Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16 - LCBio group (TS189)

This dataset comprises the molecular dynamics (MD) simulation data generated by the LCBio group (TS189) for the CASP16 RNA-water/ion prediction challenge. The collection provides the underlying simulation data used to derive the submitted predictions for target R1260. The data were generated using a simulation pipeline performed with Amber 22 (pmemd.cuda), focusing on: - System Preparation: System topology was generated using Amber's tleap, solvating the RNA (based on PDB 7EZ0) in a truncated octahedral box with a 10 Å buffer and neutralizing it with Na+ ions. - Simulation Protocol: The process included heating from 100K to 300K over 500ps with backbone restraints, followed by a four-phase NVT equilibration and a 10ns production run. - Trajectory Analysis: 1000 frames were selected for the final analysis. While the final submitted predictions had water molecules beyond 5 Å from the RNA stripped, the trajectories provided in this repository retain all water molecules and ions. This dataset explicitly supports the findings reported in the article "Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16" and provides the raw molecular dynamics trajectories used to generate the submitted water/ion predictions. It serves as a valuable resource for researchers interested in benchmarking solvation prediction methods, analyzing RNA-ion interactions, or studying the structural dynamics of the specific targets involved in the CASP16 challenge.