Explicit-Solvent All-Atom Molecular Dynamics of Peptide AggregationComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics 541–558, 2019.
Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force FieldsInternational Journal of Molecular Sciences 20, , 2019.
Protein Dynamics Simulations Using Coarse-Grained ModelsComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics 61–87, 2019.
Protein Structure Prediction Using Coarse-Grained ModelsComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics 27–59, 2019.
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structuresNucleic Acids Research, gky356 , 2018.
CABS-flex standalone: a simulation environment for fast modeling of protein flexibilityBioinformatics bty685, 2018.
Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold AssemblyJournal of Chemical Theory and Computation 14 (4), 2277–2287, 2018.
Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational studyThe Journal of Chemical Physics 148, 215106, 2018.
Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network ModelsInternational Journal of Molecular Sciences 19, , 2018.
Protein–peptide docking using CABS-dock and contact informationBriefings in Bioinformatics bby080, 2018.
The GOR Method of Protein Secondary Structure Prediction, and its Application as Protein Aggregation Prediction ToolMethods in Molecular Biology 1484, 7-24, 2017.
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, 16:71 , 2017.
Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible modelPhysical Chemistry Chemical Physics 19, 2990-9, 2017.
One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS ModelMethods in Molecular Biology 1484, 83-113, 2017.
Predicting real-valued protein residue fluctuation using FlexPredMethods in Molecular Biology 1484, 175-186, 2017.
A protocol for CABS-dock protein–peptide docking driven by side-chain contact informationBioMedical Engineering OnLine, 16:73 , 2017.
SURPASS Low-Resolution Coarse-Grained Protein ModelingJournal of Chemical Theory and Computation 13(11), 5766-5779, 2017.
Switch from thermal to force-driven pathways of protein refoldingThe Journal of Chemical Physics 146, 135101, 2017.