Publications
Pages
Lattice models of protein folding. Dynamics and thermodynamicsLattice models of protein folding. Dynamics and thermodynamics, Austin, TX, Chapman & Hall. (Chapman & Hall.: Austin, TX, 1996).
Ab initio modelingStructural Genomics and High Throughput Structural Biology 137-162, 2006.
Application of reduced models to protein structure predictionTheoretical and Computational Chemistry: Computational Molecular Biology 8, 397–440, 1999.
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 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.
Contact mapEncyclopedia of Molecular Biology 567–571, 1999.
Dynamics of dense polymer systems: Computer simulations and analytic theoriesAdvances in Chemical Physics 77, 223–278, 1990.
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.
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.
Lattice polymers and protein modelsMultiscale Approaches to Protein Modeling 1-20, 2011.
Monte Carlo approaches to the protein folding problemAdvances in Chemical Physics: Monte Carlo Methods in Chemical Physics 105, 203–242, 1999.
Monte Carlo lattice dynamics and the prediction of protein foldsComputer Simulations of Biomolecular Systems. Theoretical and Experimental Applications pp, 395–429, 1997.
Multiscale approach to protein folding dynamicsMultiscale Approaches to Protein Modeling 281-294, 2011.
Multiscale protein and peptide dockingMultiscale Approaches to Protein Modeling 21-34, 2011.
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.
PrefaceMultiscale Approaches to Protein Modeling , 2011.
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.
Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex StructuresProtein Structure Prediction 273–287, 2020.
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.
Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASSProtein Structure Prediction 337–353, 2020.
Template-free predictions of three-dimensional protein structures: From first principles to knowledge-based potentialsPrediction of Protein Structures, Functions, and Interactions 117-142, 2008.
Theoretical models and simulations of polymer chainsPhysical Properties of Polymers Handbook , 2006.