Congratulations to Lauren Winkler who won one of three best poster awards on the International Society of Quantum Biology and Pharmacology President's meeting
Congratulations to Lauren Winkler who won one of three best poster awards on the International Society of Quantum Biology and Pharmacology President's meeting.
Lauren’s short summary “Benchmarking New and Emerging Nucleic Acid Force Fields Using DNA Mini-Dumbbells” poster:
Molecular dynamics (MD) simulations of duplex DNA repeatedly show convergence and agreement with experimental data. However, many of the most interesting and functional nucleic acid (NA) structures, such as noncanonical DNA motifs or RNA, are not pure helical duplexes and are highly sensitive to the balance of forces between water, ions, and NA atoms. Despite significant advances in simulation methods and available force fields (FF), none of the currently available FFs are able to consistently and accurately model non-duplex NAs. This greatly limits MD simulation in its application to drug development and biological discovery. Thus, in an effort to understand current FF limitations and focus FF development, this project has benchmarked eight of the newest FFs (BSC0, BSC1, OL15, OL21, Tumuc1, HBFIX/CuFIX, Charmm36, and Drude Polarizable) and three FF modifications using the DNA mini-dumbbell model. Benchmarking two of these DNA mini-dumbbell sequences at the microsecond timescale showed surprisingly good results with some of the newest NA FFs. These include a high percentage of trajectory frames with less than 1 Å agreement to NMR re-refined structures and torsional angles modeled close to experimental measurements. This project, and understanding the current state of NA FFs, has implications in focusing FF development so that noncanonical NAs and RNA may be one day be modeled with the accuracy that has now been achieved with duplex DNA.