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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
PMCID: 5713875
PMID: 29199978
DOI: 10.1107/S2059798317016436

[…] 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 […]

library_books

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

2016
PMCID: 5860252
PMID: 28171606
DOI: 10.1093/bioinformatics/btw618

[…] set of predictions. pconsc2 was shown to obtain higher precision when compared to psicov, plmdca and pconsc on three different sets. a second consensus method, metapsicov, 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 () […]

library_books

Assembling the Tat protein translocase

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

[…] 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 […]


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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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