GalaxyRefineComplex statistics

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GalaxyRefineComplex specifications

Information


Unique identifier OMICS_17442
Name GalaxyRefineComplex
Interface Web user interface
Restrictions to use None
Input data A protein structure file.
Input format PDB, TXT
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Chaok Seok <>

Publication for GalaxyRefineComplex

GalaxyRefineComplex in publications

 (3)
PMCID: 5581167
PMID: 28863193
DOI: 10.1371/journal.pone.0184190

[…] in the same conformation of the pdb file provided by suzuki et al. [] by using the matchmaker chimera tool for structure superimposition. then, the tetramer was energy minimized in vacuo, using the galaxyrefinecomplex utility [], preserving the conformation of the transmembrane domains and relaxing the extracellular domains. the resulting conformation is shown in . we remark that, […]

PMCID: 5325476
PMID: 28234935
DOI: 10.1371/journal.pone.0172217

[…] stable []. prior to docking, the structure of each peptide was predicted by using pep-fold server []. the initially docked peptide-protein complexes resulted from cluspro server were refined using galaxyrefinecomplex web tool (http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=complex)., several physicochemical properties of the peptides including molecular weight, net charge at ph 7, pi, water […]

PMCID: 5150636
PMID: 27941820
DOI: 10.1038/srep38426

[…] energy minimisations were carried out with galaxyrefine, and the model with the lowest molprobity score was assembled into a tetramer by structural alignment with attpc1, and further refined using galaxyrefinecomplex. the pore interior cavity was visualised using hole., electrostatic potential energy calculations using the poisson-boltzmann equation were carried out using apbsmem, as described […]


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GalaxyRefineComplex institution(s)
Department of Chemistry, Seoul National University, Seoul, Korea
GalaxyRefineComplex funding source(s)
This study was funded by grants from the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT, & Future Planning (2016R1A2A1A05005485 and 2012M3C1A6035362), and Korea Institute of Science and Technology Information supercomputing center (KSC-2015-C2-045).

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