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References¶
This page collects references to the methods, packages, and protocols related to CABS-flex standalone 3.
Coarse-grained protein modeling review¶
Kmiecik S., Gront D., Kolinski M., Wieteska L., Dawid A. E., Kolinski A. Coarse-grained protein models and their applications. Chemical Reviews, 2016, 116(14), 7898–7936. DOI: https://doi.org/10.1021/acs.chemrev.6b00163
Detailed CABS model description¶
Kolinski A. Protein modeling and structure prediction with a reduced representation. Acta Biochimica Polonica, 2004, 51, 349–371.
CABS-flex standalone¶
Kurcinski M., Oleniecki T., Ciemny M. P., Kuriata A., Kolinski A., Kmiecik S. CABS-flex standalone: a simulation environment for fast modeling of protein flexibility. Bioinformatics, 2019, 35(4), 694–695. DOI: https://doi.org/10.1093/bioinformatics/bty685
CABS-dock standalone¶
Kurcinski M., Ciemny M. P., Oleniecki T., Kuriata A., Badaczewska-Dawid A. E., Kolinski A., Kmiecik S. CABS-dock standalone: a toolbox for flexible protein–peptide docking. Bioinformatics, 2019, 35(20), 4170–4172. DOI: https://doi.org/10.1093/bioinformatics/btz185
CABS-dock applications review¶
Kurcinski M., Badaczewska-Dawid A., Kolinski M., Kolinski A., Kmiecik S. Flexible docking of peptides to proteins using CABS-dock. Protein Science, 2020, 29, 211–222. DOI: https://doi.org/10.1002/pro.3771
Linear and cyclic peptide modeling¶
Badaczewska-Dawid A. E., Wróblewski K., Kurcinski M., Kmiecik S. Structure prediction of linear and cyclic peptides using CABS-flex. Briefings in Bioinformatics, 2024, 25(2), bbae003. DOI: https://doi.org/10.1093/bib/bbae003
CABS-flex 3.0 web server¶
Wróblewski K., Zalewski M., Kuriata A., Kmiecik S. CABS-flex 3.0: an online tool for simulating protein structural flexibility and peptide modeling. Nucleic Acids Research, 2025, 53(W1), W95–W101. DOI: https://doi.org/10.1093/nar/gkaf412
cg2all reconstruction¶
Heo L., Feig M. One bead per residue can describe all-atom protein structures. Structure, 2024, 32(1), 97–111.e6. DOI: https://doi.org/10.1016/j.str.2023.10.013
CABS-flex MD validation¶
Jamroz M., Orozco M., Kolinski A., Kmiecik S. Consistent view of protein fluctuations from all-atom molecular dynamics and coarse-grained dynamics with knowledge-based force-field. Journal of Chemical Theory and Computation, 2013, 9, 119–125. DOI: https://doi.org/10.1021/ct300854w
CABS-flex NMR validation¶
Jamroz M., Kolinski A., Kmiecik S. CABS-flex predictions of protein flexibility compared with NMR ensembles. Bioinformatics, 2014, 30, 2150–2154. DOI: https://doi.org/10.1093/bioinformatics/btu184
CABS-flex 2.0 web server¶
Kuriata A., Gierut A. M., Oleniecki T., Ciemny M. P., Kolinski A., Kurcinski M., Kmiecik S. CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures. Nucleic Acids Research, 2018, 46, W338–W343. DOI: https://doi.org/10.1093/nar/gky356
CABS-flex applications review¶
Nithin C., Fornari R. P., Pilla S. P., Badaczewska-Dawid A. E., Wróblewski K., Kmiecik S. Exploring protein functions from structural flexibility using CABS-flex modeling. Protein Science, 2024, 33, e5090. DOI: https://doi.org/10.1002/pro.5090
pLDDT-guided flexibility modeling¶
Wróblewski K., Kmiecik S. Integrating AlphaFold pLDDT Scores into CABS-flex for enhanced protein flexibility simulations. Computational and Structural Biotechnology Journal, 2024, 23, 4350–4356. DOI: https://doi.org/10.1016/j.csbj.2024.11.047
Aggrescan3D and Aggrescan4D¶
Kuriata A., Iglesias V., Pujols J., Kurcinski M., Kmiecik S., Ventura S. Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility. Nucleic Acids Research, 2019, 47(W1), W300–W307. DOI: https://doi.org/10.1093/nar/gkz321
Bárcenas O., Kuriata A., Zalewski M., Iglesias V., Pintado-Grima C., Firlik G., Burdukiewicz M., Kmiecik S., Ventura S. Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation. Nucleic Acids Research, 2024, 52(W1), W170–W175. DOI: https://doi.org/10.1093/nar/gkae382
CABS-based disordered protein modeling¶
Ciemny M., Badaczewska-Dawid A. E., Pikuzinska M., Kolinski A., Kmiecik S. Modeling of disordered protein structures using Monte Carlo simulations and knowledge-based statistical force fields. International Journal of Molecular Sciences, 2019, 20, 606. DOI: https://doi.org/10.3390/ijms20030606
CABS-based flexible docking of cyclic peptides¶
Zalewski M., Badaczewska-Dawid A., Kmiecik S. Flexible docking of cyclic peptides to proteins using CABS-dock. Journal of Chemical Theory and Computation, 2025, 21(17), 8249–8254. DOI: https://doi.org/10.1021/acs.jctc.5c00995
Preprint¶
The CABS-flex standalone 3 manuscript is currently in preparation. Publication details, including the official bioRxiv preprint link, DOI, and citation text, will be updated here as soon as they become available.