PDBeFold protocols

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PDBeFold specifications

Information


Unique identifier OMICS_04210
Name PDBeFold
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.59
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Evgeny Krissinel <>

Publication for PDBeFold

PDBeFold in pipelines

 (11)
2017
PMCID: 5233953
PMID: 28084396
DOI: 10.1038/srep40408

[…] was protonated according to ph 7.4. the maximum esp for the colour range was 100 kcal/mol. comparative structure-based homology analysis of the frpd structure was carried out using dali, cath, and pdbefold. figures were prepared with pymol (http://www.pymol.org)., saxs data were collected on the beamline x33 embl at doris-iii in hamburg, germany. the concentrations of frpd […]

2017
PMCID: 5770620
PMID: 29375490
DOI: 10.3389/fmicb.2017.02441

[…] of docking orientations between two proteins. the top docking model of the kpglpk-kpn00353 complex was superimposed with the e. coli glpk-crr complex structure (pdb accession code: 1gla) using the pdbefold server () to produce structural figures. the models of the kpn00353 mutants were generated by the coot software (). the interface residues of all complex structures were determined […]

2016
PMCID: 4729829
PMID: 26739236
DOI: 10.1038/ncomms10292

[…] conservation calculation were performed using consurf, with default settings. pbd codes for the deubad domains are 4uem and 4uf5. the structures of the deubad domains where superimposed using pdbefold., multi-angle laser light scattering experiments were performed using a minidawn light scattering detector (wyatt technologies) in line with either a superdex s75 10/30 (asxl1deu), superose […]

2016
PMCID: 5131608
PMID: 27612581
DOI: 10.1016/j.jsb.2016.08.006

[…] and β1 in tt122238-123; β2 in tt121836-123 aligns with β1 in tt122238-123, and there is no equivalent of β4 from tt122238-123 in tt121836-123., we used the protein structure comparison service pdbefold at the european bioinformatics institute (), hhpred () and dali () to search for pilins with similar folds (). the closest structure identified was the type ii secretion pseudopilin epsi […]

2015
PMCID: 4381287
PMID: 25423369
DOI: 10.1042/BSR20140174

[…] because it had better defined electron density and thus more complete models at the c-termini., a search for known protein structures with a fold similar to that of comfb was performed using pdbefold and dali [,]. analyses of contact surface areas between comfb protomers in the crystal lattice were done on the pisa server []. figures were generated in pymol (schrödinger, llc)., starter […]


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PDBeFold in publications

 (180)
PMCID: 5923319
PMID: 29649119
DOI: 10.3390/toxins10040153

[…] [,,]., structural sequence alignment. structure based sequence alignment of hca1 (chain b from 4jra) [] and hca2 (chain a from 6es1) binding to sv2c-l4 was generated using pdbefold []. graphic representation was generated using espript 3.0 [] with the secondary structure from hca2 (chain a from 6es1)., sequence alignment. sequence alignment of the fourth luminal […]

PMCID: 5895659
PMID: 29675007
DOI: 10.3389/fmicb.2018.00649

[…] ). although we could not interpret this density, we hypothesize that it may correspond to a compound present in the crystallization solution, such as peg. search for structural homologs in the pdbefold server indicated that the closest structure to mab_4384 corresponds to the lfrr tetr transcriptional regulator from mycobacterium smegmatis bound to proflavin (pdb id : 2v57) () […]

PMCID: 5871853
PMID: 29593310
DOI: 10.1038/s41598-018-22986-3

[…] 2, the enzyme adopts an open α/β structure fold, similar to the glutaminase domain from a wide range of gatases. indeed, using the gatd model as input in the protein structure comparison service pdbefold at european bioinformatics institute (http://www.ebi.ac.uk/msd-srv/ssm), several class i triad gatases were identified (table ). the most similar structure found is the thermotoga maritima […]

PMCID: 5795435
PMID: 29300333
DOI: 10.3390/v10010022

[…] of these viruses (pdb ids: cpv, 2cas; fpv, 1c8e; h-1pv, 4gbt; luiii, 6b8q; mvm, 1z14; ppv, 1k3v) [,,,,,] were compared to the buv1 vp2 structure by secondary structure matching (ssm) in the pdbefold program []. distance differences at regions of non-overlapping cα positions, due to deletions and insertions, were measured as described above. variable regions among the protoparvoviruses […]

PMCID: 5829564
PMID: 29309642
DOI: 10.1093/nar/gkx1299

[…] has residues in the disallowed region of the ramachandran map. the dna conformation was analyzed with 3dna (). atomic coordinates were aligned based on matching cα positions with the online server pdbefold (). figures were generated with pymol and espript., the binding reaction mixture (final volume of 10 μl) contained binding buffer (20 mm hepes–naoh ph 7.4, 100 mm nacl, 2 mm dtt and 5% (w/v) […]


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PDBeFold institution(s)
European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge, UK
PDBeFold funding source(s)
Supported by the research grant 721/B19544 from the Biotechnology and Biological Sciences Research Council (BBSRC) UK.

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