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Nucleic Acids Research, 2003, Vol. 31, No. 13 3370-3374
© 2003 Oxford University Press

LGA: a method for finding 3D similarities in protein structures

Adam Zemla*

Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA

*Tel: +1 925 423 5571; Fax: +1 925 422 2133; Email: adamz{at}llnl.gov

We present the LGA (Local-Global Alignment) method, designed to facilitate the comparison of protein structures or fragments of protein structures in sequence dependent and sequence independent modes. The LGA structure alignment program is available as an online service at http://PredictionCenter.llnl.gov/local/lga. Data generated by LGA can be successfully used in a scoring function to rank the level of similarity between two structures and to allow structure classification when many proteins are being analyzed. LGA also allows the clustering of similar fragments of protein structures.


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