Fig 1. The system flowchart that is used for predicting protein tertiary structure.

At the first stage, NiDelta constructs both training dataset and MSA for Phsior and residue-contacts estimator, respectively. The predicted torsion angles (ϕ, ψ) and estimated residue-contacts are used as restraints for parallelly launching 500 Upside simulations, each of which starts with an extended model represented by a simplified structure for sampling its conformation space.