Eugene Shakhnovich

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Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the inferred effective Potts Hamiltonian and real protein structure and energetics remain untested so far. Here we use(More)
have made it hard to synthesize ELPs with widely ranging compositions and lengths, hampering exploration of the relationships between phase-transition behaviour, protein sequence, chain length and coacervate secondary and tertiary structure. Using OERCA, Chilkoti and colleagues show the synthesis of an ELP gene library with large breadths of sequences and(More)
To assess the mutational robustness of nucleic acids, many genome- and protein-level studies have been performed, where nucleic acids are treated as genetic information carriers and transferrers. However, the molecular mechanisms through which mutations alter the structural, dynamic, and functional properties of nucleic acids are poorly understood. Here we(More)
We study solutions of statistically neutral polyampholyte chains containing a large fraction of neutral monomers. It is known that such solutions phase separate at very low concentrations, even if the quality of the solvent with respect to the neutral monomers is good. The precipitate is semidilute if the chains are weakly charged. This paper considers(More)
In the recent Letter [1] we reported the results of simulations concerning chain length dependence of protein folding time. We argued that first order phase transition scenario where nucleus size does not depend on chain length and the role of surface energy is played by loop entropy (which depends logarithmically on chain length) may explain the observed(More)
To isolate functional nucleic acids that bind to defined targets with high affinity and specificity, which are known as aptamers, the systematic evolution of ligands by exponential enrichment (SELEX) methodology has emerged as the preferred approach. Here, we propose a computational approach, SELEX in silico, that allows the sequence space to be more(More)
The mechanical unfolding of proteins under a stretching force has an important role in living systems and is a logical extension of the more general protein folding problem. Recent advances in experimental methodology have allowed the stretching of single molecules, thus rendering this process ripe for computational study. We use all-atom Monte Carlo(More)
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