Andrzej Kolinski Research Group

Coarse-grained protein modeling

Read our new review on coarse-grained modeling

Modeling Software & Servers

Try the CABSdock for protein-peptide docking

Biomolecules — dynamics & interactions

Read relevant publications
0
-1
-2
-3
Previous Pause Next

Publications of this author

[256]
Highly flexible protein-peptide docking using CABS-dock
Author(s): M. Ciemny, M. Kurcinski, K. Kozak, A. Koliński, S. Kmiecik
Methods in Molecular Biology, 1561:69-94, 2017
[255]
The GOR Method of Protein Secondary Structure Prediction, and its Application as Protein Aggregation Prediction Tool
Author(s): M. Kouza, E. Faraggi, A. Koliński, A. Kloczkowski
Methods in Molecular Biology, 1484:7-24, 2017
[254]
One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model
Author(s): S. Kmiecik, A. Koliński
Methods in Molecular Biology, 1484:83-113, 2017
[253]
Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction
Author(s): M. Ciemny, A. Debinski, M. Paczkowska, A. Koliński, M. Kurcinski, S. Kmiecik
Scientific Reports, 6:37532, 2016
[252]
Coarse-grained simulations of membrane insertion and folding of small helical proteins using CABS model
Author(s): W. Pulawski, M. Jamroz, M. Kolinski, A. Koliński, S. Kmiecik
Journal of Chemical Information and Modeling, 56:2207–2215, 2016
[251]
Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach
Author(s): S. Rashid, S. Saraswathi, A. Kloczkowski, S. Sundaram, A. Koliński
BMC Bioinformatics, 17:2016
[250]
Ensemble-based evaluation for protein structure models
Author(s): M. Jamroz, A. Koliński, D. Kihara
Bioinformatics, 32:i314–i321, 2016
[249]
Coarse-Grained Protein Models and Their Applications
Author(s): S. Kmiecik, D. Gront, M. Kolinski, L. Wieteska, A. Dawid, A. Koliński
Chemical Reviews, 116:7898–7936, 2016
[248]
Flexible protein-peptide docking using CABS-dock with knowledge about the binding site
Author(s): M. Kurcinski, M. Ciemny, M. Blaszczyk, A. Koliński, S. Kmiecik
Proceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 195-201, arXiv:1605.09269, 2016
[247]
Towards protein-protein docking with significant structural changes using CABS-dock
Author(s): M. Ciemny, M. Kurcinski, A. Koliński, S. Kmiecik
Proceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 207-213, arXiv:1605.09266, 2016
[246]
5-HT2 receptor affinity, docking studies and pharmacological evaluation of a series of 1,3-disubstituted thiourea derivatives
Author(s): A. Bielenica, E. Kedzierska, M. Kolinski, S. Kmiecik, A. Koliński, F. Fiorino, B. Severino, E. Magli, I. Rossi, P. Massarelli, A.E. Kozioł, A. Sawczenko, M. Struga
European Journal of Medicinal Chemistry, 116:173–186, 2016
[245]
Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking
Author(s): M. Blaszczyk, M. Kurcinski, M. Kouza, L. Wieteska, A. Debinski, A. Koliński, S. Kmiecik
Methods, 93:72–83, 2016
[244]
Coarse-Grained Modeling of Peptide Docking Associated With Large Conformation Transitions of The Binding Protein: Troponin I Fragment–Troponin C System
Author(s): J. Wabik, M. Kurcinski, A. Koliński
Molecules, 20:10763-10780, 2015
[243]
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models
Author(s): M. Kouza, N.Truong Co, P.Hoang Nguyen, A. Koliński, M.Suan Li
The Journal of Chemical Physics, 142:145104 , 2015
[242]
Improving thermal stability of thermophilic l-threonine aldolase from Thermotoga maritima.
Author(s): L. Wieteska, M. Ionov, J. Szemraj, C. Feller, A. Koliński, D. Gront
Journal of Biotechnology, 199:69-76, 2015
[241]
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
Author(s): M. Kurcinski, M. Jamroz, M. Blaszczyk, A. Koliński, S. Kmiecik
Nucleic Acids Research, 43 (W1):W419-W424, 2015
[240]
Mechanical unfolding of DDFLN4 studied by the coarse-grained knowledge-based CABS model
Author(s): M. Kouza, M. Jamroz, D. Gront, S. Kmiecik, A. Koliński
TASK Quarterly, 18: 373–378, 2014
[239]
Coarse-grained modeling of protein structure, dynamics and protein-protein interactions
Author(s): A. Koliński, S. Kmiecik, M. Jamroz, M. Blaszczyk, M. Kouza, M. Kurcinski
TASK Quarterly, 18:219–229, 2014
[238]
Flexible docking of the fragment of the troponin I to the troponin C
Author(s): J. Wabik, M. Kurcinski, A. Koliński
IWBBIO 2014 (2nd International Work-Conference on Bioinformatics and Biomedical Engineering), 2014
[237]
Mechanism of Folding and Binding of an Intrinsically Disordered Protein as Revealed by Ab Initio Simulations
Author(s): M. Kurcinski, A. Koliński, S. Kmiecik
Journal of Chemical Theory and Computation, 10:2224–2231, 2014
[236]
CABS-flex predictions of protein flexibility compared with NMR ensembles
Author(s): M. Jamroz, A. Koliński, S. Kmiecik
Bioinformatics, 30:2150-2154, 2014
[235]
BioShell-Threading: versatile Monte Carlo package for protein 3D threading.
Author(s): P. Gniewek, A. Koliński, A. Kloczkowski, D. Gront
BMC Bioinformatics, 15:22, 2014
[234]
Coarse-Grained Modeling of Protein Dynamics
Author(s): S. Kmiecik, J. Wabik, M. Kolinski, M. Kouza, A. Koliński
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed., 1:55-79, 2014
[233]
Coarse-Grained Protein Models in Structure Prediction
Author(s): M. Blaszczyk, D. Gront, S. Kmiecik, K. Ziolkowska, M. Panek, A. Koliński
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed., 1:25-53, 2014
[232]
Protocols for efficient simulations of long time protein dynamics using coarse-grained CABS model
Author(s): M. Jamroz, A. Koliński, S. Kmiecik
Protein structure prediction (3rd Edition), Methods in Molecular Biology, Daisuke Kihara, Ed., 1137:235-250, 2014

Pages