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Protocols

AL2CO specifications

Information


Unique identifier OMICS_15454
Name AL2CO
Interface Web user interface
Restrictions to use None
Input data A protein sequence alignment.
Input format CLUSTAL
Programming languages C
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Nick Grishin

Publication for AL2CO

AL2CO citations

 (31)
library_books

Structurally distinct Mre11 domains mediate MRX functions in resection, end tethering and DNA damage resistance

2018
Nucleic Acids Res
PMCID: 5888019
PMID: 29420790
DOI: 10.1093/nar/gky086

[…] of mre11 and rad50 (atp-bound) on the tetrameric complex structure from m. jannaschii (pdb id: 5f3w) (). this structure was then refined by molecular dynamics. a multiple alignment based on al2co structural conservation () of scmre11 with mre11 orthologs from homo sapiens (pdb id:3t1i), schizosaccharomyces pombe (pdb id:4fcx), chaetomium thermophilum (pdb id:4kye and 5da9 for rbd […]

library_books

LAR RPTP Clustering Is Modulated by Competitive Binding between Synaptic Adhesion Partners and Heparan Sulfate

2017
PMCID: 5645493
PMID: 29081732
DOI: 10.3389/fnmol.2017.00327

[…] on il1rapl1 also participate in a broad range of interactions with the ptpδ* ig3 domain. a sequence conservation analysis was performed on the sequences listed in supplementary table s3, using the al2co (pei and grishin, ; pettersen et al., ). it showed that the key residues at interface i and interface ii involved in the lateral interaction are highly conserved (supplementary figure s3c)., […]

library_books

Protein sites with more coevolutionary connections tend to evolve slower, while more variable protein families acquire higher coevolutionary connections

2017
F1000Res
PMCID: 5506539
PMID: 28751967
DOI: 10.5256/f1000research.12138.r21733

[…] sites. similarly, spatial proximity between the coevolved sites might provide additional reliability about the predicted coevolved sites . we examined the evolutionary conservation using the popular al2co program within 19,736, 35,514, 50,217, and 56,879 coevolved site pairs (located within 10å spatial distance), which were identified by approaches, such as mutual information (mip program ), […]

library_books

The DREAM complex through its subunit Lin37 cooperates with Rb to initiate quiescence

2017
eLife
PMCID: 5602299
PMID: 28920576
DOI: 10.7554/eLife.26876.022

[…] approximately 30,000 cells were examined., lin37 protein sequences of nine deuterostomes were aligned with clustal omega (rrid:scr_001591) () and amino acid conservation scores were calculated using al2co ()., this paper was supported by the following grants:, http://dx.doi.org/10.13039/501100001659deutsche forschungsgemeinschaft mu 3798/1-1 to gerd a müller., […]

library_books

Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti cancer proteins

2016
F1000Res
PMCID: 5247789
PMID: 28163896
DOI: 10.5256/f1000research.10527.r19231

[…] sequences were collected using blast (pmid: 9254694) of the nr database with nsp1 as a query (default settings), keeping subject sequences with over 90% coverage. conservations were calculated using al2co (pmid: 11524371) from a mafft (pmid: 24170399) alignment of the following: pieridae nsp1 and nsp2, together with aar84202.1, aby88944.1, abx39547.1, abx39554.1, aby88945.1, abx39555.1, […]

library_books

Evolution of Protein Domain Repeats in Metazoa

2016
Mol Biol Evol
PMCID: 5100051
PMID: 27671125
DOI: 10.1093/molbev/msw194

[…] regions indeed show more divergence within the treefamrepdis set compared with the treefamrepstruc set, we compared amino acid conservation by calculating normalized conservation scores using the al2co program (). the distribution of conservation scores for disordered and structured repeats is shown in the supplementary figure s2, supplementary material online. indeed, we find […]


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AL2CO institution(s)
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA

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