AMAS protocols

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AMAS specifications

Information


Unique identifier OMICS_07155
Name AMAS
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for AMAS

AMAS in pipeline

2018
PMCID: 5849740
PMID: 29535397
DOI: 10.1038/s41598-018-22804-w

[…] observe the conservation of these sequences in three species. the alignment was visualized to overview identical positions and then analyzed (calculating conservation to show similarity based on the amas method of a multiple sequence alignment analysis; adding sequence features such as active sites, important sites for hydrolytic activity, dimerization, and ligase activity, ubiquitin-binding […]


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AMAS in publications

 (8)
PMCID: 5849740
PMID: 29535397
DOI: 10.1038/s41598-018-22804-w

[…] observe the conservation of these sequences in three species. the alignment was visualized to overview identical positions and then analyzed (calculating conservation to show similarity based on the amas method of a multiple sequence alignment analysis; adding sequence features such as active sites, important sites for hydrolytic activity, dimerization, and ligase activity, ubiquitin-binding […]

PMCID: 5784254
PMID: 29362235
DOI: 10.1128/mBio.02119-17

[…] using the methods described above. all identified gpcr-pipk sequences are listed in  in the supplemental material., the degree of conservation of gpcr-pipks was calculated in jalview using the amas method (), and those data are presented as a sliding moving average calculated over 50 positions. the weblogo for the lrxgi motif was plotted using the ggseqlogo package () in r v3.3.2., […]

PMCID: 5740498
PMID: 29269382
DOI: 10.15252/msb.20177908

[…] as weighted by measurement confidence. conservation‐based features included blosum62 (henikoff & henikoff, ), sift (ng & henikoff, ) and provean (choi et al, ) scores, and position‐specific amas (livingstone & barton, ) conservation. chemicophysical features included mass and hydrophobicity of the original and wild‐type amino acids, and the difference between them. structural […]

PMCID: 5531542
PMID: 28750021
DOI: 10.1371/journal.pone.0182056

[…] v2.7 [] with the muscle [] webserver and default parameters. from this alignment, a sequence conservation score was computed at each position in jalview. the score is based on the one used in amas [] and in case of variation takes into account the number of conserved physico-chemical properties at a position. the conservation is scored from 0 (not conserved) to 11 (completely conserved)., […]

PMCID: 3695027
PMID: 23826277
DOI: 10.1371/journal.pone.0067362

[…] dataset. model quality was evaluated using molprobity and figures were prepared using pymol . sequence conservation of tae4 as well as tai4 homologous proteins was determined using the amas-server and illustrated using alscript . molecular interaction surfaces were calculated and analyzed using the pisa server and contact . the atomic coordinates and structure factor amplitudes […]


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AMAS institution(s)
Genomics Support Group, SmithKline Beecham Pharmaceuticals, Harlow, Essex, UK

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