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bbcontacts specifications

Information


Unique identifier OMICS_08918
Name bbcontacts
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU Affero General Public License version 3
Computer skills Advanced
Stability Stable
Requirements
Numpy, Scipy
Maintained Yes

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Maintainer


  • person_outline Johannes Soeding <>

Publication for bbcontacts

bbcontacts in publications

 (5)
PMCID: 5414403
PMID: 28512576
DOI: 10.1107/S2052252517005115

[…] unassisted models, those informed by the predictions from the general method pconsc2 (skwark et al., 2014), and those guided by a novel combination of pconsc2 with a β-sheet-specific method, bbcontacts (andreani & söding, 2015). in a set of 21 cases, spanning sizes of 62–221 residues, resolutions of 1.0–2.3 å and all fold classes, they found multiple targets that could only be solved […]

PMCID: 5428263
PMID: 28303031
DOI: 10.1038/s41598-017-00320-7

[…] with the goal of predicting e1e2 ectodomain tertiary and quaternary structures, we first sought to determine β-strands pairing for all the unsolved domains by applying the recently developed bbcontacts algorithm. at first, the algorithm was fed with e1e2 secondary structure and raptorx predicted contact map to test its predictive power; bbcontacts succeeded in correctly identifying five […]

PMCID: 5860252
PMID: 28171606
DOI: 10.1093/bioinformatics/btw618

[…] uses predictions output by freecontact (a mfdca implementation) (), psicov and ccmpred. resulting contact predictions are used as features in a two-layer neural network., specialist predictors like bbcontacts () have been developed, in this case, to infer only beta-strand pairing based on the output of ccmpred. it has been shown to achieve 50% precision for β–β residue pairs at 50% recall using […]

PMCID: 5031224
PMID: 27318187
DOI: 10.1002/prot.25088

[…] using the comec duf4131 sequence obtained from uniprot, evolutionary covariance analysis was used to predict residue‐residue contacts with pconsc2 and a specialist β‐strand filtering protocol bbcontacts. pconsc2 is a meta‐predictor that takes 16 predictions as input: the psicov or plmdca (ekeberg et al. 2013, 2014) results from eight alignments, derived by jackhmmer against the uniref100 […]

PMCID: 4937781
PMID: 27437113
DOI: 10.1107/S2052252516008113

[…] an additional contact map for β-structure-containing targets was predicted using ccmpred (seemayer et al., 2014) and reduced to β-sheet contact pairs using the ccmpred-specific filtering protocol bbcontacts (andreani & söding, 2015). each msa for ccmpred contact predictions was obtained using hhblits v.2.0.15 (remmert et al., 2012). this entailed two sequence-search iterations […]


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bbcontacts institution(s)
Gene Center, LMU Munich, Munich, Germany; Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

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