Computational prediction of disordered binding regions

Comparative evaluation of AlphaFold2 and disorder predictors for prediction of intrinsic disorder, disorder content and fully disordered proteins

“…In recent years, the disorder prediction field has moved towards prediction of functional types of IDRs [91] , [92] , [93] , [94] . The main focus is on the regions that interact with ligands that include peptides, proteins, DNA, RNA and lipids [91] , [92] , [95] , however, some tools also predict disordered linkers [96] , [97] . There are over three dozen of predictors of binding IDRs, with majority of them targeting protein and peptide binding IDRs [91] .…”

“…The main focus is on the regions that interact with ligands that include peptides, proteins, DNA, RNA and lipids [91] , [92] , [95] , however, some tools also predict disordered linkers [96] , [97] . There are over three dozen of predictors of binding IDRs, with majority of them targeting protein and peptide binding IDRs [91] . Example popular methods include ANCHOR [81] , [98] , [99] , MoRFpred [100 ] , MoRF chibi [101] , [102] , and DISOPRED3 [67] that predict protein and peptide binding IDRs; DisoRDPbind that predicts DNA, RNA and protein-binding IDRs; and SLiMFinder [103 ] and SLiMSearch [104] , [105] , [106] that predict short linear sequence motifs (SLiMs) that are often involved in the protein-protein and protein-nucleic acids interactions.…”

Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery

“…Short sequence regions. Significant efforts have been devoted to exploring short sequence regions that facilitate specific interactions between disordered regions and various biomolecules [ 116 ]. Two major categories of these regions are molecular recognition fragments (MoRFs) and short linear motifs (SLiMs).…”

“…MoRF can undergo a disorder-to-order transition upon binding to their partner and can be predicted using various methods with sequence lengths ranging from 5 to 25 amino acids [ 117 , 118 , 119 , 120 , 121 ]. On the other hand, SLiMs are short sequence patches each containing 3 to 15 amino acids that are often found within the disordered regions of diverse proteins and can be highly conserved [ 116 , 122 , 123 , 124 , 125 ]. Such sequence conservation, e.g., within low-complexity disordered regions, suggests potential coevolution with binding partners for specific functions.…”

The role of intrinsic disorder in binding of plant microtubule‐associated proteins to the cytoskeleton

“…A multitude of available online‐based tools is available to identify intrinsic disorder in proteins and new, improved tools are published on a regular basis. Available tools were discussed and summarized previously (Basu et al, 2023; Han et al, 2023; Liu et al, 2017).…”