PPM Server statistics

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Protocols

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PPM Server specifications

Information


Unique identifier OMICS_06356
Name PPM Server
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Andrei L. Lomize <>

Publication for PPM Server

PPM Server in pipelines

 (2)
2014
PMCID: 4434415
PMID: 28324295
DOI: 10.1007/s13205-014-0231-z

[…] its molecular function. we used pocasa (yu et al. ), pocket-finder (laurie and jackson ) and firestar server (lopez et al. ) for prediction of functionally important residues in hp and the ppm server for calculating rotational as well as translational positions of transmembrane and peripheral proteins in cell membranes (lomize et al. ). it can be applied to newly determine experimental […]

2014
PMCID: 4569619
PMID: 28324524
DOI: 10.1007/s13205-014-0274-1

[…] the catalytic residues in hps. furthermore, active pocket sites in the predicted structures of hps were identified using pocasa (yu et al. ) and pocket-finder (laurie and jackson, ) servers. the ppm server (lomize et al. ) was used for calculating spatial positions in membranes of hps. the profunc (laskowski et al. ) web server was used for structure-based function annotation […]


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PPM Server in publications

 (24)
PMCID: 5935710
PMID: 29728606
DOI: 10.1038/s41467-018-04139-2

[…] putative transmembrane segment of the c10 symmetric yaxab complex consists of 40 staggered helices, jointly contributed from yaxa and yaxb foot domains (fig. ). analysis of the pore model using the ppm server (which positions the protein in a bilayer and calculates the corresponding hydrophobic thickness) confirms the amphipathic nature of the foot domain helices (fig. ). together, […]

PMCID: 5849751
PMID: 29535329
DOI: 10.1038/s41598-018-22476-6

[…] of protein embedding over a database confirms good results, protein in/out topologies in pdbtm are inconsistently handled. a more recent method that coherently accounts for topology is the ppm server used by the opm database. while opm is widely used also for derivation of other methods, comparison of protein embedding for larger databases between pdbtm and opm indicates inferior […]

PMCID: 5840332
PMID: 29511171
DOI: 10.1038/s41467-018-02927-4

[…] estimation method for membrane proteins that assesses the best ranks for those regions of the nmdar that lay within the cell membrane. these regions of the nmdar were previously identified using the ppm server. the most energy-favourable model that emerged, and was used in this study, was finally assessed by ranking according to the ‘borda score’. for this score, each model fit (i) within […]

PMCID: 5725538
PMID: 27919210
DOI: 10.2174/1567201814666161205131213

[…] the membed [] protocol was used to embed it in a dipalmitoylphosphatidylcholine(dppc) pre-equilibrated and extended bilayer provided by slipid []. the position of membrane was calculated using the ppm server [, ] and vmd [] was used to align the bilayer to the protein. the slipid parameters in conjunction with amber ff99sb [] forcefield modified for gromacs (ffamber) [, ]. simulation […]

PMCID: 5654971
PMID: 29066778
DOI: 10.1038/s41598-017-13714-4

[…] simulation, an already published model based of the quasipore structure was used. the protein-membrane system was built with the charmm-gui server, using the membrane positioning as suggested by the ppm server. the system was simulated using a similar procedure of that of the prepore with membrane, but simulating for a longer time of 250 ns., two methods were here used to explore the main […]


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PPM Server institution(s)
Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA

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