Eun-Jong Hong

Learn More
BACKGROUND By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. RESULTS Here we describe(More)
We have evaluated the fate of misfolded protein domains in the Saccharomyces cerevisiae secretory pathway by fusing mutant forms of the NH2-terminal domain of lambda repressor protein to the secreted protein invertase. The hybrid protein carrying the wild-type repressor domain is mostly secreted to the cell surface, whereas hybrid proteins with amino acid(More)
We present an exact method for the global minimum energy conformation (GMEC) search of protein side-chains. Our method consists of a branch-and-bound (B&B) framework and a new subproblem-pruning scheme. The pruning scheme consists of upper/lower-bounding methods and problem-size reduction techniques. We explore a way of using the tree-reweighted max-product(More)
The search for the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a NP-hard optimization problem. Dead-end elimination (DEE) methods combined with systematic A* search (DEE/A*) has proven useful, but may(More)
—The prediction of energetically favorable side-chain conformations is a fundamental element in homology modeling of proteins and the design of novel protein sequences. The space of side-chain conformations can be approximated by a discrete space of probabilistically representative side-chain conformations (called rotamers). The problem is, then, to find a(More)
The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Abstract Background: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type(More)
  • 1