Results 21 to 30 of about 167,696 (254)
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
Molecular Dynamics Simulation [PDF]
, 2014 The contributions collected in this book move from the quantum-statistical description to the validity of classical modeling; they present some perspectives in the algorithmic and in the enhanced sampling approaches, tackling some longstanding challenges to simulation in the area of non-equilibrium, rare events, mesoscale and quantum-classical ...
Ciccotti, Giovanni +2 more
openaire +3 more sources
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
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
Applications of Molecular Dynamics Simulation in Protein Study
Membranes, 2022 Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study ...
Siddharth Sinha +2 more
doaj +1 more source
Time after time – circadian clocks through the lens of oscillator theory
FEBS Letters, EarlyView.Oscillator theory bridges physics and circadian biology. Damped oscillators require external drivers, while limit cycles emerge from delayed feedback and nonlinearities. Coupling enables tissue‐level coherence, and entrainment aligns internal clocks with environmental cues.
Marta del Olmo +2 more
wiley +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
Sequence determinants of RNA G‐quadruplex unfolding by Arg‐rich regions
FEBS Letters, EarlyView.We show that Arg‐rich peptides selectively unfold RNA G‐quadruplexes, but not RNA stem‐loops or DNA/RNA duplexes. This length‐dependent activity is inhibited by acidic residues and is conserved among SR and SR‐related proteins (SRSF1, SRSF3, SRSF9, U1‐70K, and U2AF1).
Naiduwadura Ivon Upekala De Silva +10 more
wiley +1 more source
FEBS Letters, EarlyView.The Ile181Asn variant of human UDP‐xylose synthase (hUXS1), associated with a short‐stature genetic syndrome, has previously been reported as inactive. Our findings demonstrate that Ile181Asn‐hUXS1 retains catalytic activity similar to the wild‐type but exhibits reduced stability, a looser oligomeric state, and an increased tendency to precipitate ...
Tuo Li +2 more
wiley +1 more source
Structural insights into an engineered feruloyl esterase with improved MHET degrading properties
FEBS Letters, EarlyView.A feruloyl esterase was engineered to mimic key features of MHETase, enhancing the degradation of PET oligomers. Structural and computational analysis reveal how a point mutation stabilizes the active site and reshapes the binding cleft, expading substrate scope.
Panagiota Karampa +5 more
wiley +1 more source