POODLE: tools predicting intrinsically disordered regions of amino acid sequence.

Protein intrinsic disorder, a widespread phenomenon characterized by a lack of stable three-dimensional structure, is thought to play an important role in protein function. In the last decade, dozens of computational methods for predicting intrinsic disorder from amino acid sequences have been developed. They are widely used by structural biologists not only for analyzing the biological function of intrinsic disorder but also for finding flexible regions that possibly hinder successful crystallization of the full-length protein. In this chapter, I introduce Prediction Of Order and Disorder by machine LEarning (POODLE), which is a series of programs accurately predicting intrinsic disorder. After giving the theoretical background for predicting intrinsic disorder, I give a detailed guide to using POODLE. I then also briefly introduce a case study where using POODLE for functional analyses of protein disorder led to a novel biological findings.