FreeContact: fast and free software for protein contact prediction from residue co-evolution
Background 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-f...
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| Published in | BMC bioinformatics Vol. 15; no. 1; p. 85 |
|---|---|
| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
BioMed Central
26.03.2014
BioMed Central Ltd Springer Nature B.V |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1471-2105 1471-2105 |
| DOI | 10.1186/1471-2105-15-85 |
Cover
| Abstract | Background
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.
Results
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.
Conclusions
FreeContact
provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud). |
|---|---|
| AbstractList | 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.BACKGROUND20 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.RESULTSHere, 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).CONCLUSIONSFreeContact provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud). Doc number: 85 Abstract Background: 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. Results: 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. Conclusions: FreeContact provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud). 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). Background 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. Results 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. Conclusions FreeContact provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud). Keywords: Protein structure prediction, Protein sequence analysis, Fast protein contact prediction, 2D prediction, Open-source software, EVfold, EVcouplings, PSICOV, mfDCA, BioXSD, Debian package Background 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. Results 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. Conclusions FreeContact provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud). Background: 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. Results: 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. Conclusions: FreeContact provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud). 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). |
| ArticleNumber | 85 |
| Audience | Academic |
| Author | Rost, Burkhard Hopf, Thomas A Kalaš, Matúš Kaján, László Marks, Debora S |
| AuthorAffiliation | 5 Institute of Advanced Study (TUM-IAS), Lichtenbergstr. 2a, Garching/Munich 85748, Germany 2 Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA 4 Department of Informatics, University of Bergen, Bergen 5008, Norway 1 Department for Bioinformatics and Computational Biology, TU Munich, Boltzmannstraße 3, Garching 85748, Germany 6 WZW – Weihenstephan, Alte Akademie 8, Freising, Germany 3 Computational Biology Unit, Uni Computing, Bergen 5008, Norway |
| AuthorAffiliation_xml | – name: 4 Department of Informatics, University of Bergen, Bergen 5008, Norway – name: 6 WZW – Weihenstephan, Alte Akademie 8, Freising, Germany – name: 1 Department for Bioinformatics and Computational Biology, TU Munich, Boltzmannstraße 3, Garching 85748, Germany – name: 2 Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA – name: 5 Institute of Advanced Study (TUM-IAS), Lichtenbergstr. 2a, Garching/Munich 85748, Germany – name: 3 Computational Biology Unit, Uni Computing, Bergen 5008, Norway |
| Author_xml | – sequence: 1 givenname: László surname: Kaján fullname: Kaján, László organization: Department for Bioinformatics and Computational Biology, TU Munich – sequence: 2 givenname: Thomas A surname: Hopf fullname: Hopf, Thomas A organization: Department for Bioinformatics and Computational Biology, TU Munich, Department of Systems Biology, Harvard Medical School – sequence: 3 givenname: Matúš surname: Kalaš fullname: Kalaš, Matúš organization: Computational Biology Unit, Uni Computing, Department of Informatics, University of Bergen – sequence: 4 givenname: Debora S surname: Marks fullname: Marks, Debora S organization: Department of Systems Biology, Harvard Medical School – sequence: 5 givenname: Burkhard surname: Rost fullname: Rost, Burkhard email: assistant@rostlab.org organization: Department for Bioinformatics and Computational Biology, TU Munich, Institute of Advanced Study (TUM-IAS), Lichtenbergstr. 2a, WZW – Weihenstephan |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/24669753$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | Kaján et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( ) applies to the data made available in this article, unless otherwise stated. COPYRIGHT 2014 BioMed Central Ltd. 2014 Kaján et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Copyright © 2014 Kaján et al.; licensee BioMed Central Ltd. 2014 Kaján et al.; licensee BioMed Central Ltd. |
| Copyright_xml | – notice: Kaján et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( ) applies to the data made available in this article, unless otherwise stated. – notice: COPYRIGHT 2014 BioMed Central Ltd. – notice: 2014 Kaján et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. – notice: Copyright © 2014 Kaján et al.; licensee BioMed Central Ltd. 2014 Kaján et al.; licensee BioMed Central Ltd. |
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| DOI | 10.1186/1471-2105-15-85 |
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| Keywords | EVcouplings PSICOV mfDCA EVfold 2D prediction Open-source software Protein structure prediction BioXSD Debian package Protein sequence analysis Fast protein contact prediction |
| Language | English |
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20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated... 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations... Background 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated... Doc number: 85 Abstract Background: 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein... Background: 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated... |
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| SubjectTerms | Algorithms Bioinformatics Biology Biomedical and Life Sciences C plus plus Colleges & universities Computational Biology - methods Computational Biology/Bioinformatics Computer Appl. in Life Sciences Internet service providers Life Sciences Methods Microarrays Programming languages Protein Conformation Protein structure prediction Proteins Proteins - chemistry Proteins - genetics Public software Sequence analysis (applications) Sequence Analysis, Protein - methods Software Technology application |
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| Title | FreeContact: fast and free software for protein contact prediction from residue co-evolution |
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