FreeContact: fast and free software for protein contact prediction from residue co-evolution
20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein three-dimensional structure. The method EVfold broke new ground using mean-field Direct...
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| Veröffentlicht in: | BMC bioinformatics 2014-03, Vol.15 (1), p.85-85, Article 85 |
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| creator | Kaján, László Hopf, Thomas A Kalaš, Matúš Marks, Debora S Rost, Burkhard |
| description | 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein three-dimensional structure. The method EVfold broke new ground using mean-field Direct Coupling Analysis (EVfold-mfDCA); the method PSICOV applied a related concept by estimating a sparse inverse covariance matrix. Both methods (EVfold-mfDCA and PSICOV) are publicly available, but both require too much CPU time for interactive applications. On top, EVfold-mfDCA depends on proprietary software.
Here, we present FreeContact, a fast, open source implementation of EVfold-mfDCA and PSICOV. On a test set of 140 proteins, FreeContact was almost eight times faster than PSICOV without decreasing prediction performance. The EVfold-mfDCA implementation of FreeContact was over 220 times faster than PSICOV with negligible performance decrease. EVfold-mfDCA was unavailable for testing due to its dependency on proprietary software. FreeContact is implemented as the free C++ library "libfreecontact", complete with command line tool "freecontact", as well as Perl and Python modules. All components are available as Debian packages. FreeContact supports the BioXSD format for interoperability.
FreeContact provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud). |
| doi_str_mv | 10.1186/1471-2105-15-85 |
| format | Article |
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Here, we present FreeContact, a fast, open source implementation of EVfold-mfDCA and PSICOV. On a test set of 140 proteins, FreeContact was almost eight times faster than PSICOV without decreasing prediction performance. The EVfold-mfDCA implementation of FreeContact was over 220 times faster than PSICOV with negligible performance decrease. EVfold-mfDCA was unavailable for testing due to its dependency on proprietary software. FreeContact is implemented as the free C++ library "libfreecontact", complete with command line tool "freecontact", as well as Perl and Python modules. All components are available as Debian packages. FreeContact supports the BioXSD format for interoperability.
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Here, we present FreeContact, a fast, open source implementation of EVfold-mfDCA and PSICOV. On a test set of 140 proteins, FreeContact was almost eight times faster than PSICOV without decreasing prediction performance. The EVfold-mfDCA implementation of FreeContact was over 220 times faster than PSICOV with negligible performance decrease. EVfold-mfDCA was unavailable for testing due to its dependency on proprietary software. FreeContact is implemented as the free C++ library "libfreecontact", complete with command line tool "freecontact", as well as Perl and Python modules. All components are available as Debian packages. FreeContact supports the BioXSD format for interoperability.
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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kaján, László</au><au>Hopf, Thomas A</au><au>Kalaš, Matúš</au><au>Marks, Debora S</au><au>Rost, Burkhard</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>FreeContact: fast and free software for protein contact prediction from residue co-evolution</atitle><jtitle>BMC bioinformatics</jtitle><addtitle>BMC Bioinformatics</addtitle><date>2014-03-26</date><risdate>2014</risdate><volume>15</volume><issue>1</issue><spage>85</spage><epage>85</epage><pages>85-85</pages><artnum>85</artnum><issn>1471-2105</issn><eissn>1471-2105</eissn><abstract>20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein three-dimensional structure. The method EVfold broke new ground using mean-field Direct Coupling Analysis (EVfold-mfDCA); the method PSICOV applied a related concept by estimating a sparse inverse covariance matrix. Both methods (EVfold-mfDCA and PSICOV) are publicly available, but both require too much CPU time for interactive applications. On top, EVfold-mfDCA depends on proprietary software.
Here, we present FreeContact, a fast, open source implementation of EVfold-mfDCA and PSICOV. On a test set of 140 proteins, FreeContact was almost eight times faster than PSICOV without decreasing prediction performance. The EVfold-mfDCA implementation of FreeContact was over 220 times faster than PSICOV with negligible performance decrease. EVfold-mfDCA was unavailable for testing due to its dependency on proprietary software. FreeContact is implemented as the free C++ library "libfreecontact", complete with command line tool "freecontact", as well as Perl and Python modules. All components are available as Debian packages. FreeContact supports the BioXSD format for interoperability.
FreeContact provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud).</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>24669753</pmid><doi>10.1186/1471-2105-15-85</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | BMC bioinformatics, 2014-03, Vol.15 (1), p.85-85, Article 85 |
| issn | 1471-2105 1471-2105 |
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| source | MEDLINE; SpringerLink Journals; PubMed Central Open Access; Springer Nature OA Free Journals; TestCollectionTL3OpenAccess; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Algorithms Bioinformatics Biology C plus plus Colleges & universities Computational Biology - methods Internet service providers Methods Programming languages Protein Conformation Protein structure prediction Proteins Proteins - chemistry Proteins - genetics Public software Sequence Analysis, Protein - methods Software Technology application |
| title | FreeContact: fast and free software for protein contact prediction from residue co-evolution |
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