Publications
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Analysis and optimization of interactions between peptides mimicking the GD2 ganglioside and the monoclonal antibody 14G2aInternational Journal of Molecular Medicine 28, 47–57, 2011.
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.
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.
Highly flexible protein-peptide docking using CABS-dockMethods in Molecular Biology 1561, 69-94, 2017.
Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins.Journal of Physicak Chemistry Letters 4, 180-188, 2013.
Key Factors Governing Fibril Formation Of Proteins: Insights From Simulations And ExperimentsTask Quarterly 18, 245–254, 2014.
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.
Mechanical strength of 17,134 model proteins and cysteine slipknots.PLoS Comput Biol 5, e1000547, 2009.
Mechanical stretching of proteins—a theoretical survey of the Protein Data BankJournal of Physics: Condensed Matter 19, , 2007.
Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulationsBiophys J 99, 238-47, 2010.
Modeling EphB4-EphrinB2 protein–protein interaction using flexible docking of a short linear motifBioMedical Engineering OnLine, 16:71 , 2017.
Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force FieldsInternational Journal of Molecular Sciences 20, , 2019.
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom modelsThe Journal of Chemical Physics 142, 145104 , 2015.
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.
Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interactionScientific Reports 6, 37532, 2016.
Protein–peptide docking using CABS-dock and contact informationBriefings in Bioinformatics bby080, 2018.
A protocol for CABS-dock protein–peptide docking driven by side-chain contact informationBioMedical Engineering OnLine, 16:73 , 2017.
On the remarkable mechanostability of scaffoldins and the mechanical clamp motif.Proceedings of the National Academy of Sciences of the United States of America 106, 13791-6, 2009.
On the remarkable mechanostability of scaffoldins and the mechanical clamp motif.Proceedings of the National Academy of Sciences of the United States of America 106, 13791-6, 2009.