Identifying affinity classes of inorganic materials binding sequences via a graph-based model

Nan Du, Marc R. Knecht, Mark T. Swihart, Zhenghua Tang, Tiffany R. Walsh, Aidong Zhang

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Rapid advances in bionanotechnology have recently generated growing interest in identifying peptides that bind to inorganic materials and classifying them based on their inorganic material affinities. However, there are some distinct characteristics of inorganic materials binding sequence data that limit the performance of many widely-used classification methods when applied to this problem. In this paper, we propose a novel framework to predict the affinity classes of peptide sequences with respect to an associated inorganic material. We first generate a large set of simulated peptide sequences based on an amino acid transition matrix tailored for the specific inorganic material. Then the probability of test sequences belonging to a specific affinity class is calculated by minimizing an objective function. In addition, the objective function is minimized through iterative propagation of probability estimates among sequences and sequence clusters. Results of computational experiments on two real inorganic material binding sequence data sets show that the proposed framework is highly effective for identifying the affinity classes of inorganic material binding sequences. Moreover, the experiments on the structural classification of proteins (SCOP) data set shows that the proposed framework is general and can be applied to traditional protein sequences.

Original languageEnglish (US)
Article number6808499
Pages (from-to)193-204
Number of pages12
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Issue number1
StatePublished - Jan 1 2015


  • classification
  • Inorganic material
  • peptide sequences

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Applied Mathematics


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