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ArchPRED specifications

Information


Unique identifier OMICS_08515
Name ArchPRED
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline András Fiser <>

Publication for ArchPRED

ArchPRED in publications

 (6)
PMCID: 5932063
PMID: 29720613
DOI: 10.1038/s41598-018-25329-4

[…] whatif program. the unresolved structural segments in the crystal structures were modeled using modeller program program. we then employed template-based loop prediction approaches modloop and the archpred to reconstruct and refine the linker region in the yeast hsp82 and human hsp90β structures, as well as src-loop residues f329-d339 in chain a, and a597-k611 in both protomers of the yeast […]

PMCID: 4736830
PMID: 27493864
DOI: 10.2142/biophysico.12.0_145

[…] the program ranch [], and the missing residues connecting two separate regions in tni (tni138–147) were also complemented as loop structures using a template-based loop structure prediction server archpred []., in the model thus constructed, the pivot points, around which the structures can rotate freely, were set around the central region in the it arm (gly91 (tnc), ser42 (tni), gly137 (tni), […]

PMCID: 4111215
PMID: 24969589
DOI: 10.1021/ja503546j

[…] amide proton to the nearest point on the surface of hgh were obtained using the crystal structure of hgh (3hhr). initially, conformations of the missing loop at residues 149–153 were built using the archpred server and protons were added to the crystal structure. subsequently, the msms computer program was used to calculate the solvent excluded surface of hgh using a probe size of 0.35 nm, […]

PMCID: 4629667
PMID: 27493547
DOI: 10.2142/biophysics.9.99

[…] also removed from the methylated lysine residues in the crystal structure. the missing residues in the crystal structure were complemented using a template-based loop structure prediction server archpred., the scattering curve calculated from the crystal structure of s1 was found not to fit well to the experimental curve regardless of the hydration shell (data not shown). a saxs study […]

PMCID: 3350225
PMID: 22494242
DOI: 10.1021/jp301726s

[…] at a site near residues n310, d312, and t92 as identified in ref (). for the ofcc, residues missing from the tm3–4 loop were modeled with the template-based loop structure prediction software archpred., for the “md2” simulations we constructed trimer intermediates, termed “mdi.x” (x = 2, 4, 5, 11), from each selected monomer pri.x and added the substrate (aspartate) and sodium ions […]


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ArchPRED institution(s)
Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, Bronx, NY, USA

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