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Citations per year

Number of citations per year for the bioinformatics software tool FreeContact
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Tool usage distribution map

This map represents all the scientific publications referring to FreeContact per scientific context
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Protocols

FreeContact specifications

Information


Unique identifier OMICS_03520
Name FreeContact
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
Autotools, Boost, BLAS, LAPACK, Xerces, CodeSynthesis XSD
Maintained Yes

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Maintainer


  • person_outline Burkhard Rost

Publication for FreeContact

FreeContact citations

 (3)
library_books

Approaches to ab initio molecular replacement of α helical transmembrane proteins

2017
Acta Crystallogr D Struct Biol
PMCID: 5713875
PMID: 29199978
DOI: 10.1107/S2059798317016436

[…] m, 2017). A contact meta-prediction using MetaPSICOV v.1.04 (Jones et al., 2015) was generated, which in turn used the following contact-prediction pipelines: CCMPRED v.0.3.2 (Seemayer et al., 2014), FreeContact v.1.0.21 (Kaján et al., 2014) and PSICOV v.2.1b3 (Jones et al., 2012). The predictions from MetaPSICOV stage 1 (MetaPSICOV_S1) were used as the contact predictions for MetaPSICOV as recomm […]

call_split

Comparing co evolution methods and their application to template free protein structure prediction

2016
Bioinformatics
PMCID: 5860252
PMID: 28171606
DOI: 10.1093/bioinformatics/btw618
call_split See protocol

[…] Mean Field Direct Coupling Analysis (mfDCA) is a class of contact predictors based on a maximum entropy model. For the analyses described in this work, we used both Freecontact version 1.0.21, with standard parameters () and PSICOV version 2.1 with a target precision matrix sparsity of 0.03 and default parameters ().MfDCA and PSICOV are significantly different in […]

library_books

Assembling the Tat protein translocase

2016
eLife
PMCID: 5201420
PMID: 27914200
DOI: 10.7554/eLife.20718.030

[…] rganism was removed from the analysis. PSICOV () was used to predict the co-evolving residue pairs shown in the main text. Evolutionary couplings calculated using the alternative programs CCMPRED (), FreeContact (), and MetaPSICOV () resulted in similar contact predictions (). Topologically implausible contacts were removed by retaining only contacts that were less than 15 Å apart along the membra […]


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FreeContact institution(s)
Department for Bioinformatics and Computational Biology, TU Munich, Garching, Germany; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Computational Biology Unit, Uni Computing, Bergen 5008, Norway; Department of Informatics, University of Bergen, Bergen, Norway; Institute of Advanced Study (TUM-IAS),Munich, Germany; WZW – Weihenstephan, Freising, Germany

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