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Many biological sequence databases have redundant sequences which are not helpful to statistical analysis and require more computational time and resources to process. This lead us to design a new and fast program to generate a non-redundant sequence set. A graph theoretic algorithm was designed to process BLAST output and remove redundant proteins from a protein sequence database. We have developed...
Side-chain positioning is a central component of homology modeling and protein design. A simple solution is introduced by assuming a fixed backbone and discretizing the amino acid side-chain conformations into energetically favorable rotamers. For each possible combination of rotamers, an energy function is used to evaluate its fitness for the target conformation. While constructing complete energy...
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