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Protocols

SuperPose specifications

Information


Unique identifier OMICS_30167
Name SuperPose
Interface Web user interface
Restrictions to use None
Input data Some text files (from a user’s hard drive) or PDB accession numbers or any combination of both.
Input format PDB
Output data A PDB file containing the coordinates of the superimposed molecules; a PDB file containing the backbone coordinates of a single averaged structure (if all sequences match identically); a sequence or secondary structure alignment (pairwise or multiple) file of the sequences used in the alignment; a difference distance matrix (if only two molecules are superimposed); an RMSD report that contains the calculated RMSD values (in Angstroms) between the superimposed molecules; a still image (PNG, portable network graphics file) of the superimposed molecules generated using MolScript; and a WebMol applet view of the superimposed molecules.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline David Wishart

Publication for SuperPose

SuperPose citations

 (68)
library_books

Bleogens: Cactus Derived Anti Candida Cysteine Rich Peptides with Three Different Precursor Arrangements

2017
Front Plant Sci
PMCID: 5743680
PMID: 29312404
DOI: 10.3389/fpls.2017.02162

[…] th antimicrobial peptides such as MJ-AMP1 from Mirabilis jalapa and PAFP-S from Phytolacca americana (; ; Figure ). Protein tertiary structure comparison with PAFP-S (PDB entry: 1DKC) conducted using SuperPose software Version 1.0 () showed that PAFP-S has a similar structural fold as bleogen pB1 (Figure ). The RMSD values between the superimposed structures of PAFP-S and bleogen pB1 were 0.681 Å […]

call_split

Mechanism of formation of a toroid around DNA by the mismatch sensor protein

2017
Nucleic Acids Res
PMCID: 5758902
PMID: 29182773
DOI: 10.1093/nar/gkx1149
call_split See protocol

[…] re 26.8 and 23.4%, respectively for the NgoS–ADP complex. The final Rfree and Rwork values are 25.9 and 21.2%, respectively for the NgoS–AMPPNP complex. All structural comparisons were done using the Superpose tool in Coot and the interactions between the clamp regions were mapped using CONTACT in CCP4 (,). All figures were prepared using PyMol (Schrödinger Corp.) and the movies were prepared in P […]

library_books

Distinct roles of Pcf11 zinc binding domains in pre mRNA 3′ end processing

2017
Nucleic Acids Res
PMCID: 5737669
PMID: 28973460
DOI: 10.1093/nar/gkx674

[…] dues 538 to 608 (PDB ID 2NAX; ()) displays the same overall fold, with a global RMSD between the two ensembles of 0.7 and 1.3 Å for the backbone and all heavy atoms, respectively, calculated by using SuperPose ().A search of the available structures by using DALI () failed to find a close structural homologue, but instead identified local homology (Z-score > 2) to one of the two zinc-binding sites […]

library_books

Predicting the functional consequences of non synonymous single nucleotide polymorphisms in IL8 gene

2017
Sci Rep
PMCID: 5529537
PMID: 28747718
DOI: 10.1038/s41598-017-06575-4

[…] sease associated nsSNPs had been found to be located in surface pockets of protein structures.Figure 6 We superimposed the 8 mutant IL-8 proteins onto the PDB structure of the wild type protein using SuperPose ver 1.0 server (Fig. ). We found that the substitutions (such as E31A and E31K) in the N-terminal receptor binding ELR31–33 motif of the IL-8 protein entail local conformation changes as wel […]

call_split

Identification of Histamine H3 Receptor Ligands Using a New Crystal Structure Fragment based Method

2017
Sci Rep
PMCID: 5500575
PMID: 28684785
DOI: 10.1038/s41598-017-05058-w
call_split See protocol

[…] or residue and interacting ligand moiety, from GPCR crystal structure complexes. Herein, we uploaded our H3 receptor model to GPCRdb to identify conserved residues represented in this library, and to superpose the backbones of the corresponding fragments. The pharmacophore elements were placed using Phase at the highest density of the (multiple) fragment moieties. The vectors of the hydrogen bondi […]

library_books

Evolution of strigolactone receptors by gradual neo functionalization of KAI2 paralogues

2017
BMC Biol
PMCID: 5490202
PMID: 28662667
DOI: 10.1186/s12915-017-0397-z

[…] irm that both methods generated similar models, root-mean-square deviation (RMSD) values for the SWISSMODEL- and I-TASSER-generated models were then calculated for the 10 pairs of sequences using the SuperPose server based on the Cα coordinates (http://wishart.biology.ualberta.ca/superpose/) []. The RMSD values confirmed that both model-generating servers converged on essentially the same result ( […]

Citations

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SuperPose institution(s)
Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB, Canada
SuperPose funding source(s)
Supported by the Protein Engineering Network of Centres of Excellence (PENCE Inc.) and Genome Prairie (a division of Genome Canada).

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