+ Translate
+ Most Popular
Gaucher's disease;thirty-two years experience at Siriraj Hospital
A study of Macrobathra Meyrick from China (Lepidoptera, Cosmopterigidae)
First occurrence in ores of tetragonal chalcocite
Effects of trace element nutrition on sleep patterns in adult women
N.Z. range management guidelines. 2. Design of grazing management systems for tussock country
A case of lipoma of the esophagus
A revision of world Acanthosomatidae (Heteroptera: Pentatomidae): keys to and descriptions of subfamilies, tribes and genera, with designation of types
Life history of the coronate scyphozoan Linuche unguiculata (Swartz, 1788)
Perceptual restoration of obliterated sounds
Mutagenicity studies on two chromium(III) coordination compounds
The formation of the skeleton. I. Growth of a long bone. 1st appearance of a center of calcification
Leucopenia and abnormal liver function in travellers on malaria chemoprophylaxis
The joint commission: four key root causes loom large in sentinel event data
Treatment of vitiligo with topical 15% lactic acid solution in combination with ultra violet-A
Behaviour of dairy cows within three hours after feed supply: I. Influence of housing type and time elapsing after feed supply
Observations of the propagation velocity and formation mechanism of burst fractures caused by gunshot
Management and control of patients with type 2 diabetes mellitus in Lebanon: results from the International Diabetes Management Practices Study (IDMPS)
The diet composition and nutritional knowledge of patients with anorexia nervosa
Physoporella croatica Herak, 1958 of the Slovak karst Anisian (Slovakia, the West Carpathians Mts.)
Bright lights, big noise. How effective are vehicle warning systems?
Ein Plesiosaurier-Rest mit Magensteinen aus mittlerem Lias von Quedlinburg
Incidence of Chlamydia trachomatis in patients with sterility
Monster soup: the microscope and Victorian fantasy
Preliminary tests with residual sprays against poultry lice
Duration of the life of plants in phylogeny

PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence

PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence

Bioinformatics 34(19): 3289-3299

ISSN/ISBN: 1367-4803

PMID: 29726965

DOI: 10.1093/bioinformatics/bty352

Machine learning plays a substantial role in bioscience owing to the explosive growth in sequence data and the challenging application of computational methods. Peptide-recognition domains (PRDs) are critical as they promote coupled-binding with short peptide-motifs of functional importance through transient interactions. It is challenging to build a reliable predictor of peptide-binding residue in proteins with diverse types of PRDs from protein sequence alone. On the other hand, it is vital to cope up with the sequencing speed and to broaden the scope of study. In this paper, we propose a machine-learning-based tool, named PBRpredict, to predict residues in peptide-binding domains from protein sequence alone. To develop a generic predictor, we train the models on peptide-binding residues of diverse types of domains. As inputs to the models, we use a high-dimensional feature set of chemical, structural and evolutionary information extracted from protein sequence. We carefully investigate six different state-of-the-art classification algorithms for this application. Finally, we use the stacked generalization approach to non-linearly combine a set of complementary base-level learners using a meta-level learner which outperformed the winner-takes-all approach. The proposed predictor is found competitive based on statistical evaluation. PBRpredict-Suite software: Supplementary data are available at Bioinformatics online.

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 065393229

Download citation: RISBibTeXText

Related references

Fractional crystallization of the basaltic suite of Usu volcano, southwest Hokkaido, Japan, and its relationships with the associated felsic suite - Cristallisation fractionnée de la suite basaltique du Volcan Usu, au sud ouest de Hokkaido et ses relations avec la suite felsique associée. Lithos (Oslo. Print) 19(2): 129-140, 1986

Domain of EPI suite biotransformation models. Sar and Qsar in Environmental Research 21(5-6): 415-443, 2010

Petrografia da Suite Metaultramafica da sequencia vulcano-sedimentar Morro do Ferro na regiao de sul a oeste de Alpinopolis, MG (dominio norte do Complexo Campos Gerais)--Petrography of the meta-ultramafic suite of the Morro do Ferro volcano-sedimentary sequence in the southwestern Alpinopolis region, Minas Gerais (northern domain of the Campos Gerais Complex). Boletim IG-USP, Serie Cientifica 28: 160-162, 1997

A Transfinite Sequence of O-Models une Suite Transfinie d'o-Modeles. J. Symb. Logic 37(1): 96-102, 1972

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. Bmc Evolutionary Biology 8: 255, 2008

Logistic regression models to predict solvent accessible residues using sequence- and homology-based qualitative and quantitative descriptors applied to a domain-complete X-ray structure learning set. Journal of Applied Crystallography 48(Part 6): 1976-1984, 2015

Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite. Methods in Molecular Biology 1561: 235-254, 2017

SEQSEE: a comprehensive program suite for protein sequence analysis. Computer Applications in the Biosciences: Cabios 10(2): 121-132, 1994

Etude systematique de l'os penien des Mammiferes (suite). Rongeurs, famille des Sciurides (suite). Mammalia, Paris: 67-74, 1953

Notes on the delimitation between Nordhausen suite and Bernburg suite of the lower Bunter Sandstone. Zeitschrift fuer Geologische Wissenschaften 13(2): 179-184, 1985

Comparison of the Khanabad suite in the Paleogene of Tadzhikistan with the Chegan suite of the Aral region. Doklady Akademii Nauk SSSR: 145: 1341-1343, 1962

De Quelques Monuments Antiques Relatifs a la Suite des Affaires Criminelles (Suite). Revue Archéologique (Troisième Série) 13: 145-162, 1889

The BioTools Suite. A comprehensive suite of platform-independent bioinformatics tools. Molecular Biotechnology 19(1): 59-77, 2001

BioImage Suite: An integrated medical image analysis suite: An update. Insight Journal 2006: 209, 2006

The problem of distinguishing suite subdivisions in reef facies (on the example of the Usinsk Suite). Soviet Geology and Geophysics 28(4): 12-17, 1987