Results 21 to 30 of about 34,460 (284)

Using VMD: An Introductory Tutorial [PDF]

Current Protocols in Bioinformatics, 2008
AbstractVMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. This unit will serve as an introductory VMD tutorial. We will present several step‐by‐step examples of some of VMD's most popular features, including visualizing ...
Jen, Hsin, Anton, Arkhipov, Ying, Yin, John E, Stone, Klaus, Schulten   +4 more
openaire   +2 more sources

MEMBPLUGIN: studying membrane complexity in VMD [PDF]

Bioinformatics, 2014
AbstractSummary: Computer simulations are giving way to more complex and accurate studies of biological membranes by molecular dynamics (MD) simulations. The analysis of MD trajectories comprises the biophysical characterization of membrane properties or the study of protein–lipid interactions and dynamics.
Ramon Guixà-González, Ismael Rodriguez-Espigares, Juan Manuel Ramírez-Anguita, Pau Carrió-Gaspar, Hector Martinez-Seara, Toni Giorgino, Jana Selent   +6 more
openaire   +4 more sources

Research on Multi-Domain Fault Diagnosis of Gearbox of Wind Turbine Based on Adaptive Variational Mode Decomposition and Extreme Learning Machine Algorithms

Energies, 2020
Since variational mode decomposition (VMD) was proposed, it has been widely used in condition monitoring and fault diagnosis of mechanical equipment. However, the parameters K and α in the VMD algorithm need to be set before decomposition, which ...
Hui Li, Bangji Fan, Rong Jia, Fang Zhai, Liang Bai, Xingqi Luo   +5 more
doaj   +1 more source

MHD Free Convective Heat and Mass Transfer Flow from a Vertical Porous Surface with Variable Thermal Conductivity, Variable Mass Diffusivity and Thermal Diffusion Including Viscous Dissipation and Chemical Reaction

International Journal of Applied Mechanics and Engineering, 2022
An analysis is carried out to study chemically reactive, viscous dissipative effects of an incompressible and electrically conducting fluid with MHD free convection adjacent to a vertical surface with variable thermal conductivity (VTD) and variable mass
J. Phakirappa, S. Priyanka, P.H. Veena, V.K. Pravin   +3 more
doaj   +1 more source

Growth prediction of Microcystis aeruginosa based on a secondary decomposition integration model

Water Science and Technology, 2023
Microcystis aeruginosa is the dominant species in the blooms of eutrophic lakes such as Taihu Lake in China. Chlorophyll-a is one of the most common indicators to characterize its biomass.
Juan Huan, Beier Yang, Mingbao Li, Hao Zhang, Wendi Sun, Bing Shi   +5 more
doaj   +1 more source

Short-term prediction of the significant wave height and average wave period based on the variational mode decomposition–temporal convolutional network–long short-term memory (VMD–TCN–LSTM) algorithm [PDF]

Ocean Science, 2023
The present work proposes a prediction model of significant wave height (SWH) and average wave period (APD) based on variational mode decomposition (VMD), temporal convolutional networks (TCNs), and long short-term memory (LSTM) networks.
Q. Ji, L. Han, L. Jiang, Y. Zhang, M. Xie, Y. Liu, Y. Liu   +6 more
doaj   +1 more source

Software pipeline for predicting and analyzing the structure of the receptor–ligand

Учёные записки Казанского университета: Серия Физико-математические науки, 2022
It is of fundamental importance in pharmacology and theoretical biology to analyze the binding of ligands to receptors. A better understanding of this process and its outcomes can help predict the following: how the protein interacts with ligands ...
A.S. Kozlova, A.R. Mukhametgalieva, A.N. Fattakhova, N.I. Akberova   +3 more
doaj   +1 more source

VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program [PDF]

Bioinformation, 2014
The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its ...
Yahyavi, Masoumeh, Falsafi-Zadeh, Sajad, Karimi, Zahra, Kalatarian, Giti, Galehdari, Hamid   +4 more
openaire   +2 more sources

Fusion of GNSS and Speedometer Based on VMD and Its Application in Bridge Deformation Monitoring

Sensors, 2020
Real-time dynamic displacement and spectral response on the midspan of Jiangyin Bridge were calculated using Global Navigation Satellite System (GNSS) and a speedometer for the purpose of understanding the dynamic behavior and the temporal evolution of ...
Ruicheng Zhang, Chengfa Gao, Shuguo Pan, Rui Shang   +3 more
doaj   +1 more source

VMD DisRg: New User-Friendly Implement for calculation distance and radius of gyration in VMD program [PDF]

Bioinformation, 2012
Molecular dynamic simulation is a practical and powerful technique for analysis of protein structure. Several programs have been developed to facilitate the mentioned investigation, under them the visual molecular dynamic or VMD is the most frequently used programs.
Falsafi-Zadeh, Sajad, Karimi, Zahra, Galehdari, Hamid   +2 more
openaire   +2 more sources