Eun-Jong Hong

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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. Here we describe the release of PFAAT(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)
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 subproblempruning 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 prediction of energetically favorable sidechain 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)
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