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A New Graph Theoretic Approach for Protein Threading

Song Y., Qu J., Xu Y., Cai L.

Fundamenta Informaticae

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2016

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Vol. 145, nr 2

151--170

EN

In this paper, we develop a novel graph theoretic approach for protein threading. In order to perform the protein sequence-structure alignment in threading both efficiently and accurately, we develop a graph model to describe the tertiary structure of a protein family and the alignment between a sequence and a family can be efficiently computed with a dynamic programming algorithm when the tree width of the graph model is a small integer. Our experiments show that this new approach is significantly faster than existing tools for threading and can achieve comparable prediction accuracy.

2

Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling?

Bryliński M.

Bio-Algorithms and Med-Systems

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2015

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Vol. 11, no. 1

1--7

EN

The Protein Data Bank (PDB) undergoes an exponential expansion in terms of the number of macromolecular structures deposited every year. A pivotal question is how this rapid growth of structural information improves the quality of three-dimensional models constructed by contemporary bioinformatics approaches. To address this problem, we performed a retrospective analysis of the structural coverage of a representative set of proteins using remote homology detected by COMPASS and HHpred. We show that the number of proteins whose structures can be confidently predicted increased during a 9-year period between 2005 and 2014 on account of the PDB growth alone. Nevertheless, this encouraging trend slowed down noticeably around the year 2008 and has yielded insignificant improvements ever since. At the current pace, it is unlikely that the protein structure prediction problem will be solved in the near future using existing template-based modeling techniques. Therefore, further advances in experimental structure determination, qualitatively better approaches in fold recognition, and more accurate template-free structure prediction methods are desperately needed.

3

Implementation and evaluation of new protocol for comparative modeling of protein structures

Strumillo M., Dawid A. E., Szczasiuk A., Gront D.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2014

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Vol. 18, No 4

379--384

EN

Template-based modeling (termed also Comparative or Homology Modeling) of a protein structure is one of ubiquitous tasks of structural bioinfor matics. The method can deliver model structures important for testing biological hypotheses, virtual docking and drug design. The performance of these methods is evaluated every two years during a Critical Assessment of Protein Structure Prediction (CASP) experiment. In this contribution we present a new automated protocol for template-base d modeling, which combines computational tools recently developed in our laboratory: the dat abase of protein domain structures (BDDB) with one dimensional and three dimensional thread ing applications. The protocol was tested during a CASP11 experiment.