loopy protocols

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loopy specifications

Information


Unique identifier OMICS_26610
Name loopy
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Registration required Yes
Maintained Yes

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Maintainers


  • person_outline Barry Honig <>
  • person_outline Jackal Team <>

Publication for loopy

loopy in pipelines

 (2)
2018
PMCID: 5893540
PMID: 29636462
DOI: 10.1038/s41467-018-03314-9

[…] and an engineered g protein (pdb 5g53)., extracellular ligands, water molecules, and other solvents resolved in crystal structures were removed. missing backbone atoms were modeled with the program loopy,. missing side chain atoms and side chain reversions to wild-type were modeled with the program scwrl4. disulfide bonds (c71-c159, c74-c146, c77-c166, and c259-c262) and all hydrogen atoms […]

2011
PMCID: 3136923
PMID: 21779343
DOI: 10.1371/journal.pone.0021871

[…] structural overlap due to the sequence dissimilarity with t. thermophilus if1, but a better overlap was obtained manually. the manually oriented insert was then connected to the rest of if2mt using loopy for prediction of linker region structures. the complete model was then optimized using a series of restrained minimization and dynamics steps performed with charmm . if the 49 aa insert […]


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loopy in publications

 (16)
PMCID: 5893540
PMID: 29636462
DOI: 10.1038/s41467-018-03314-9

[…] and an engineered g protein (pdb 5g53)., extracellular ligands, water molecules, and other solvents resolved in crystal structures were removed. missing backbone atoms were modeled with the program loopy,. missing side chain atoms and side chain reversions to wild-type were modeled with the program scwrl4. disulfide bonds (c71-c159, c74-c146, c77-c166, and c259-c262) and all hydrogen atoms […]

PMCID: 5829636
PMID: 29385534
DOI: 10.1093/nar/gky031

[…] the structure determined here of the polymerase domain with a bound magnesium ion (pdb id: 5vtp). 6-his tags were added to the n-termini of the polymerase domains using the loop-modeling program loopy (). at this stage, these models were used in the ld simulations of the polymerase domain alone. for the simulations of the full-length protein, further model building was performed. a homology […]

PMCID: 5757960
PMID: 29261665
DOI: 10.1371/journal.pcbi.1005909

[…] generated by removing inter-helical loop residues 24–29, rotating h1 or h2 about its long axis by ±10°, ±20°, ±30°, ±40° and ±50°, and then modeling loop residues using the prediction program loopy []. secondary structure is maintained while allowing changes in helical rotation and separation by applying intra-helical distance restraints on all backbone atom pairs with force constants […]

PMCID: 5312500
PMID: 28228926
DOI: 10.1016/j.csbj.2017.01.010

[…] sample the conformational space sufficiently; and their prediction accuracy decreases with loop length (as the number of degrees of freedom increases). ab initio algorithms include plop , modeller , loopy , loopbuilder , leap , and the loop modelling routine within rosetta ., the idea of a hybrid loop modelling algorithm, combining knowledge-based and ab initio approaches, has been explored. […]

PMCID: 4833398
PMID: 26689967
DOI: 10.1038/nsmb.3144

[…] used to model the complex consisting of the prefusion hiv-1 env trimer and cap256-vrc26.09 antibody. to begin, any loop regions on the hiv-1 env prefusion trimer were modeled in using the program loopy. we then added mannose 5 to each sequon position. a model for the cap256-vrc26.09 antibody was obtained by threading the amino acid sequence of cap256-vrc26.09 onto the cap256.vrc26.03 antibody […]


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loopy institution(s)
Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
loopy funding source(s)
Supported by National Institutes of Health Grant GM-30518.

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