New Monte Carlo Based Technique To Study DNA-Ligand Interactions.

摘要: We present a new all-atom Monte Carlo technique capable of performing quick and accurate DNA-ligand conformational sampling. In particular, using the PELE software as frame, we have introduced an additional force field, implicit solvent, anisotropic network model to effectively map DNA energy landscape. With these additions, successfully generated conformations for test set composed six fragments A-DNA B-DNA. Moreover, trajectories cisplatin its hydrolysis products identified best interacting compound binding site, producing analogous results microsecond molecular dynamics simulations. Furthermore, combination with Markov State Models produced noncovalent free energies in good agreement published results, at significantly lower computational cost. Overall our approach will allow but sampling interactions.