A novel algorithm reported August 2 in the PNAS could help uncover better methods to compare three-dimensional protein structures, say authors of the report. In addition, they say, it could help in the development of ways to determine whether proteins can assume more than one biologically active conformation.

There are two main techniques used to quantify similarity of the three-dimensional structures of a pair of proteins, Rachel Kolodny, of Stanford University, Calif., and Nathan Linial, of Hebrew University, Jerusalem, explain in their paper. The first—including the most commonly used three-dimensional protein structure comparison server, Dali—computes the distances between corresponding locations in each of the proteins and then compares these distances. The second in essence superimposes each protein on the other and measures how close they match.

The new approach aligns proteins for comparison via the second approach. It is not heuristic; instead, it exhaustively computes all the ways...

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