Molecular dynamics simulations for "Ancestral structure prediction reveals the conformational impact of the RuBisCO small subunit across time"

This repository contains the molecular dynamics simulation files for the extant and ancestral RuBisCOs, presented in Amritkar2024 et. al.

There is a total of 60 files, out of which 30 are the simulation trajectory `.dcd` files and the other 30 are the `.pdb` for their corresponding protein structures.

The trajectory files are dried, i.e. water molecules have been removed from them.

The data encompasses over 5 extant (pdb ids: 1BWV, 3ZXW, 6FTL, 6URA, 8RUC) and 7 ancestral (Anc-I/I', Anc-I', Anc-I, Anc-IAB, Anc-ICD, Anc-IA, Anc-IB) RuBisCO complexes.

Three types of simulations were performed in this study: with water molecules (labeled as exp01), with water + CO2 molecules (labeled as exp02), and with water + O2 molecules (labeled as exp04). exp02 and exp04 files are not present for the RbcS-less (Anc-I/I', Anc-I', and 6URA) RuBisCOs.

Each file is named "RuBisCO-system"."simulation-type".md01.dry."pdb or dcd".

The files are named with respect to each RuBisCO-id in small (No caps). Anc-I/I' is represented as "anciip" and Anc-I' is represented as "ancip".