, Barbara Kirchner, Fabrice Leroux
Software Mentions: 3
Published: over 7 years ago
10.1002/2211-5463.12053
A disulfide bridge in the calcium binding site of a polyester hydrolase increases its thermal stability and activity against polyethylene terephthalateCited by: 80
Author(s): Johannes Then, Ren Wei, Thorsten Oeser, André Gerdts, Juliane Schmidt, Markus Barth, Wolfgang Zimmermann
Software Mentions: 3
Published: over 8 years ago
10.1116/1.4971381
Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulationsCited by: 25
Author(s): Elisa T. Harrison, Tobias Weidner, David G. Castner, Gianluca Interlandi
Software Mentions: 3
Published: almost 8 years ago
10.3390/e22111259
Modeling the Device Behavior of Biological and Synthetic Nanopores with Reduced ModelsCited by: 7
Author(s): Dezső Boda, Mónika Valiskó, Dirk Gillespie
Software Mentions: 2
Published: about 4 years ago
10.1111/febs.13517
Interactions between N‐linked glycosylation and polymerisation of neuroserpin within the endoplasmic reticulumCited by: 18
Author(s): Claudia Moriconi, Adriana Ordóñez, Giuseppe Lupo, Bibek Gooptu, James A. Irving, Rosina Noto, Vincenzo Martorana, Mauro Manno, Valentina Timpano, Noemi Antonella Guadagno, Louise Dalton, Stefan J. Marciniak, David A. Lomas, Elena Miranda
Software Mentions: 2
Published: about 9 years ago
10.1002/1873-3468.13994
The first intracellular loop is essential for the catalytic cycle of the human ABCG2 multidrug resistance transporterCited by: 3
Author(s): Narakorn Khunweeraphong, Karl Kuchler
Software Mentions: 2
Published: about 4 years ago
10.3389/fgene.2016.00014
Structural and Dynamic Characterization of the C313Y Mutation in Myostatin Dimeric Protein, Responsible for the “Double Muscle” Phenotype in Piedmontese CattleCited by: 6
Author(s): Silvia Bongiorni, Alessio Valentini, Giovanni Chillemi
Software Mentions: 2
Published: almost 9 years ago
10.1038/srep09200
The Glycan Role in the Glycopeptide Immunogenicity Revealed by Atomistic Simulations and Spectroscopic Experiments on the Multiple Sclerosis Biomarker CSF114(Glc)Cited by: 12
Author(s): Annalisa Bruno, Mario Scrima, Ettore Novellino, Gerardino D’Errico, Anna Maria D’Ursi, Vittorio Limongelli
Software Mentions: 2
Published: over 9 years ago
10.3390/molecules23112794
A Novel Integrated Way for Deciphering the Glycan Code for the FimH LectinCited by: 11
Author(s): Tetiana Dumych, Clarisse Bridot, Sébastien G. Gouin, Marc F. Lensink, Solomiya Paryzhak, Sabine Szunerits, Ralf Blossey, Rostyslav Bilyy, Julie Bouckaert, Eva‐Maria Krammer
Software Mentions: 2
Published: about 6 years ago
10.7717/peerj.5412
NMR structure of the C-terminal domain of TonB protein from <i>Pseudomonas aeruginosa</i>Cited by: 10
Author(s): Jesper S. Oeemig, O. H. Samuli Ollila, Hideo Iwaï
Software Mentions: 2
Published: about 6 years ago
10.1111/tpj.12575
The pattern of xylan acetylation suggests xylan may interact with cellulose microfibrils as a twofold helical screw in the secondary plant cell wall of <i>Arabidopsis thaliana</i>Cited by: 222
Author(s): Marta Busse‐Wicher, Thiago C. F. Gomes, Theodora Tryfona, Nino Nikolovski, Katherine Stott, Nicholas J. Grantham, David N. Bolam, Munir S. Skaf, Paul Dupree
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0027994
Concentration Dependent Ion Selectivity in VDAC: A Molecular Dynamics Simulation StudyCited by: 28
Author(s): Eva‐Maria Krammer, Fabrice Homblé, Martine Prévost
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0121746
Dual Mechanism of Ion Permeation through VDAC Revealed with Inorganic Phosphate Ions and Phosphate MetabolitesCited by: 19
Author(s): Eva‐Maria Krammer, Giang T. H. Vu, Fabrice Homblé, Martine Prévost
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0160219
Unveiling the Mechanism of Arginine Transport through AdiC with Molecular Dynamics Simulations: The Guiding Role of Aromatic ResiduesCited by: 15
Author(s): Eva‐Maria Krammer, Kassem Ghaddar, Brunó André, Martine Prévost
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0026014
Molecular Basis of Bcl-XL-p53 Interaction: Insights from Molecular Dynamics SimulationsCited by: 29
Author(s): Nagakumar Bharatham, Seung‐Wook Chi, Ho Sup Yoon
Software Mentions: 2
Published: about 13 years ago
10.1016/j.celrep.2014.01.013
Destruction of Full-Length Androgen Receptor by Wild-Type SPOP, but Not Prostate-Cancer-Associated MutantsCited by: 202
Author(s): Jian An, Chenji Wang, Yibin Deng, Yu Liu, Haojie Huang
Software Mentions: 2
Published: almost 11 years ago
10.1039/d0sc05249c
Ferro-self-assembly: magnetic and electrochemical adaptation of a multiresponsive zwitterionic metalloamphiphile showing a shape-hysteresis effectCited by: 4
Author(s): Stefan Bitter, Moritz Schlötter, Markus Schilling, Marina Krumova, Sebastian Polarz, Rainer F. Winter
Software Mentions: 2
Published: almost 4 years ago