MoRFchibi SYSTEM: software tools for the identification of MoRFs in protein sequences

Abstract

Molecular recognition features, MoRFs, are short segments within longer disordered protein regions that bind to globular protein domains in a process known as disorder-to-order transition. MoRFs have been found to play a significant role in signaling and regulatory processes in cells. High-confidence computational identification of MoRFs remains an important challenge. In this work, we introduce MoRFchibi SYSTEM that contains three MoRF predictors: MoRFCHiBi, a basic predictor best suited as a component in other applications, MoRFCHiBi_Light, ideal for high-throughput predictions and MoRFCHiBi_Web, slower than the other two but best for high accuracy predictions. Results show that MoRFchibi SYSTEM provides more than double the precision of other predictors. MoRFchibi SYSTEM is available in three different forms: as HTML web server, RESTful web server and downloadable software at: http://www.chibi.ubc.ca/faculty/joerg-gsponer/gsponer-lab/software/morf_chibi/

Understanding the penetrance of intrinsic protein disorder in rotavirus proteome

“…For intrinsically disordered regions (IDPRs) and MoRF analysis, numerous technologically advanced predictors are available, such as IUPred [38], ANCHOR [39], MoRFPred [40], MoRFchibi_web [41], DisEMBL [42], GlobPlot [43], DisoPred [44], PONDR Ò pool [including predictors, such as PONDR Ò VLXT [45], PONDR Ò VLS2 [46], and PONDR Ò VL3 [47], as well as a meta-predictor PONDR Ò FIT [48], and several others [49]. Critical Assessment of Protein Structure Prediction (CASP) was used to examine the accuracy of several disorder predictors, and several of the software mentioned above were compared using CASP [50].…”

“…In general, MoRFs are the short (5-25 residues) protein binding sites within disordered region sometimes longer also (more than 50 residues) and may have the potential to undergo disorder to order transitions upon interaction with other partners [53]. In our study, four standard MoRF predictors were used as: ANCHOR [39], MoRFPred [40], MoRFchibi_web [41] and Disopred [54]. All these predictors utilize different types of algorithms to predict MoRFs, so we have used four predictors to completely characterized these regions in rotavirus proteome.…”

Sequence characteristics responsible for protein‐protein interactions in the intrinsically disordered regions of caseins, amelogenins, and small heat‐shock proteins

“…They generally comprise 3‐11 residues and have a low affinity for their interaction partners with dissociation constants of 1‐150 μM making the interactions transient and reversible . Automated tools for identifying SLiMs are in common use . Since SLiMs are short and degenerate, over‐prediction is common and many putative SLiMs are false positives.…”

OPAL+: Length‐Specific MoRF Prediction in Intrinsically Disordered Protein Sequences

“…The EXP53 set was assembled by combining sequences from three different studies and includes sequences containing experimentally validated MoRFs that are disordered in isolation. These sets were previously used to develop predictors including OPAL, MoRFchibi‐web, MoRFpred‐plus, MoRFchibi, and MoRFpred . Altogether, there were 938 sequences in training and test sets.…”

“…MoRFpred‐plus targets the properties of upstream/downstream flank residues of a query residue to predict MoRFs. More accurate predictors like MoRFchibi‐web and OPAL are constructed by combining multiple component predictors. Specifically, MoRFchibi‐web uses scores of MoRFchibi, Espirtz, a disorder predictor, and conservation information derived from PSI‐BLAST .…”