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Protocols

RCSB PDB specifications

Information


Unique identifier OMICS_03036
Name RCSB PDB
Alternative names The Research Collaboratory for Structural Bioinformatics Protein Data Bank, RCSB PDB Mobile, RCSB Protein Data Bank
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainers


  • person_outline Peter Rose
  • person_outline Christine Zardecki

Additional information


https://www.rcsb.org/pages/help/index

Publications for The Research Collaboratory for Structural Bioinformatics Protein Data Bank

RCSB PDB citations

 (188)
library_books

Determination of genotypic and clinical characteristics of Colombian patients with mucopolysaccharidosis IVA

2018
PMCID: 5926073
PMID: 29731656
DOI: 10.2147/TACG.S141881

[…] Each mutant was modeled by homology with SWISS-model using a 4FDI wild-type GALNS template from the RCSB-PDB database, and then the models were refined at PyMOL. summarizes the RMSD and ASA measures for each of the models.RMSD was calculated by overlapping all mutant GALNS models with 4FDI wild-typ […]

library_books

Lignin peroxidase ligand access channel dysfunction in the presence of atrazine

2018
Sci Rep
PMCID: 5902622
PMID: 29662099
DOI: 10.1038/s41598-018-24478-w

[…] 1.1). The docking procedure was carried out with the DockingServer web-based application, and the results were analyzed with AutoDockTools (v1.5.6). The applied enzyme structure was obtained from the RCSB PDB database (PDB: 1B82) with a resolution of 1.8 Å. The structure contained a non-relevant R114A mutation. MD simulations of lignin peroxidase were performed with NAMD software (v2.12) using the […]

library_books

Analysis of HIV 1 envelope evolution suggests antibody mediated selection of common epitopes among Chinese former plasma donors from a narrow source outbreak

2018
Sci Rep
PMCID: 5893620
PMID: 29636501
DOI: 10.1038/s41598-018-23913-2

[…] elling was implemented through SWISS-MODEL– to map the translated SM cohort Gp120 consensus sequence to a cryo-electron microscopy (cryo-EM) crystal structure of a glycosylated HIV-1 envelope trimer (RCSB PDB 3J5M). The sites of interest were annotated on the modelled structure in PyMOL v1.7.4 (Schrödinger, LLC.). […]

call_split

Glucose regulated protein 78 substrate binding domain alters its conformation upon EGCG inhibitor binding to nucleotide binding domain: Molecular dynamics studies

2018
Sci Rep
PMCID: 5882873
PMID: 29615633
DOI: 10.1038/s41598-018-22905-6
call_split See protocol

[…] full length ATP-bound state of 78-kDa Glucose-regulated Protein (GRP78) and its isolated SBD, respectively, was downloaded from Research Collaboratory in Structural Bioinformatics Protein Data Bank (RCSB PDB) (http://www.rcsb.org/pdb/home.do). EGCG inhibitor structure was downloaded from PubChem database in .sdf format. OpenBabel (http://openbabel.org/wiki/main_page) was used to convert this file […]

library_books

New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET) Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes

2018
Appl Environ Microbiol
PMCID: 5881046
PMID: 29427431
DOI: 10.1128/AEM.02773-17

[…] search was carried out using the HMMER (http://hmmer.org/) webpage or a local version of the software (v3.1b2) with downloaded data sets. Structural information on the enzymes was retrieved from the RCSB-PDB () database.Sequence data were processed using BioEdit and the Clone Manager suite version 9 (Sci-Ed Software, Denver, USA). Neighbor-joining phylogenetic trees based on amino acid sequence a […]

library_books

The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex specific ORFs across order Unionoida

2018
BMC Genomics
PMCID: 5870820
PMID: 29587633
DOI: 10.1186/s12864-018-4583-3

[…] To ensure that the amino acid chain within Respiratory Complex 1 that corresponds to NAD5 was correctly selected for analysis, sequence for NAD5 from A. anatina was aligned to protein sequence in the RCSB PDB using BLAST [–]. This protein BLAST analysis also served as a complementary test for our annotation of NAD5. NAD5’s protein features were assigned in our figures using the annotations reporte […]


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RCSB PDB institution(s)
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, CA, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA; The Scripps Research Institute, La Jolla, CA, USA
RCSB PDB funding source(s)
Supported by the National Science Foundation [NSF-DBI 1338415]; the National Institute of General Medical Sciences; National Cancer Institute; and the U.S. Department of Energy.

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