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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 citations

 (25)
library_books

Structure and mechanism of the two component α helical pore forming toxin YaxAB

2018
Nat Commun
PMCID: 5935710
PMID: 29728606
DOI: 10.1038/s41467-018-04139-2

[…] e 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, these helices […]

library_books

Statistically derived asymmetric membrane potentials from α helical and β barrel membrane proteins

2018
Sci Rep
PMCID: 5849751
PMID: 29535329
DOI: 10.1038/s41598-018-22476-6

[…] inspection 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 embedd […]

library_books

Disease associated missense mutations in GluN2B subunit alter NMDA receptor ligand binding and ion channel properties

2018
Nat Commun
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 a group […]

library_books

Structure function relationships in ABCG2: insights from molecular dynamics simulations and molecular docking studies

2017
Sci Rep
PMCID: 5686161
PMID: 29138424
DOI: 10.1038/s41598-017-15452-z

[…] s in the presence of cholesterol prior to the crystallization step and ii) it provides an optimal hydrophobic environment to accommodate the hydrophobic thickness for the ABCG2 transmembrane domains (PPM server prediction: 28.6 ± 0.9 Å). After membrane insertion, the system was water soaked (59.982 molecules) and neutralized with 22 chlorine ions, originating a system with 221.728 atoms. The syste […]

library_books

Three dimensional Modelling of the Voltage gated Sodium Ion Channel from Anopheles gambiae Reveals Spatial Clustering of Evolutionarily Conserved Acidic Residues at the Extracellular Sites

2017
PMCID: 5725538
PMID: 27919210
DOI: 10.2174/1567201814666161205131213

[…] d. 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 was carrie […]

call_split

Structural, physicochemical and dynamic features conserved within the aerolysin pore forming toxin family

2017
Sci Rep
PMCID: 5654971
PMID: 29066778
DOI: 10.1038/s41598-017-13714-4
call_split See protocol

[…] 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. […]

Citations

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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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