LGA: a method for finding 3D similarities in protein structures
Open accessAbstract
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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Domain accuracies in CASP are reported as GDT.
“Domain accuracies in CASP are reported as GDT33”
From Highly accurate protein structure prediction with AlphaFold (2021) · cites this paper as [33]
The section “Evaluating Structure Similarity Between Proteins” says that GDT was tested in CASP and helped rank evaluated 3D models. It does not say that CASP reports domain accuracies as GDT; the domain-specific reporting claim is unsupported. No page number is available in our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measuredFinal relaxation by gradient descent in the Amber force field does not improve accuracy as measured by GDT or lDDT-Cα but removes stereochemical violations without loss of accuracy.
“Empirically, this final relaxation does not improve the accuracy of the model as measured by the global distance test (GDT)33 or lDDT-Cα34 but does remove distracting stereochemical violations without the loss of accuracy.”
From Highly accurate protein structure prediction with AlphaFold (2021) · cites this paper as [33]
The threshold of 90 GDT_TS corresponds to approximately 1.5 Angstroms RMSD, and 80 corresponds to about 2.5 Angstroms (all residues included, calculated with LGA 24).
“The threshold of 90 GDT_TS corresponds to approximately 1.5 Angstroms RMSD, and 80 corresponds to about 2.5 Angstroms (all residues included, calculated with LGA 24).”
From Critical assessment of methods of protein structure prediction (CASP)—Round <scp>XIV</scp> (2021) · cites this paper as [24]
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“In the Table 4 we compare results of LGA to those of four methods available as web services and which are frequently used by the scientific community: VAST (8), DALI (1), CE (9) and ProSup (10).”
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BackgroundMethodInfluential
- Authors
- Zemla, A.
- Affiliations
- Lawrence Livermore National Laboratory (US)
- Corresponding author
- Zemla, A.
- ORCID
- Zemla, A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-07-01
- Volume
- 31
- Issue
- 13
- Pages
- 3370-3374
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC168977
- OpenAlex
- W2110483430
- Cited by
- 1,069
- References
- 1
- Citations by year
- 2026: 28 · 2025: 52 · 2024: 51 · 2023: 66 · 2022: 50 · 2021: 79 · 2020: 51 · 2019: 51 · 2018: 37 · 2017: 40 · 2016: 50 · 2015: 40 · 2014: 40 · 2013: 58 · 2012: 61
- FWCI
- 8.29
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Energy (W-7405, -7405-ENG-48)
- Lawrence Livermore National Laboratory (W-7405-ENG 48, -7405-Eng-48)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein structure alignment, protein fragments, structural classification
- MeSH terms
- Algorithms, Computer Graphics, Models, Molecular, Proteins, Software, Molecular Structure, Sequence Alignment, Nuclear Magnetic Resonance, Biomolecular, Internet, Databases, Protein, Structural Homology, Protein
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