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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2018
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structuresKuriata, A. et al.Nucleic Acids Research, gky356 , 2018.
Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold AssemblyDawid, A., Gront, D. & Koliński, A.Journal of Chemical Theory and Computation 14 (4), 2277–2287, 2018.
In silico analysis of cytochrome P450 monooxygenases in chronic granulomatous infectious fungus Sporothrix schenckii: Special focus on CYP51.Matowane, R.Godfrey et al.Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1866(1), 166-177, 2018.
Protein-peptide docking: opportunities and challengesCiemny, M.Pawel et al.Drug Discovery Today, doi:10.1016/j.drudis.2018.05.006 , 2018.
Synthesis, structural and antimicrobial studies of type II topoisomerase-targeted copper(II) complexes of 1,3-disubstituted thiourea ligandsBielenica, A. et al.Journal of Inorganic Biochemistry 182, 61 - 70, 2018.
2017
Biofunctionalisation of p-doped silicon with cytochrome c553 minimises charge recombination and enhances photovoltaic performance of the all-solid-state photosystem I-based biophotoelectrodeOlmos, J.David Jann et al.RSC Advances 7, 47854-47866, 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, 16:71 , 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, 16:73 , 2017.
SURPASS Low-Resolution Coarse-Grained Protein ModelingDawid, A., Gront, D. & Koliński, A.Journal of Chemical Theory and Computation 13(11), 5766-5779, 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.
Toward more efficient simulations of slow processes in large biomolecular systems: Comment on "Ligand diffusion in proteins via enhanced sampling in molecular dynamics" by Jakub Rydzewski and Wieslaw Nowak.Koliński, A.Physics of Life Reviews 22–23, 85-87, 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.

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