Maciej Ciemny

PhD candidate

Contact

Publications

12. Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force FieldsInternational Journal of Molecular Sciences, 20: 606, 2019Ciemny Maciej, Badaczewska-Dawid A. E., Pikuzinska M., Kolinski A., Kmiecik Sebastian
13. Protein Structure Prediction Using Coarse-Grained ModelsComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: 27-59, 2019Błaszczyk Maciej, Gront Dominik, Kmiecik Sebastian, Kurciński Mateusz, Kolinski Michal, Ciemny Maciej, Ziolkowska Katarzyna, Panek Marta, Kolinski Andrzej
14. CABS-flex 2.0: a web server for fast simulations of flexibility of protein structuresNucleic Acids Res, 46: W338-W343, 2018Kuriata Aleksander, Gierut A. M., Oleniecki T., Ciemny Maciej, Kolinski A., Kurciński Mateusz, Kmiecik Sebastian
15. CABS-flex standalone: a simulation environment for fast modeling of protein flexibilityBioinformatics, 4: 694–695, 2018Kurciński Mateusz, Oleniecki T., Ciemny Maciej, Kuriata Aleksander, Kolinski A., Kmiecik Sebastian
16. Protein-peptide docking using CABS-dock and contact informationBriefings in Bioinformatics, 2018Błaszczyk Maciej, Ciemny Maciej, Kolinski A., Kurciński Mateusz, Kmiecik Sebastian
17. Protein-peptide docking: opportunities and challengesDrug Discovery Today, 23: 1530-1537, 2018Ciemny Maciej, Kurciński Mateusz, Kamel Karol, Kolinski Andrzej, Alam Nawsad, Schueler-Furman Ora, Kmiecik Sebastian
18. A protocol for CABS-dock protein-peptide docking driven by side-chain contact informationBiomedical Engineering Online, 16, 2017Kurciński Mateusz, Błaszczyk Maciej, Kolinski Andrzej, Kmiecik Sebastian, Ciemny Maciej
19. Highly Flexible Protein-Peptide Docking Using CABS-DockMethods in Molecular Biology, 1561: 69-94, 2017Ciemny Maciej, Kurciński Mateusz, Konrad Kozak, Andrzej Kolinski, Kmiecik Sebastian
20. Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motifBiomedical Engineering Online, 16, 2017Kurciński Mateusz, Błaszczyk Maciej, Kolinski Andrzej, Kmiecik Sebastian, Ciemny Maciej
21. Flexible protein-peptide docking using CABS-dock with knowledge about the binding siteProceedings Of The International Work-conference On Bioinformatics And Biomedical Engineering (iwwbio) In Granada, Spain, 195-201, Arxiv:1605.09269, 2016Kurciński Mateusz, Ciemny Maciej, Błaszczyk Maciej, Andrzej Koliński, Kmiecik Sebastian
22. Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interactionScientific Reports, 6, 2016Ciemny Maciej, Aleksander Debinski, Marta Paczkowska, Andrzej Kolinski, Kurciński Mateusz, Kmiecik Sebastian
23. Towards protein-protein docking with significant structural changes using CABS-dockProceedings Of The International Work-conference On Bioinformatics And Biomedical Engineering (iwwbio) In Granada, Spain, 207-213, Arxiv:1605.09266, 2016Ciemny Maciej, Kurciński Mateusz, Andrzej Koliński, Kmiecik Sebastian