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P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features

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Algorithms for Computational Biology (AlCoB 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9199))

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Abstract

The knowledge of protein-ligand binding sites is vital prerequisite for any structure-based virtual screening campaign. If no prior knowledge about binding sites is available, the ligand-binding site prediction methods are the only way to obtain the necessary information. Here we introduce P2RANK, a novel machine learning-based method for prediction of ligand binding sites from protein structure. P2RANK uses Random Forests learner to infer ligandability of local chemical neighborhoods near the protein surface which are represented by specific near-surface points and described by aggregating physico-chemical features projected on those points from neighboring protein atoms. The points with high predicted ligandability are clustered and ranked to obtain the resulting list of binding site predictions. The new method was compared with a state-of-the-art binding site prediction method Fpocket on three representative datasets. The results show that P2RANK outperforms Fpocket by 10 to 20 % points on all the datasets. Moreover, since P2RANK does not rely on any external software for computation of various complex features, such as sequence conservation scores or binding energies, it represents an ideal tool for inclusion into future structural bioinformatics pipelines.

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Acknowledgments

This work was supported by the Czech Science Foundation grant 14-29032P and by project SVV-2015-260222 and by the Charles University in Prague, project GA UK No. 174615.

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Authors and Affiliations

  1. FMP, Department of Software Engineering, Charles University in Prague, Malostranské nám. 25, 118 00, Prague, Czech Republic

    Radoslav Krivák & David Hoksza

Authors
  1. Radoslav Krivák
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  2. David Hoksza
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Correspondence to Radoslav Krivák .

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Editors and Affiliations

  1. Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

    Adrian-Horia Dediu

  2. Faculty of Science, National Autonomous University of Mexico - UNAM, Mexico City, Mexico

    Francisco Hernández-Quiroz

  3. Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

    Carlos Martín-Vide

  4. Institute for Research in Applied Mathematics and Systems – IIMAS, National Autonomous University of Mexico - UNAM, Mexico City, Mexico

    David A. Rosenblueth

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Krivák, R., Hoksza, D. (2015). P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features. In: Dediu, AH., Hernández-Quiroz, F., Martín-Vide, C., Rosenblueth, D. (eds) Algorithms for Computational Biology. AlCoB 2015. Lecture Notes in Computer Science(), vol 9199. Springer, Cham. https://doi.org/10.1007/978-3-319-21233-3_4

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  • DOI: https://doi.org/10.1007/978-3-319-21233-3_4

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  • Publisher Name: Springer, Cham

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