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SPalign specifications

Information


Unique identifier OMICS_03687
Name SPalign
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format PDB
Programming languages C++
Computer skills Basic
Stability Stable
Maintained No

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Information


Unique identifier OMICS_03687
Name SPalign
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format PDB
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained No

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Publication for SPalign

SPalign in publications

 (6)
PMCID: 5746772
PMID: 29088096
DOI: 10.3390/bios7040049

[…] the antigenic sites of glycoproteins e1 and e2. the authors searched and filtered potential scaffolds using a matrix meta-server method composed of six different databases: tm-align(f), tm-align(c), spalign, click, fast, and mammoth. then, the authors used md simulations to study the dynamics of potential epitope scaffolds in solution. the selected epitope scaffolds were his-tagged, transiently […]

PMCID: 5343507
PMID: 28262665
DOI: 10.1038/ncomms14614

[…] suite provided by bioinformatics.org. pdb accession codes used for structural analyses were 2c3z for ssigps, 1i4n for tmigps and 1vc4for ttigps. rmsds of structural alignments were performed using spalign. structural figures were generated using pymol molecular graphics system v1.8.2.0. accessible surface area (asa) was calculated using ebi pisa tool. rsa was calculated from asa using […]

PMCID: 5278169
PMID: 27895130
DOI: 10.1128/IAI.00898-16

[…] accession number af226499), and metq of e. coli strain mg1655 (genbank accession number nc_000913; locus tag, b0197). the structural similarity between the metq homologues was investigated using the spalign server ()., the metq knockout construct was made by cloning the ngag_00171 gene from the genome of n. gonorrhoeae 1291 (using primers 5′-gccgtctgaacgccgaatccggacggc-3′ […]

PMCID: 4609302
PMID: 26313554
DOI: 10.1002/prot.24915

[…] b), and made use of the non‐redundant representative subsets of scop domains, which are provided in astral. for example, yang and colleagues developed a new structure alignment method called spalign, which they developed and tested on pairs of domains from the same scop fold, but with <20% sequence identity. although the authors didn't state their reasons for choosing scop over cath, […]

PMCID: 4533164
PMID: 26238798
DOI: 10.1038/srep12501

[…] are identical, suggesting that the two algorithms identified a set of different but overlapping scaffolds. we then included four more structural alignment algorithms—a c implementation of tm-align, spalign, click, and fast, which identified 539, 331, 74, and 152 scaffolds, respectively (). together, six scaffolding algorithms yielded 1,003 non-redundant scaffolds with a pairwise overlap […]


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SPalign institution(s)
Indiana University Purdue University, Indianapolis, IN and Center for computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA

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