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Protocols

PDBsum specifications

Information


Unique identifier OMICS_02951
Name PDBsum
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/PDBsum

Maintainers


  • person_outline Tjaart A. P. de Beer
  • person_outline Roman Laskowski

Additional information


https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=doc_about.html

Publications for PDBsum

library_books

PDBsum additions

2014 Nucleic Acids Res
PMCID: 3965036
PMID: 24153109
DOI: 10.1093/nar/gkt940
library_books

PDBsum new things

2009 Nucleic Acids Res
PMCID: 2686501
PMID: 18996896
DOI: 10.1093/nar/gkn860

PDBsum citations

 (178)
library_books

A new insight into identification of in silico analysis of natural compounds targeting GPR120

2018
PMCID: 5951878
PMID: 29780684
DOI: 10.1007/s13721-018-0166-0

[…] s by combining its confidence scores with predicted or identified secondary structures and local sequence identity. Secondary structural conformations for the developed GPR120 model were predicted by Pdbsum (Laskowski et al. ). […]

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

[…] ured or disallowed regions, the number of glycine and proline residues and orientation of their backbone dihedral angles including the phi (φ) and psi (ψ) angles with using the PROCHECK module of the PDBsum server http://www.ebi.ac.uk/pdbsum/ []. Furthermore, qualitative assessment measured in terms of stability and reliability of the predicted models was evaluated through the RAMPAGE server http: […]

library_books

SMAR1 inhibits Wnt/β catenin signaling and prevents colorectal cancer progression

2018
Oncotarget
PMCID: 5940383
PMID: 29765542
DOI: 10.18632/oncotarget.25093

[…] and ΔS is the entropy changes. The interaction of SMAR1 with AT-01C and AT-01D was also analyzed by an in silico docking AutoDock. Amino acid residues involved in the interaction were analyzed using PDBsum. The structures of the peptides were generated using Swiss PDB [] while the SMAR1 structure was used from the already reported structure earlier from our lab []. […]

call_split

Genetic characterization of Chikungunya virus 2009 isolates from South India

2018
Bioinformation
PMCID: 5953859
DOI: 10.6026/97320630014106
call_split See protocol

[…] The secondary structure of the protein was predicted by PDBSUM []. The entire protein structure was unavailable in PDB; an ab-initio structure prediction was carried out using ITASSER []. The best model was selected using confidence score (C-score) and val […]

call_split

Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members

2018
Sci Rep
PMCID: 5829257
PMID: 29487297
DOI: 10.1038/s41598-018-21798-9
call_split See protocol

[…] collection, structure solution, and refinement are given in SMI, while statistics from processing/refinement are given in Table . Analysis of the structures were performed with PyMOL, Dali server and PDBsum. […]

call_split

Characterization of indole 3 pyruvic acid pathway mediated biosynthesis of auxin in Neurospora crassa

2018
PLoS One
PMCID: 5805262
PMID: 29420579
DOI: 10.1371/journal.pone.0192293
call_split See protocol

[…] All the predicted structures generated by I-TASSER or SWISS-MODEL were evaluated in the PDBsum database using PROCHECK analysis []. As two independent approaches (Ab initio and homology modeling) were used for structure prediction, we further checked the consistency and reliability of th […]

Citations

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PDBsum institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland; National Centre for Biomolecular Research, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University Brno, Brno-Bohunice, Czech Republic
PDBsum funding source(s)
Supported by the Ministry of Education, Youth and Sports of the Czech Republic; Grant number: CEITEC 2020 (LQ1601).

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