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References¶
This page collects references to the methods, packages, and protocols related to CABS-flex standalone 3.
Preprint¶
Nithin C., Wróblewski K., Szukalo P., Fasemire A., Kuriata A., Kurcinski M., Kolinski A., Kmiecik S. CABS-flex standalone 3: an open command-line platform for protein flexibility simulation, peptide structure modeling, and protein-peptide docking. arXiv, 2026, arXiv:2606.24487 [q-bio.BM]. DOI: https://doi.org/10.48550/arXiv.2606.24487
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
CABS-dock contact-guided docking¶
Blaszczyk M., Ciemny M., Kolinski A., Kurcinski M., Kmiecik S. Protein–peptide docking using CABS-dock and contact information. Briefings in Bioinformatics, 2018, 19(6), 1346–1355. DOI: https://doi.org/10.1093/bib/bby080
GPCR extracellular loop modeling¶
Kmiecik S., Jamroz M., Kolinski M. Structure prediction of the second extracellular loop in G-protein-coupled receptors. Biophysical Journal, 2014, 106(11), 2408–2416. DOI: https://doi.org/10.1016/j.bpj.2014.04.032
CABS-dock all-atom reconstruction and refinement¶
Badaczewska-Dawid A. E., Khramushin A., Kolinski A., Schueler-Furman O., Kmiecik S. Protocols for all-atom reconstruction and high-resolution refinement of protein–peptide complex structures. In Protein Structure Prediction (pp. 273–287). Humana, New York, NY. DOI: https://doi.org/10.1007/978-1-0716-0708-4_17
CABS-based peptide folding and binding mechanism¶
Kurcinski M., Kolinski A., Kmiecik S. Mechanism of folding and binding of an intrinsically disordered protein as revealed by ab initio simulations. Journal of Chemical Theory and Computation, 2014, 10(5), 2224–2231. DOI: https://doi.org/10.1021/ct401083s