Protein-peptide docking: opportunities and challenges
Open accessAbstract
Peptides have recently attracted much attention as promising drug candidates. Rational design of peptide-derived therapeutics usually requires structural characterization of the underlying protein-peptide interaction. Given that experimental characterization can be difficult, reliable computational tools are needed. In recent years, a variety of approaches have been developed for 'protein-peptide docking', that is, predicting the structure of the protein-peptide complex, starting from the protein structure and the peptide sequence, including variable degrees of information about the peptide binding site and/or conformation. In this review, we provide an overview of protein-peptide docking methods and outline their capabilities, limitations, and applications in structure-based drug design. Key challenges are also briefly discussed, such as modeling of large-scale conformational changes upon binding, scoring of predicted models, and optimal inclusion of varied types of experimental data and theoretical predictions into an integrative modeling process.
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Other types of molecules interacting with proteins, as well as protein-protein interactions in membranes, have been studied extensively through the years.
“While other types of molecules interacting with proteins, as well as protein-protein interactions in membranes, have been studied extensively through the years [14–18]”
From Challenges in protein docking (2020) · cites this paper as [18]
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- Authors
- Ciemny, M., Kurcinski, M., Kamel, K., Kolinski, A., Alam, N., Schueler-Furman, O., & Kmiecik, S.
- Affiliations
- University of Warsaw (PL)
- Institute of Bioorganic Chemistry, Polish Academy of Sciences (PL)
- Hebrew University of Jerusalem (IL)
- Corresponding author
- Kmiecik, Sebastian
- Venue
- Drug Discovery Today
- Publisher
- Elsevier BV
- Published
- 2018-08
- Volume
- 23
- Issue
- 8
- Pages
- 1530-1537
- ISSN
- 1359-6446 (ISSN-L)
- OpenAlex
- W2800677598
- Cited by
- 306
- References
- 69
- Citations by year
- 2026: 31 · 2025: 40 · 2024: 32 · 2023: 41 · 2022: 52 · 2021: 39 · 2020: 39 · 2019: 26 · 2018: 6
- FWCI
- 2.70
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Drug Discovery Today (publishedVersion, cc-by)
- PubMed (publishedVersion)
- ReIn UW (University of Warsaw) (submittedVersion, cc-by-nc-nd)
- Funders
- National Science Center (NCN, Poland) (MAESTRO2014/14/A/ST6/00088)
- Topics
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- protein-peptide docking, protein-peptide interactions, peptide therapeutics, structure-based drug design, docking scoring, integrative modeling, experimental data integration
- MeSH terms
- Animals, Binding Sites, Humans, Peptides, Protein Binding, Protein Conformation, Structure-Activity Relationship, Drug Design, Molecular Docking Simulation
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