Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2003 Jul 1;31(13):3370-4.
doi: 10.1093/nar/gkg571.

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

Adam Zemla  1
Affiliations

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

Adam Zemla. Nucleic Acids Res. .

Abstract

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
(A) C-alpha–C-alpha distance deviation bars from one LGA superposition under a 3.0 Å distance cutoff. Residues superimposed below 1.0 Å are in green, below 2.0 Å in yellow, below 3.0 Å in orange, below 4.0 Å in brown and residues at or above 4.0 Å in red. (C) RasMol plot of two superimposed structures: 1m2f_A_2 and 1m2e_A. Colors correspond to the fourth bar from (A). (B) C-alpha–C-alpha deviation bars for multiple LGA superpositions. (D) RasMol plot of superimposed structures 1m2f_A_2 and 1m2e_A corresponding to fourth bar representation from (B) where >85.0% of equivalent residues under distance cutoff=1.5 Å are in green, >70.0%: yellow, >50.0%: orange, >20.0%: brown and ≤20.0%: red.
Figure 1
Figure 1
(A) C-alpha–C-alpha distance deviation bars from one LGA superposition under a 3.0 Å distance cutoff. Residues superimposed below 1.0 Å are in green, below 2.0 Å in yellow, below 3.0 Å in orange, below 4.0 Å in brown and residues at or above 4.0 Å in red. (C) RasMol plot of two superimposed structures: 1m2f_A_2 and 1m2e_A. Colors correspond to the fourth bar from (A). (B) C-alpha–C-alpha deviation bars for multiple LGA superpositions. (D) RasMol plot of superimposed structures 1m2f_A_2 and 1m2e_A corresponding to fourth bar representation from (B) where >85.0% of equivalent residues under distance cutoff=1.5 Å are in green, >70.0%: yellow, >50.0%: orange, >20.0%: brown and ≤20.0%: red.
Figure 1
Figure 1
(A) C-alpha–C-alpha distance deviation bars from one LGA superposition under a 3.0 Å distance cutoff. Residues superimposed below 1.0 Å are in green, below 2.0 Å in yellow, below 3.0 Å in orange, below 4.0 Å in brown and residues at or above 4.0 Å in red. (C) RasMol plot of two superimposed structures: 1m2f_A_2 and 1m2e_A. Colors correspond to the fourth bar from (A). (B) C-alpha–C-alpha deviation bars for multiple LGA superpositions. (D) RasMol plot of superimposed structures 1m2f_A_2 and 1m2e_A corresponding to fourth bar representation from (B) where >85.0% of equivalent residues under distance cutoff=1.5 Å are in green, >70.0%: yellow, >50.0%: orange, >20.0%: brown and ≤20.0%: red.
Figure 1
Figure 1
(A) C-alpha–C-alpha distance deviation bars from one LGA superposition under a 3.0 Å distance cutoff. Residues superimposed below 1.0 Å are in green, below 2.0 Å in yellow, below 3.0 Å in orange, below 4.0 Å in brown and residues at or above 4.0 Å in red. (C) RasMol plot of two superimposed structures: 1m2f_A_2 and 1m2e_A. Colors correspond to the fourth bar from (A). (B) C-alpha–C-alpha deviation bars for multiple LGA superpositions. (D) RasMol plot of superimposed structures 1m2f_A_2 and 1m2e_A corresponding to fourth bar representation from (B) where >85.0% of equivalent residues under distance cutoff=1.5 Å are in green, >70.0%: yellow, >50.0%: orange, >20.0%: brown and ≤20.0%: red.
Figure 2
Figure 2
Bar representation of the results from sequence independent LGA superpositions, and a RasMol plot of superimposed first template 1a04_B and T0138. Residues superimposed below 2.0 Å are in green, below 4.0 Å in yellow, below 6.0 Å in orange and residues at or above 6.0 Å or not superimposed are in red (target) and in white (template).
Figure 2
Figure 2
Bar representation of the results from sequence independent LGA superpositions, and a RasMol plot of superimposed first template 1a04_B and T0138. Residues superimposed below 2.0 Å are in green, below 4.0 Å in yellow, below 6.0 Å in orange and residues at or above 6.0 Å or not superimposed are in red (target) and in white (template).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Holm L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123–138. - PubMed
    1. Feng Z.K. and Sippl,M.J. (1996) Optimum superimposition of protein structures: ambiguities and implications. Fold Des., 1, 123–132. - PubMed
    1. Zemla A., Venclovas,C., Reinhardt,A., Fidelis,K. and Hubbard,T.J. (1997) Numerical criteria for the evaluation of ab initio predictions of protein structure. Proteins, S1, 140–150. - PubMed
    1. Zemla A., Venclovas,C., Moult,J. and Fidelis,K. (1999) Processing and analysis of CASP3 protein structure predictions. Proteins, S3, 22–29. - PubMed
    1. Orengo C.A., Bray,J.E., Hubbard,T., LoConte,L. and Sillitoe,I. (1999) Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins, S3, 149–170. - PubMed

Publication types

-