DeepAlign protocols

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DeepAlign specifications


Unique identifier OMICS_03689
Name DeepAlign
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Sheng Wang <>


Unique identifier OMICS_03689
Name DeepAlign
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++
Computer skills Advanced
Version 1.2
Stability Stable
Source code URL
Maintained Yes



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  • person_outline Sheng Wang <>

Publication for DeepAlign

DeepAlign in pipeline

PMCID: 4524716
PMID: 26241330
DOI: 10.1371/journal.pone.0132863

[…] located in table a in ., structure-guided alignments were made from sets of pp2c sequences with solved structures using the 3dcomb function of the raptorx server ([, ]; solved structures used were: ((1a6q, 2p8e, 2i0o, 2iq1 –eukaryotic pp2cs); (1txo, 2pk0, 2jfr, 2j82 –bacterial group i); (3es2, 3w40, 3zt9 –bacterial group ii)). additional […]

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DeepAlign in publications

PMCID: 5825884
PMID: 29492339
DOI: 10.7717/peerj.4396

[…] was performed for pb263r model 1a, and the 10 highest-ranked structural analogs of the predicted model were identified with the raptorx structure alignment server at ( and visualized using jalview v.2.10.1 () to infer function and identify conserved residues. go terms () predicted with the i-tasser server were used to infer the pb263r model 1a […]

PMCID: 5662722
PMID: 29085020
DOI: 10.1038/s41598-017-14533-3

[…] structure based sequence alignment for ha described in literature was used. as for na, crystal structures of n1 to n9 were downloaded from pdb database and aligned with structure alignment tool deepalign., given a column of two aligned sequence sets (set a and set b), the frequencies of residues of the column in each set were counted. the dscore was defined to assess the difference […]

PMCID: 4982684
PMID: 27517583
DOI: 10.1371/journal.pone.0161254

[…] comparison, met the criteria., there are many excellent servers available for protein structure comparisons, including ce [], fatcat-flexible [], tm-align [], dali [], vast [], structal [] and deepalign [], more information and the details of each method can found in systematic review [, ]. in the current work, only three widely used methods (ce, fatcat-flexible and tm-align) were employed […]

PMCID: 4833381
PMID: 27082872
DOI: 10.1371/journal.ppat.1005564

[…] structures. our rough predictions of the structures of hcmv tr gh/gl involved comparisons to hsv-1 and ebv gh/gl sequences using the raptorx structure alignment server ( this produced a crude 3d structure of hcmv gh/gl that was used along with primary sequence alignments between hcmv, hsv-1, and ebv gh/gl molecules [] to design mutations in hcmv gh/gl […]

PMCID: 5065317
PMID: 27572256
DOI: 10.7554/eLife.18017.029

[…] piston. 2 fs time steps were used. all analysis was carried out in vmd1.9.2. protein structures were aligned using multiseq stamp () implemented in vmd1.9.2; structures in were aligned using deepalign ( structural comparisons to hv1 fl were conducted on chain a of the dimer, which is not identical to chain b (). coordinates for ci vsdu (pdb: […]

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DeepAlign institution(s)
Provides automatic protein structure alignment. DeepAlign uses amino acid and local substructure substitution matrices, which are derived from evolutionarily-related protein pairs, and generate alignments highly consistent with manually-curated alignments. The interest of this method lies in its scoring function, which considering not only 3D geometric similarity, but also evolutionary information at the sequence and local substructure levels as well as hydrogen bonding similarity.
DeepAlign funding source(s)
Supported by the National Institutes of Health grant R01GM089753, the National Science Foundation grant DBI-0960390 and the National Science Foundation CAREER award CCF-1149811.

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