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Protocols

PMDB specifications

Information


Unique identifier OMICS_21438
Name PMDB
Alternative name Protein Model Database
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes

Maintainers


  • person_outline Anna Tramontano
  • person_outline PMDB Team

Additional information


https://bioinformatics.cineca.it/PMDB/help.php

Publication for Protein Model Database

PMDB citations

 (69)
library_books

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

2018
PLoS One
PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] re, the result of motif composition analysis revealed the strong conservation of these four strands across all the members in the tomato family. The protein models predicted were further submitted to PMDB (https://bioinformatics.cineca.it/PMDB/) [] and were provided with submission identities including PM0080926 (WRKY33_NTD) and PM0081236 (WRKY33 NTD), PM0080775 (WRKY33 CTD) and PM0080776 (WRKY37) […]

library_books

The Candida albicans ENO1 gene encodes a transglutaminase involved in growth, cell division, morphogenesis, and osmotic protection

2018
PMCID: 5868267
PMID: 29386353
DOI: 10.1074/jbc.M117.810440

[…] was deposited in the Protein Model Database from CASPUR and the Biocomputing Group of the Department of Biochemical Sciences of the University of Rome “LA Sapienza” (https://bioinformatics.cineca.it/PMDB/),5 with the identifier PM0081054. To determine the surface electrostatic potential (EP) of CaEno1p and ScEno1p, the PDB files were converted to a PQR format using the PDB2PQR (version 2.1.1) ser […]

library_books

Iodide Binding in Sodium Coupled Cotransporters

2017
J Chem Inf Model
PMCID: 5744185
PMID: 29131623
DOI: 10.1021/acs.jcim.7b00521

[…] ined by their superposition onto that of vSGLT, which was determined with the Orientation of Proteins in Membranes (OPM) server. The final representative hNIS and hSMCT1 models are available from the Protein Model DataBase (https://bioinformatics.cineca.it/PMDB/) with accession number PM0080745 and PM0080746, respectively. […]

library_books

Structural and functional characterization of the Helicobacter pylori cytidine 5′ monophosphate pseudaminic acid synthase PseF: molecular insight into substrate recognition and catalysis mechanism

2017
PMCID: 5638570
PMID: 29062238
DOI: 10.2147/AABC.S139773

[…] cy and stereochemical features of the final 3D model were checked by the RAM-PAGE and ERRAT servers. PPI networks analysis was carried out by the STRING database. The HpPseF model was achieved in the Protein Model Database under the access code of PM0080987. Structure figures were prepared using PYMOL (http://www.pymol.org/). […]

call_split

Molecular details of secretory phospholipase A2 from flax (Linum usitatissimum L.) provide insight into its structure and function

2017
Sci Rep
PMCID: 5593939
PMID: 28894144
DOI: 10.1038/s41598-017-10969-9
call_split See protocol

[…] the most favoured regions of the Ramachandran Plot. Structure visualization was performed with pymol (http://www.pymol.org). The predicted models of proteins were submitted to Protein Model Database (PMDB) and have been assigned identifier PM0080416 (LusPLA2I) and PM0080415 (LusPLA2II). […]

library_books

Identification of a type I nitroreductase gene in non virulent Trypanosoma rangeli

2017
PMCID: 5452488
PMID: 28591312
DOI: 10.1590/0074-02760160532

[…] TRs from all the strains exhibited conservation of the NTR domain and critical residues involved in FMN interactions: R74, S76, R78, Q131, G247, and F248 (). In addition, a structural homology model (PMDB ID: PM0080571, https://bioinformatics.cineca.it/PMDB/) was constructed from amino acid residues 65 to 298 (). The N-terminal region between amino acid residues 32 and 68 is particularly rich in g […]

Citations

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PMDB institution(s)
CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita e Ricerca, Rome, Italy; Department of Biochemical Sciences, University ‘La Sapienza’, Rome, Italy; Istituto Pasteur—Fondazione Cenci Bolognetti, University ‘La Sapienza’, Rome, Italy
PMDB funding source(s)
Supported by the EU funded BioSapiens Network of Excellence, contract number LHSGCT-203-503265, and by the AIRC funded BICG Project “Bioinformatics tools for identifying, understanding and 60 attacking targets in cancer”.

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