i3Drefine is software for reliable and computationally efficient protein structure refinement. The goal of i3Drefine is to perform consistent and simultaneous improvement in both global and local structural qualities of the initial models to bring it closer to the native state in a computationally inexpensive manner. The name i3Drefine stands for iterative three-dimensional (3D) protein structure refinement.
The i3Drefine method employs a iterative refinement based on two steps of process. The first step is based on optimization of hydrogen bonding (HB) network and the second step applies atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields. The starting structure is refined by the algorithm and the refined structure is recursively refined by the same protocol to generate multiple refined structures. This is done primarily to avoid getting stuck in local minima in protein's multidimensional energy landscape (Figure 1).
Figure 1. Workflow of the i3Drefine protocol.