Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interactionScientific Reports 6, 37532, 2016.
Towards protein-protein docking with significant structural changes using CABS-dockProceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 207-213, arXiv:1605.09266 , 2016.
AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structuresNucleic 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 siteNucleic Acids Research 43 (W1), W419-W424, 2015.
Improving thermal stability of thermophilic l-threonine aldolase from Thermotoga maritima.Journal of Biotechnology 199, 69-76, 2015.
KnotProt: a database of proteins with knots and slipknotsNucleic Acids Research 43, D306-D314, 2015.
Prediction of the optimal set of contacts to fold the smallest knotted protein.J Phys Condens Matter 27, 354109, 2015.
BioShell-Threading: versatile Monte Carlo package for protein 3D threading.BMC Bioinformatics 15, 22, 2014.
CABS-flex predictions of protein flexibility compared with NMR ensemblesBioinformatics 30, 2150-2154, 2014.
Coarse-Grained Modeling of Protein DynamicsComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed. 1, 55-79, 2014.
Coarse-grained modeling of protein structure, dynamics and protein-protein interactionsTASK Quarterly 18, 219–229, 2014.
Coarse-Grained Protein Models in Structure PredictionComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed. 1, 25-53, 2014.
Connecting thermal and mechanical protein (un)folding landscapesBiophysical Journal 107(12), 2950-61, 2014.
Flexible docking of the fragment of the troponin I to the troponin CIWBBIO 2014 (2nd International Work-Conference on Bioinformatics and Biomedical Engineering) , 2014.
Key Factors Governing Fibril Formation Of Proteins: Insights From Simulations And ExperimentsTask Quarterly 18, 245–254, 2014.
Mechanical unfolding of DDFLN4 studied by the coarse-grained knowledge-based CABS modelTASK Quarterly 18, 373–378, 2014.
Mechanism of Folding and Binding of an Intrinsically Disordered Protein as Revealed by Ab Initio SimulationsJournal of Chemical Theory and Computation 10, 2224–2231, 2014.
Protocols for efficient simulations of long time protein dynamics using coarse-grained CABS modelProtein structure prediction (3rd Edition), Methods in Molecular Biology, Daisuke Kihara, Ed. 1137, 235-250, 2014.
CABS-flex: server for fast simulation of protein structure fluctuationsNucleic Acids Research 41, W427-W431, 2013.