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Protein-Folding Dynamics: Overview of Molecular Simulation TechniquesTopology of Type II REases revisited; structural classes and the common conserved coreMultiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides.Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides.Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds.A united residue force-field for calcium-protein interactions.Lessons from application of the UNRES force field to predictions of structures of CASP10 targetsImprovement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.WeFold: a coopetition for protein structure predictionAn improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. IIInvestigation of protein folding by coarse-grained molecular dynamics with the UNRES force fieldImplementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.Coarse-grained force field: general folding theory.Kinks, loops, and protein folding, with protein A as an example.Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interactionFurther evidence for the absence of polyproline II stretch in the XAO peptide.In situ data analytics and indexing of protein trajectories.Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: comparison between theory and experiment.Conformational studies of the alpha-helical 28-43 fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus.Conformational studies of the C-terminal 16-amino-acid-residue fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus.Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure.Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force FieldPotential of mean force of association of large hydrophobic particles: toward the nanoscale limit.Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin-binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein.Accounting for a mirror-image conformation as a subtle effect in protein folding.Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chainsbeta-hairpin-forming peptides; models of early stages of protein folding.A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field.Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures.Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular proteinA unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field.PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics.Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins.DNA Duplex Formation with a Coarse-Grained ModelSimple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains.Common functionally important motions of the nucleotide-binding domain of Hsp70
P50
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Józef Adam Liwo
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Józef Adam Liwo
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