Publications
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Correlated fluctuations of microparticles in viscoelastic solutions: quantitative measurement of material properties by microrheology in the presence of optical traps.Phys Rev E Stat Nonlin Soft Matter Phys 73, 061501, 2006.
Computational reconstruction of atomistic protein structures from coarse-grained modelsComputational and Structural Biotechnology Journal 18, 162-176, 2020.
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.
CABS-fold: server for the de novo and consensus-based prediction of protein structureNucleic Acids Research 41, W406-W411, 2013.
Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold AssemblyJournal of Chemical Theory and Computation 14 (4), 2277–2287, 2018.
Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein SolubilityMolecular Pharmaceutics 15, 3846-3859, 2018.
Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamicsBiophysical Journal 99, 3507–16, 2010.
Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energyJournal of Chemical Physics 113, 5065–5071, 2000.
Clustering as a supporting tool for structural drug designActa Poloniae Pharmaceutica. Drug Research 63, 436-8, 2006.
Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-FieldJournal of Chemical Theory and Computation 9, 119 - 125, 2013.
CABS-flex: server for fast simulation of protein structure fluctuationsNucleic Acids Research 41, W427-W431, 2013.
CABS-flex predictions of protein flexibility compared with NMR ensemblesBioinformatics 30, 2150-2154, 2014.
Computational study of binding of epothilone A to β-tubulinActa Biochimica Polonica 58, 255–60, 2011.
Characterization of protein-folding pathways by reduced-space modelingProceedings of the National Academy of Sciences of the United States of America 104, 12330–5, 2007.
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.
Comment on "Local knot model of entangled polymer chains"The Journal of Physical Chemistry 97, 3450, 1993.
Collapse Transition of Semiflexible Polymers in 2-dimensional SystemsActa Physica Polonica 79, 601-612, 1991.
Comparative modeling without implicit sequence alignmentsBioinformatics (Oxford, England) 23, 2522–7, 2007.
Coarse-grained Protein Modeling: Dynamics, Folding Pathways and Mechanical UnfoldingFrom Computational Biophysics to Systems Biology (CBSB11) Proceedings 8, 83–90, 2012.