Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Modeling Software & Servers

Try the CABSdock for protein-peptide docking

Biomolecules — dynamics & interactions

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2017
Fast and Accurate Accessible Surface Area Prediction Without a Sequence ProfileFaraggi, E., Kouza, M., Zhou, Y. & Kloczkowski, A.Methods in Molecular Biology 1484, 127-136, 2017.
The GOR Method of Protein Secondary Structure Prediction, and its Application as Protein Aggregation Prediction ToolKouza, M., Faraggi, E., Koliński, A. & Kloczkowski, A.Methods in Molecular Biology 1484, 7-24, 2017.
Highly flexible protein-peptide docking using CABS-dockCiemny, M., Kurcinski, M., Kozak, K., Koliński, A. & Kmiecik, S.Methods in Molecular Biology 1561, 69-94, 2017.
Modeling EphB4-EphrinB2 protein–protein interaction using flexible docking of a short linear motifCiemny, M., Kurcinski, M., Blaszczyk, M., Koliński, A. & Kmiecik, S.BioMedical Engineering OnLine, doi: 10.1186/s12938-017-0362-7 , 2017.
Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible modelKouza, M., Banerji, A., Koliński, A., Buhimschi, I.A. & Kloczkowski, A.Physical Chemistry Chemical Physics 19, 2990-9, 2017.
One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS ModelKmiecik, S. & Koliński, A.Methods in Molecular Biology 1484, 83-113, 2017.
Predicting real-valued protein residue fluctuation using FlexPredPeterson, L., Jamroz, M., Koliński, A. & Kihara, D.Methods in Molecular Biology 1484, 175-186, 2017.
A protocol for CABS-dock protein–peptide docking driven by side-chain contact informationKurcinski, M., Blaszczyk, M., Ciemny, M., Koliński, A. & Kmiecik, S.BioMedical Engineering OnLine, doi:10.1186/s12938-017-0363-6 , 2017.
Switch from thermal to force-driven pathways of protein refoldingKouza, M., Lan, P.Dang, Gabovich, A.M., Koliński, A. & Li, M.SuanThe Journal of Chemical Physics 146, 135101, 2017.
2016
5-HT2 receptor affinity, docking studies and pharmacological evaluation of a series of 1,3-disubstituted thiourea derivativesBielenica, A. et al.European Journal of Medicinal Chemistry 116, 173–186, 2016.
Coarse-Grained Protein Models and Their ApplicationsKmiecik, S. et al.Chemical Reviews 116, 7898–7936, 2016.
Coarse-grained simulations of membrane insertion and folding of small helical proteins using CABS modelPulawski, W., Jamroz, M., Kolinski, M., Koliński, A. & Kmiecik, S.Journal of Chemical Information and Modeling 56, 2207–2215, 2016.
Ensemble-based evaluation for protein structure modelsJamroz, M., Koliński, A. & Kihara, D.Bioinformatics 32, i314–i321, 2016.
Flexible protein-peptide docking using CABS-dock with knowledge about the binding siteKurcinski, M., Ciemny, M., Blaszczyk, M., Koliński, A. & Kmiecik, S.Proceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 195-201, arXiv:1605.09269 , 2016.
Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible dockingBlaszczyk, M. et al.Methods 93, 72–83, 2016.
Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approachRashid, S., Saraswathi, S., Kloczkowski, A., Sundaram, S. & Koliński, A.BMC Bioinformatics 17, , 2016.
Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interactionCiemny, M. et al.Scientific Reports 6, 37532, 2016.
Towards protein-protein docking with significant structural changes using CABS-dockCiemny, M., Kurcinski, M., Koliński, A. & Kmiecik, S.Proceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 207-213, arXiv:1605.09266 , 2016.
2015
AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structuresZambrano, R. et al.Nucleic Acids Research 43 (W1), W306-W313, 2015.
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding siteKurcinski, M., Jamroz, M., Blaszczyk, M., Koliński, A. & Kmiecik, S.Nucleic Acids Research 43 (W1), W419-W424, 2015.
Coarse-Grained Modeling of Peptide Docking Associated With Large Conformation Transitions of The Binding Protein: Troponin I Fragment–Troponin C SystemWabik, J., Kurcinski, M. & Koliński, A.Molecules 20, 10763-10780, 2015.
Improving thermal stability of thermophilic l-threonine aldolase from Thermotoga maritima.Wieteska, L. et al.Journal of Biotechnology 199, 69-76, 2015.
KnotProt: a database of proteins with knots and slipknotsJamroz, M. et al.Nucleic Acids Research 43, D306-D314, 2015.
Prediction of the optimal set of contacts to fold the smallest knotted protein.Dabrowski-Tumanski, P., Jarmolinska, A.I. & Sulkowska, J.I.J Phys Condens Matter 27, 354109, 2015.
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom modelsKouza, M., Co, N.Truong, Nguyen, P.Hoang, Koliński, A. & Li, M.SuanThe Journal of Chemical Physics 142, 145104 , 2015.

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