IDRWalker: A Random Walk based Modeling Tool for Disordered Regions in Proteins

Abstract

MotivationWith the advancement of structural biology techniques, the elucidation of increasingly large protein structures has become possible. However, the structural modeling of intrinsically disordered regions in proteins remains challenging. Particularly in the case of large protein complexes, it is difficult to rapidly construct models for all intrinsically disordered regions using existing methods. In the nuclear pore complex, a gigantic protein machine of interest, intrinsically disordered regions play a crucial role in the function of the nuclear pore complex. Therefore, there is a need to develop a modeling tool suitable for intrinsically disordered regions in large protein complexes. ResultsWe have developed a program named IDRWalker based on self-avoiding random walks, enabling convenient and rapid modeling of intrinsically disordered regions in large protein complexes. Using this program, modeling of all disordered regions within the nuclear pore complex can be completed in a matter of minutes. Furthermore, we have addressed issues related to peptide chain connectivity and knot that may arise during the application of random walks. Availability and implementationIDRWalker is an open-source Python package. Its source code is publicly accessible on GitHub (https://github.com/zyzhangGroup/IDRWalker).