Natural language processing in text mining for structural modeling of protein complexes
Open accessAbstract
BACKGROUND: Structural modeling of protein-protein interactions produces a large number of putative configurations of the protein complexes. Identification of the near-native models among them is a serious challenge. Publicly available results of biomedical research may provide constraints on the binding mode, which can be essential for the docking. Our text-mining (TM) tool, which extracts binding site residues from the PubMed abstracts, was successfully applied to protein docking (Badal et al., PLoS Comput Biol, 2015; 11: e1004630). Still, many extracted residues were not relevant to the docking. RESULTS: We present an extension of the TM tool, which utilizes natural language processing (NLP) for analyzing the context of the residue occurrence. The procedure was tested using generic and specialized dictionaries. The results showed that the keyword dictionaries designed for identification of protein interactions are not adequate for the TM prediction of the binding mode. However, our dictionary designed to distinguish keywords relevant to the protein binding sites led to considerable improvement in the TM performance. We investigated the utility of several methods of context analysis, based on dissection of the sentence parse trees. The machine learning-based NLP filtered the pool of the mined residues significantly more efficiently than the rule-based NLP. Constraints generated by NLP were tested in docking of unbound proteins from the DOCKGROUND X-ray benchmark set 4. The output of the global low-resolution docking scan was post-processed, separately, by constraints from the basic TM, constraints re-ranked by NLP, and the reference constraints. The quality of a match was assessed by the interface root-mean-square deviation. The results showed significant improvement of the docking output when using the constraints generated by the advanced TM with NLP. CONCLUSIONS: The basic TM procedure for extracting protein-protein binding site residues from the PubMed abstracts was significantly advanced by the deep parsing (NLP techniques for contextual analysis) in purging of the initial pool of the extracted residues. Benchmarking showed a substantial increase of the docking success rate based on the constraints generated by the advanced TM with NLP.
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Automated procedures like text mining of publicly available online publications face copyright restrictions and are hindered by still limited amount of open-access publications.
“Such automated procedures, like text mining of publicly available online publications [47] face copyright restrictions and are hindered by still limited amount of open-access publications.”
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Sorted by citations
Vakser, I. A. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.07.001 · Cited by 62 · see citing works
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- Authors
- Badal, V. D., Kundrotas, P. J., & Vakser, I. A.
- Affiliations
- University of Kansas (US)
- Corresponding author
- Kundrotas, Petras J.
- Vakser, Ilya A.
- Venue
- BMC Bioinformatics
- Published
- 2018-03-05
- Volume
- 19
- Issue
- 1
- Pages
- 84-84
- ISSN
- 1471-2105 (ISSN-L)
- PMC
- PMC5838950
- OpenAlex
- W2794764013
- Cited by
- 34
- References
- 58
- Citations by year
- 2025: 3 · 2024: 4 · 2023: 4 · 2022: 5 · 2021: 6 · 2020: 5 · 2019: 4 · 2018: 3
- FWCI
- 1.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Bioinformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- KU ScholarWorks (University of Kansas) (submittedVersion, cc-by)
- Funders
- National Institutes of Health (R01GM074255)
- National Science Foundation (DBI1262621, DBI1565107)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- text mining, natural language processing, protein-protein interaction, protein docking, binding site residues, contextual analysis, parse trees, keyword dictionary, protein complexes, PubMed abstracts
- MeSH terms
- Machine Learning, Models, Molecular, Natural Language Processing, Protein Binding, Proteins, Semantics, Data Mining, Support Vector Machine
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