Prediction of cis/trans isomerization using feature selection and support vector machines
Φόρτωση...
Ημερομηνία
Συγγραφείς
Exarchos, K. P.
Papaloukas, C.
Exarchos, T. P.
Troganis, A. N.
Fotiadis, D. I.
Τίτλος Εφημερίδας
Περιοδικό ISSN
Τίτλος τόμου
Εκδότης
Περίληψη
Τύπος
Είδος δημοσίευσης σε συνέδριο
Είδος περιοδικού
peer reviewed
Είδος εκπαιδευτικού υλικού
Όνομα συνεδρίου
Όνομα περιοδικού
J Biomed Inform
Όνομα βιβλίου
Σειρά βιβλίου
Έκδοση βιβλίου
Συμπληρωματικός/δευτερεύων τίτλος
Περιγραφή
In protein structures the peptide bond is found to be in trans conformation in the majority of the cases. Only a small fraction of peptide bonds in proteins is reported to be in cis conformation. Most of these instances (>90%) occur when the peptide bond is an imide (X-Pro) rather than an amide bond (X-nonPro). Due to the implication of cis/trans isomerization in many biologically significant processes, the accurate prediction of the peptide bond conformation is of high interest. In this study, we evaluate the effect of a wide range of features, towards the reliable prediction of both proline and non-proline cis/trans isomerization. We use evolutionary profiles, secondary structure information, real-valued solvent accessibility predictions for each amino acid and the physicochemical properties of the surrounding residues. We also explore the predictive impact of a modified feature vector, which consists of condensed position-specific scoring matrices (PSSMX), secondary structure and solvent accessibility. The best discriminating ability is achieved using the first feature vector combined with a wrapper feature selection algorithm and a support vector machine (SVM). The proposed method results in 70% accuracy, 75% sensitivity and 71% positive predictive value (PPV) in the prediction of the peptide bond conformation between any two amino acids. The output of the feature selection stage is investigated in order to identify discriminatory features as well as the contribution of each neighboring residue in the formation of the peptide bond, thus, advancing our knowledge towards cis/trans isomerization. (C) 2008 Elsevier Inc. All rights reserved.
Περιγραφή
Λέξεις-κλειδιά
peptide bond, cis/trans isomerization, support vector machines, cis-trans isomerization, secondary structure information, peptide-bond conformation, amino-acid-sequence, protein structures, evolution, residues, server
Θεματική κατηγορία
Παραπομπή
Σύνδεσμος
<Go to ISI>://000263882700015
http://ac.els-cdn.com/S1532046408000646/1-s2.0-S1532046408000646-main.pdf?_tid=0964545aa68ec6c50bc655b6adefb2e9&acdnat=1335944746_a94a9ac4429423cb145b6c57d1c9e566
http://ac.els-cdn.com/S1532046408000646/1-s2.0-S1532046408000646-main.pdf?_tid=0964545aa68ec6c50bc655b6adefb2e9&acdnat=1335944746_a94a9ac4429423cb145b6c57d1c9e566
Γλώσσα
en
Εκδίδον τμήμα/τομέας
Όνομα επιβλέποντος
Εξεταστική επιτροπή
Γενική Περιγραφή / Σχόλια
Ίδρυμα και Σχολή/Τμήμα του υποβάλλοντος
Πανεπιστήμιο Ιωαννίνων. Σχολή Επιστημών και Τεχνολογιών. Τμήμα Βιολογικών Εφαρμογών και Τεχνολογιών