Highly flexible protein-peptide docking using CABS-dockMethods in Molecular Biology 1561, 69-94, 2017.
Modeling EphB4-EphrinB2 protein–protein interaction using flexible docking of a short linear motifBioMedical Engineering OnLine, doi: 10.1186/s12938-017-0362-7 , 2017.
One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS ModelMethods in Molecular Biology 1484, 83-113, 2017.
5-HT2 receptor affinity, docking studies and pharmacological evaluation of a series of 1,3-disubstituted thiourea derivativesEuropean Journal of Medicinal Chemistry 116, 173–186, 2016.
Coarse-grained simulations of membrane insertion and folding of small helical proteins using CABS modelJournal of Chemical Information and Modeling 56, 2207–2215, 2016.
Flexible protein-peptide docking using CABS-dock with knowledge about the binding siteProceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 195-201, arXiv:1605.09269 , 2016.
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-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.
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.
CABS-fold: server for the de novo and consensus-based prediction of protein structureNucleic Acids Research 41, W406-W411, 2013.
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular DynamicsInternational Journal of Molecular Sciences 14, 9893–9905, 2013.