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Protocols

SABBAC specifications

Information


Unique identifier OMICS_22847
Name SABBAC
Alternative name Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.3
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pierre Tuffery

Publication for Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace

SABBAC citations

 (6)
library_books

Conformational Activation of Poly(ADP ribose) Polymerase 1 upon DNA Binding Revealed by Small Angle X ray Scattering

2014
Biochemistry
PMCID: 3971956
PMID: 24588584
DOI: 10.1021/bi401439n

[…] II (FIII, residues 224–359, PDB entry 4DQY), BRCT domain (residues 388–483, PDB entry 2COK), WGR domain (residues 531–644, PDB entry 4DQY), and catalytic domain (residues 662–1009, PDB entry 4DQY).,, SABBAC (online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace) was then utilized to position the missing atoms in the flexible linkers of the structural models of fu […]

call_split

Hsc70 induced Changes in Clathrin Auxilin Cage Structure Suggest a Role for Clathrin Light Chains in Cage Disassembly

2013
PMCID: 3776051
PMID: 23710728
DOI: 10.1111/tra.12085
call_split See protocol

[…] significantly better (0.70 versus 0.68). The atomic models were derived by fitting a backbone and side chains to the published alpha carbon models determined by cryo-TEM, using the programs Scit and SABBAC .The clathrin-auxilin401-910-Hsc70 map needed no resampling, but the scale of the clathrin-auxilin map was adjusted using Frealign to match the atomic model and the clathrin-auxilin401-910-Hsc7 […]

call_split

The Carboxy Terminal αN Helix of the Archaeal XerA Tyrosine Recombinase Is a Molecular Switch to Control Site Specific Recombination

2013
PLoS One
PMCID: 3646895
PMID: 23667562
DOI: 10.1371/journal.pone.0063010
call_split See protocol

[…] ing the program CRYSOL from the crystal structure by adding missing residues (8 in the N-terminal position and 13 in the C-terminal position including the His6-Tag) and using the programs BUNCH and SABBAC . The goodness of fit was characterised by the χ parameter whose square is the average of differences between experimental and calculated intensities (Iexp(q)−Icalc(q))2 weighted by the experim […]

call_split

Structural Insight into Inhibitor of Apoptosis Proteins Recognition by a Potent Divalent Smac Mimetic

2012
PLoS One
PMCID: 3499469
PMID: 23166698
DOI: 10.1371/journal.pone.0049527
call_split See protocol

[…] esidue long) were modeled as dummy residues (DRs) centered at Cα positions. The DR chains in resulting models were substituted with a polypeptide backbone and side-chains were added using the program SABBAC . The connectivity of the split 9a molecule was restored using rotational degrees of freedom around single bonds. Finally the scattering pattern of the model was recalculated using Crysol . […]

call_split

4.4 Å cryo EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus

2011
PMCID: 3173789
PMID: 21829169
DOI: 10.1038/emboj.2011.261
call_split See protocol

[…] ent bulky side-chain densities along the helices (e.g., E1-W407, E1-W409, E1-Y434 and E2-W387).Next, we converted all the de novo traced Cα models to their corresponding all-atom models of VEEV using SABBAC online server (), and then stitched the homology and de novo portions together in COOT () to generate the initial full-length E1 and E2 atomic models.Our model for the CP protease domain is tak […]

library_books

Diffusion, Crowding and Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

2010
PLoS Comput Biol
PMCID: 2832674
PMID: 20221255
DOI: 10.1371/journal.pcbi.1000694

[…] group and kindly made available to the authors by Dr. Feng Ding (UNC; personal communication). This structure contains only Cα atoms so complete backbone coordinates were first constructed using the SABBAC webserver (http://bioserv.rpbs.jussieu.fr/cgi-bin/SABBAC) before sidechain positions were constructed using SCWRL3. Owing to the structure's origins being a Cα-only model we were unable to add […]

Citations

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SABBAC institution(s)
Equipe de Bioinformatique Genomique et Moleculaire, INSERM U726, Universite Paris, Paris, France; Institut de Pharmacologie Moleculaire et Cellulaire, UMR 6097 CNRS/UNSA, Sophia Antipolis, France

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