Ruđer Bošković Institute Research Data Repository
| Title (english) | Thioxo/mercapto-tetrahydro-pyrimidin-benzenesulfonamide Hybrids as Potential BRAFV600E Inhibitors |
| Author | Jurica Novak Institut Ruđer Bošković |
| Collaborator | Prateek Pathak (Researcher) School of Pharmacy, GITAM (Deemed to be University), Hyderabad Campus, India |
| Scientific / art field, discipline and subdiscipline | NATURAL SCIENCES Chemistry Physical Chemistry |
| Methods (english) | For molecular dynamics simulation under physiological conditions (310 K, 1 atm), a minimization–heating–equilibration–production protocol was employed. The minimization process involved 10000 cycles (4000 steepest descent followed by 6000 conjugate gradient) with harmonic potential constraints (k = 10.0 kcal mol−1 Å−2) on all non-solvent molecules. A second minimization followed a similar protocol without constraints. Following energy minimization, the systems were gradually heated from 0 K to 300 K over 500 ps without constraints, followed by 500 ps of equilibration. Finally, a 300 ns MD production run was performed with a 2 fs time step at 310 K and 1 atm. Temperature was controlled using a Langevin thermostat with a collision frequency of 1 ps−1. Hydrogen atoms were constrained using the SHAKE algorithm. Long-range electrostatic interactions were managed using the particle mesh Ewald method, with a cutoff distance of 11 Å for non-bonded interactions. Periodic boundary conditions were applied in all directions. MD simulations were executed on the Supek supercomputer at the University of Zagreb, University Computing Center—SRCE, using the AMBER software suite. |
| Keywords (english) | |
| Language | croatian |
| URN:NBN | urn:nbn:hr:241:709243 |
| Publication | 2024-12-25 |
| Geolocation | Croatia |
| Publisher | Institut Ruđer Bošković Ruđer Bošković Institute |
| Access conditions | Open access |
| Terms of use |  |
| Created on | 2024-12-17 13:25:00 |
