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Open Access Research article

AMS 3.0: prediction of post-translational modifications

Subhadip Basu1 and Dariusz Plewczynski2*

Author affiliations

1 Department of Computer Science and Engineering, Jadavpur University, Kolkata - 700032, India

2 Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, 5a Street, 02-106 Warsaw, Poland

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Citation and License

BMC Bioinformatics 2010, 11:210  doi:10.1186/1471-2105-11-210

Published: 28 April 2010

Abstract

Background

We present here the recent update of AMS algorithm for identification of post-translational modification (PTM) sites in proteins based only on sequence information, using artificial neural network (ANN) method. The query protein sequence is dissected into overlapping short sequence segments. Ten different physicochemical features describe each amino acid; therefore nine residues long segment is represented as a point in a 90 dimensional space. The database of sequence segments with confirmed by experiments post-translational modification sites are used for training a set of ANNs.

Results

The efficiency of the classification for each type of modification and the prediction power of the method is estimated here using recall (sensitivity), precision values, the area under receiver operating characteristic (ROC) curves and leave-one-out tests (LOOCV). The significant differences in the performance for differently optimized neural networks are observed, yet the AMS 3.0 tool integrates those heterogeneous classification schemes into the single consensus scheme, and it is able to boost the precision and recall values independent of a PTM type in comparison with the currently available state-of-the art methods.

Conclusions

The standalone version of AMS 3.0 presents an efficient way to indentify post-translational modifications for whole proteomes. The training datasets, precompiled binaries for AMS 3.0 tool and the source code are available at http://code.google.com/p/automotifserver webcite under the Apache 2.0 license scheme.