Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders are discussed. Similar patterns for non-randomness are found

/polar model sequences and enzymes display hydrophobicity correlations that are qualitatively similar. ) irback@thep.lu.se 1 x1. Introduction The protein design problem amounts to finding an amino acid sequence given a target structure, which is stable in the target structure, and is able to fold fast

Introduction Proteins are heterogenuous chain molecules composed of sequences of amino acids. The protein folding problem amounts to given a sequence of amino acids predict the protein 3D structure. There are 20 different amino acids. In the Bioinformatics approach one aims at extracting rules

we discuss an alternative Monte Carlo approach, multisequence design, where conformation and sequence degrees of freedom are simultaneously probed. The method is explored on hydrophobic/polar models. A statistical analysis of sequence correlations is also discussed. It is found that hydrophobic

Coarse-grained protein modeling tool, CABS, is used in multiscale modeling of protein dynam-ics. It is demonstrated that the stochastic (Monte Carlo) dynamics, combined with all-atom re-finement of the coarse-grained structures follows observed in experiments folding pathways of small proteins

. The method is then successfully applied to lattice chains with up to 50 monomers, and to off-lattice 20-mers. Conclusions: The multisequence Monte Carlo method offers a new approach to sequence design in coarse-grained models. It is much more efficient than previous Monte Carlo methods, and is, as it stands

Abstract: We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After

Abstract: We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After

ABSTRACT We develop a coarse-grained protein model with a simplified amino acid interaction potential. Using this model, we perform discrete molecular dynamics folding simulations of a small 20-residue protein—Trp-cage—from a fully extended conformation. We demonstrate the ability of the Trp

Although a wide variety of proteins can assemble into amyloid fibrils, the structure of the early oligomeric species on the aggregation pathways remains unknown at an atomic level of detail. In this paper we report, using molecular dynamics simulations with the OPEP coarse-grained force field