Publications
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Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex StructuresProtein Structure Prediction 273–287, 2020.
Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASSProtein Structure Prediction 337–353, 2020.
Protein Structure Prediction Using CABS – A Consensus ApproachFrom Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 29–32, 2012.
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 docking using CABS-dock and contact informationBriefings in Bioinformatics bby080, 2018.
Protein fragment reconstruction using various modeling techniquesJournal of Computer-Aided Molecular Design 17, 725–38, 2003.
Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interactionScientific Reports 6, 37532, 2016.
Prediction of the optimal set of contacts to fold the smallest knotted protein.J Phys Condens Matter 27, 354109, 2015.
Protein modeling with reduced representation: statistical potentials and protein folding mechanismActa Biochimica Polonica 52, 741–8, 2005.
The protein folding problem: a biophysical enigmaCurrent Pharmaceutical Biotechnology 3, 329–347, 2002.
Phosphorylation of the N-terminal domain of ribosomal P-stalk protein uL10 governs its association with the ribosomeFEBS Letters 594, 3002-3019, 2020.
Protein structure prediction by tempering spatial constraintsJournal of Computer-Aided Molecular Design 19, 603–8, 2005.
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.
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.
Prediction of Experimental Phi Values in Protein Folding by Simulation with Knowledge-based Potentials: B Domain of Protein AFrom Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 79–82, 2012.
Protein modeling and structure prediction with a reduced representationActa Biochimica Polonica 51, 349–71, 2004.
Protein Folding: Flexible Lattice ModelsProgress of Theoretical Physics Supplement 138, 292–300, 2000.
PrefaceMultiscale Approaches to Protein Modeling , 2011.
Protein mechanical unfolding: Importance of non-native interactionsThe Journal of Chemical Physics 131, 215103, 2009.
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom modelsThe Journal of Chemical Physics 142, 145104 , 2015.
A protocol for CABS-dock protein–peptide docking driven by side-chain contact informationBioMedical Engineering OnLine, 16:73 , 2017.
Protein-protein docking with large-scale backbone flexibility using coarse-grained Monte-Carlo simulationsInternational Journal of Molecular Sciences 22(14), , 2021.
Protein structure prediction: combining de novo modeling with sparse experimental dataJournal of Computational Chemistry 28, 1668–76, 2007.