AL2CO protocols

View AL2CO computational protocol

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AL2CO specifications


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



  • person_outline Nick Grishin <>

Publication for AL2CO

AL2CO in pipeline

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

[…] code: cd01291). 8, 30, 20 and 46 coevolutionary connections were predicted by mip , mcbasc , dca and psicov23 methods, respectively. interestingly, in this family, the average conservation score (al2co score: 0.65) for all sites are quite low (as shown by color coding), despite having higher coevolutionary connections. hence, observations in this family support the hypothesis that a higher […]

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AL2CO in publications

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 […]

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)., […]

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 ), […]

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:, forschungsgemeinschaft mu 3798/1-1 to gerd a müller., […]

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, […]

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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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