@article {528, title = {Protein-peptide docking: opportunities and challenges}, journal = {Drug Discovery Today}, volume = {23}, year = {2018}, pages = {1530-1537}, abstract = {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 {\textquoteright}protein-peptide docking{\textquoteright}, 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.}, doi = {10.1016/j.drudis.2018.05.006}, url = {https://www.sciencedirect.com/science/article/pii/S1359644617305937}, author = {Maciej Pawel Ciemny and Mateusz Kurcinski and Karol Kamel and Andrzej Koli{\'n}ski and Nawsad Alam and Ora Schueler-Furman and Sebastian Kmiecik} }