Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 2002;11(11):2714–26. 28. Rykunov D, Fiser A. Effects of amino acid composition, finite size of proteins, and sparse statistics ...
The CXCR4 chemokine receptor is a G protein-coupled receptor that plays a role in many physiological processes and diseases, such as cancer metastasis, HIV infection, and immune response. Because of this, it may be possible to target it therapeutically.
For the atomic model of the nsP2 protein, containing both the helicase and protease subdomains, the predicted AF2 structure was used as an initial model. All-atom MD simulations were performed with the MD package Gromacs (version 2020)54,55 using the CHARMM36 force field56. The protein model...
The MD simulations provided critical insights into the structural stability and dynamic behavior of the MurM-ligand complexes and the unbound form of MurM, facilitating the identification of potential lead molecules for further experimental studies. These simulations were conducted using GROMACS (GROningen...
The PARP-1 protein was reprepared with charmm27 force field by Gromacs. The topology and parameters of each ligand for use with Gromacs were provided by SwissParam program [48]. The whole system involves a cubic box with a minimum distance of 1.2 Å from the protein-ligand complex was...
Molecular dynamics simulation To further validate the reliability of the docking proto- col, this study employed GROMACS 2022.4 software to perform all-atom molecular dynamics simulations on the protein-ligand complexes obtained from molecular docking [22]. The protein component was parameterized using ...
We introduce a family of membrane-targeted azobenzenes (MTs) with a push-pull character as a new tool for cell stimulation. These molecules are water soluble and spontaneously partition in the cell membrane. Upon light irradiation, they isomerize from tr
All the simulations in this work have been done for a system of 500 molecules and employing molecular dynamic simulations in the NVT ensemble with the package GROMACS 4.5 [21]. The equations of motion are solved using the leap-frog algorithm [22,21] and the time step used was 2 fs. The...
After completion, the simulation trajectory was analyzed using GROMACS analysis tools to extract information about the protein–ligand complex's structure, dynamics, and interactions. The root mean square deviation (RMSD) and root mean square fluctuation (RMSF), radius of gyration (Rg), solvent ...
The molecular dynamics (MD) simulations were performed with GROMACS 2024.2, CHARMM36 force field, and TIP3 water model. The simulation box was defined with a minimum distance of 1.5 nm (15 Å) between the protein and the box edge. The system was then solvated, and ions were added to ...