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Protocols

PMP specifications

Information


Unique identifier OMICS_13614
Name PMP
Alternative name Protein Model Portal
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes

Documentation


Maintainer


  • person_outline Christophe Geourjon

Publication for Protein Model Portal

PMP citations

 (27)
library_books

Mapping genetic variations to three dimensional protein structures to enhance variant interpretation: a proposed framework

2017
Genome Med
PMCID: 5735928
PMID: 29254494
DOI: 10.1186/s13073-017-0509-y

[…] ble experimentally derived structures are deposited in the Protein Data Bank (PDB) []. When experimentally determined structures are not available for proteins, structural models may be used instead. Protein Model Portal [] aggregates precomputed models from multiple resources, whereas most methods generate models interactively on request, for example, I-TASSER [], ModWeb [], Phyre2 [], HHpred [], […]

call_split

L Asparaginase of Leishmania donovani: Metabolic target and its role in Amphotericin B resistance

2017
PMCID: 5633258
PMID: 28988014
DOI: 10.1016/j.ijpddr.2017.09.003
call_split See protocol

[…] UNIPROT E9BC85), H. pylori, M. tuberculosis and human L-asparaginase was done using CLUSTAL Omega. 3D structure alignment of LdAI with L-asparaginase of M. tuberculosis and S. typhi (pre-available at Protein Model Portal at Protein Structure Initiative Knowledgebase (PSI KB)) and H. pylori (PDB id: 2WLT) was done using PyMol. For identifying potential interaction partners, STRING () analysis was d […]

call_split

Repurposing metformin as a quorum sensing inhibitor in Pseudomonas aeruginosa

2017
PMCID: 5656202
PMID: 29085409
DOI: 10.4314/ahs.v17i3.24
call_split See protocol

[…] udy was performed. The crystal structure of P. aeruginosa LasR ligand binding domain was obtained from Protein Data Bank (PDB ID: 2UV0), while the rhlr receptor model (ID: P54292.1) was achieved from protein model portal28. The interaction of metformin, the natural ligand, 3-oxo-dodecanoylhomoserine lactone and the classical quorum sensing inhibitor C30 furanone into the receptor active site was i […]

library_books

Engineering a high affinity humanized anti CD24 antibody to target hepatocellular carcinoma by a novel CDR grafting design

2017
Oncotarget
PMCID: 5584245
PMID: 28881644
DOI: 10.18632/oncotarget.17228

[…] and sequenced. Based on the sequencing results, we analyzed the cG7 epitope. The ZDOCK program (version 3.0.2) was used to dock cG7 and epitope residues on CD24 using a structure downloaded from the Protein Model Portal (PMP) [, ]. The superior modeled complex structure was analyzed by MOE and the residues that played an important role in the molecular interactions were identified. […]

library_books

Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases

2016
Sci Rep
PMCID: 5171882
PMID: 27991516
DOI: 10.1038/srep38886

[…] on the three-dimensional structure of EstDZ2 were performed by employing a variety of automated web-servers for protein structure homology modelling and applying standard protocols as implemented in “Protein Model Portal”. These include SWISS-MODEL, M4T, InFOLD2, Phyre2 and I-TASSER. Model structures of EstDZ2, were created based on templates derived from previously determined structures that exhi […]

library_books

Emergence and Evolution of Hominidae Specific Coding and Noncoding Genomic Sequences

2016
Genome Biol Evol
PMCID: 4987104
PMID: 27289096
DOI: 10.1093/gbe/evw132

[…] of DSCR4 based on Chou and Fasman algorithm () suggests the existence of potential α-Helices and β-Sheets (see supplementary fig. S3a, Supplementary Material online). Constructing the 3D structure by protein model portal () and I-TASSER () also showed evidence for the existence of α helices and β sheets in the protein coded by DSCR4 (see supplementary fig. S3b and c, Supplementary Material online) […]

Citations

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PMP institution(s)
Biozentrum University of Basel, Klingelbergstrasse, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Klingelbergstrasse, Basel, Switzerland
PMP funding source(s)
This work was supported by National Institutes of Health; National Institute of General Medical Sciences (grant n°U01 GM093324-01); Swiss Institute of Bioinformatics.

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