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Information


Unique identifier OMICS_03652
Name LGA
Alternative name Local-Global Alignment
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Local-Global Alignment

LGA citations

 (17)
library_books

Mutations in human AID differentially affect its ability to deaminate cytidine and 5 methylcytidine in ssDNA substrates in vitro

2017
Sci Rep
PMCID: 5478644
PMID: 28634398
DOI: 10.1038/s41598-017-03936-x

[…] gest number of members were further analyzed. For each of the clusters the average structure was calculated. These average structures were then compared with X-ray structure of AID variant using LGA (Local-Global Alignment) server (http://as2ts.proteinmodel.org/AS2TS/LGA/lga.html) (see Supplementary Fig. ). The same analysis was performed for models of both wt hAID and N51A variant. […]

library_books

Comparative visualization of protein secondary structures

2017
BMC Bioinformatics
PMCID: 5333176
PMID: 28251875
DOI: 10.1186/s12859-016-1449-z

[…] Visualization of Protein-Ligand Graphs (VPLG), supports several graph types and can optionally include ligand contacts.Concerning the comparison of protein structures, Zemla presented an LGA method (Local-Global Alignment) [] that facilitates both sequence dependent and independent modes to this problem. Other structure comparison programs use an adequate scoring function, mostly evaluating the s […]

library_books

Identification of Genome Wide Mutations in Ciprofloxacin Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing

2016
PLoS One
PMCID: 5036845
PMID: 27668749
DOI: 10.1371/journal.pone.0163458

[…] implied by the observed mutations, and to estimate the level of possible sequence variability in identified structurally conserved regions. Structure alignments were calculated using the program LGA (Local Global Alignment) [] and evaluation of detected structural similarities between LVS proteins and related structures from Protein Data Bank (PDB) was performed by StralSV sequence/structure varia […]

call_split

An Electrostatic Funnel in the GABA Binding Pathway

2016
PLoS Comput Biol
PMCID: 4847780
PMID: 27119953
DOI: 10.1371/journal.pcbi.1004831
call_split See protocol

[…] incorporated. This protocol was used for regions that were missing in the structure, lacked alignment to the template, or were poorly conserved. The DIG (Deletions Insertions Gaps) tool from the LGA (Local–Global Alignment) [] program was used for this additional alignment and modeling. The DIG tool analyzes protein structures, or fragments of protein structures, and can complete the missing secti […]

call_split

Benchmarking Deep Networks for Predicting Residue Specific Quality of Individual Protein Models in CASP11

2016
Sci Rep
PMCID: 4725912
PMID: 26763289
DOI: 10.1038/srep19301
call_split See protocol

[…] Sequence-dependent Local-Global Alignment (LGA) was used to superimpose a protein model with its experimental structure (i.e., native structure). After superimposition, LGA can generate a Global Distance Test Total Scor […]

call_split

Customised fragments libraries for protein structure prediction based on structural class annotations

2015
BMC Bioinformatics
PMCID: 4419399
PMID: 25925397
DOI: 10.1186/s12859-015-0576-2
call_split See protocol

[…] The main metric used to assess our structure prediction pipeline is the global distance test-total score (GDT_TS). It was introduced as a part of the LGA (Local Global Alignment) method and since then it has been widely accepted in the community mainly due the fact it is less sensitive to outliers than the popular root mean square deviation (RMSD) []. G […]

Citations

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LGA institution(s)
Lawrence Livermore National Laboratory, Livermore, CA, USA

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