SALIGN statistics

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Citations per year

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Associated diseases

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SALIGN specifications


Unique identifier OMICS_03674
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Some protein sequences and/or structures.
Output data The final alignment file, superimposed coordinates if structures were aligned, a dendrogram file if a tree was constructed, and the MODELLER input and log files.
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Andrej Sali <>
  • person_outline Mallur Srivatsan Madhusudhan <>

Additional information

SALIGN is also part of DBAli

Publications for SALIGN

SALIGN in publications

PMCID: 5786013
PMID: 29374165
DOI: 10.1038/s41467-017-02592-z

[…] peptide is aligned to the protein sequence using the needleman–wunsch algorithm. many peptides are discarded at this stage due to alignment mismatches. for the aligned peptides, an alignment score salign is computed using the blosum90 similarity matrix, which quantifies the importance of the alignment to a specific amino acid sequence. taken all the above into account, the weighted probability […]

PMCID: 5447077
PMID: 28611792
DOI: 10.3389/fpls.2017.00819

[…] server (laskowski et al., ) and further also confirmed with rampage (lovell et al., ). for the structural alignment, salign-modbase server (braberg et al., ) was used the computationally predicted models were submitted in the protein modeling database (pmdb) […]

PMCID: 5432455
PMID: 28508385
DOI: 10.1186/s13568-017-0399-9

[…] highest primary structure identities with aoxyn11a, were selected as homology modeling templates. the 3-d structures of aoxyn11a and its variants were modeled based on the three templates using the salign program ( and modeller 9.11 program (, and analyzed using the pymol software (, the 3-d structure of a mesophilic […]

PMCID: 5354106
PMID: 28316890
DOI: 10.7717/peerj.3087

[…] as the templates for our modeling. the multialignment of the chosen target (p50993, at1a2_human) sequence and the two templates (3b8e, 3kdp) for open conformation was prepared by modeller program (salign module) (; ; ; ). the choice of templates (solved crystal structures) was based on the species proximity (pig over shark) and absence of any cardioglycosides in the solved crystal structure, […]

PMCID: 5132326
PMID: 27907195
DOI: 10.1371/journal.pone.0167650

[…] the developed 3d model was validated for stereochemical quality using saves software;, and for superimposition with human arnt pas-b using salign software ( finally the predicted 3d structure was visualized by ucsf chimera (, the human er-negative mda-mb-231 and er-positive […]

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SALIGN institution(s)
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA; Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA, USA; Bioinformatics Institute, Singapore; Department of Biological Sciences, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore
SALIGN funding source(s)
Supported by National Institutes of Health (NIH), U.S.A [U54 GM094662 and R01 GM54762].

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