Results 21 to 30 of about 176,064 (165)
The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein
eLife, 2022 Spike (S) protein is the primary antigenic target for neutralization and vaccine development for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It decorates the virus surface and undergoes large motions of its receptor binding domains (
Hisham M Dokainish +5 more
doaj +1 more source
Molecular dynamics simulations of a helicase [PDF]
Proteins: Structure, Function, and Bioinformatics, 2003 AbstractHelicases are ubiquitous enzymes involved in nucleic acid metabolism. The PcrA DNA helicase is an essential bacterial protein involved in rolling circle plasmid replication and DNA repair. Recent crystal structures of PcrA bound to DNA indicate that a flexible loop mediates a functionally important rigid‐body‐domain rotation.
Katherine, Cox +3 more
openaire +2 more sources
Molecular dynamics simulation of uranium nitride oxidation [PDF]
Journal of the Serbian Chemical SocietyA molecular dynamic simulation of the uranium mononitride (UN) oxidation in an Ar–O medium in the temperature range of 373–2073 K is performed. The study is performed for UN particles with a crystalline and amorphous structure at an oxygen concentration ...
Galashev Alexander Y. +4 more
doaj +1 more source
Molecular Dynamics Simulation for All [PDF]
Neuron, 2018 The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery has expanded dramatically in recent years. These simulations capture the behavior of proteins and other biomolecules in full atomic detail and at very fine temporal resolution.
Scott A, Hollingsworth, Ron O, Dror
openaire +2 more sources
Computational and Structural Biotechnology Journal, 2023 We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations.
Angelo Felline +4 more
doaj +1 more source
Indonesian Journal of Chemistry, 2020 Erlotinib, Afatinib, and WZ4002 are quinazoline derivative compounds and classified as first, second, and third-generation EGFR inhibitor. All inhibitors have been given directly to cancer patients for many years but find some resistance.
Herlina Rasyid +2 more
doaj +1 more source
Molecular dynamics simulations of membrane proteins [PDF]
Biophysical Reviews, 2012 Membrane proteins control the traffic across cell membranes and thereby play an essential role in cell function from transport of various solutes to immune response via molecular recognition. Because it is very difficult to determine the structures of membrane proteins experimentally, computational methods have been increasingly used to study their ...
Baştuğ, Turgut, Kuyucak, Serdar
openaire +4 more sources
Dynamics of riboswitches: Molecular simulations [PDF]
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2014 Riboswitch RNAs play key roles in bacterial metabolism and represent a promising new class of antibiotic targets for treatment of infectious disease. While many studies of riboswitches have been performed, the exact mechanism of riboswitch operation is still not fully understood at the atomistic level of detail.
openaire +2 more sources
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
BMC Bioinformatics, 2023 Background The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular dynamics simulation softwares are very useful, however, most of them are used in command line form and continue
Ivo Henrique Provensi Vieira +5 more
doaj +1 more source
Molecular Dynamics Simulation of Polyacrylamide Adsorption on Calcite
Molecules, 2023 In poorly consolidated carbonate rock reservoirs, solids production risk, which can lead to increased environmental waste, can be mitigated by injecting formation-strengthening chemicals. Classical atomistic molecular dynamics (MD) simulation is employed
Keat Yung Hue +5 more
doaj +1 more source