DOI: 10.1186/1471-2105-15-85. FreeContact: fast and free software for protein contact prediction from residue co-evolution

FreeContact: fast and free software for protein contact prediction from residue co-evolution

10.1186/1471-2105-15-85

Crossref journal-article

Springer Science and Business Media LLC

BMC Bioinformatics (297)

Bibliography

KajÃ¡n, L., Hopf, T. A., KalaÅ¡, M., Marks, D. S., & Rost, B. (2014). FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics, 15(1).

Authors 5

László Kaján (first)
Thomas A Hopf (additional)
Matúš Kalaš (additional)
Debora S Marks (additional)
Burkhard Rost (additional)

References 36 Referenced 148

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The protein data bank. Nucleic Acids Res. 2000, 28 (1): 235-242. (10.1093/nar/28.1.235) / Nucleic Acids Res by HM Berman (2000)
Magrane M, Consortium U: UniProt knowledgebase: a hub of integrated protein data. Database: the journal of biological databases and curation. 2011, 2011: bar009- (10.1093/database/bar009) / Database: the journal of biological databases and curation by M Magrane (2011)
Rost B, Sander C: Bridging the protein sequence-structure gap by structure predictions. Annual review of biophysics and biomolecular structure. 1996, 25: 113-136. (10.1146/annurev.bb.25.060196.000553) / Annual review of biophysics and biomolecular structure by B Rost (1996)
Kiefer F, Arnold K, Kunzli M, Bordoli L, Schwede T: The SWISS-MODEL repository and associated resources. Nucleic Acids Res. 2009, 37 (Database issue): D387-392. (10.1093/nar/gkn750) / Nucleic Acids Res by F Kiefer (2009)
Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A: ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2011, 39 (Database issue): D465-474. (10.1093/nar/gkq1091) / Nucleic Acids Res by U Pieper (2011)
Liu J, Hegyi H, Acton TB, Montelione GT, Rost B: Automatic target selection for structural genomics on eukaryotes. Proteins. 2004, 56 (2): 188-200. (10.1002/prot.20012) / Proteins by J Liu (2004)
Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS: Three-dimensional structures of membrane proteins from genomic sequencing. Cell. 2012, 149 (7): 1607-1621. (10.1016/j.cell.2012.04.012) / Cell by TA Hopf (2012)
Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C: Protein 3D structure computed from evolutionary sequence variation. PLoS ONE. 2011, 6 (12): e28766- (10.1371/journal.pone.0028766) / PLoS ONE by DS Marks (2011)
EVcouplings and EVfold. http://evfold.org/evfold-web/evfold.do,
Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M: Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A. 2011, 108 (49): E1293-1301. (10.1073/pnas.1111471108) / Proc Natl Acad Sci U S A by F Morcos (2011)
Jones DT, Buchan DW, Cozzetto D, Pontil M: PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics. 2012, 28 (2): 184-190. (10.1093/bioinformatics/btr638) / Bioinformatics by DT Jones (2012)
Ekeberg M, Lovkvist C, Lan Y, Weigt M, Aurell E: Improved contact prediction in proteins: using pseudolikelihoods to infer potts models. Physical review E, Statistical, nonlinear, and soft matter physics. 2013, 87 (1–1): 012707- (10.1103/PhysRevE.87.012707) / Physical review E, Statistical, nonlinear, and soft matter physics by M Ekeberg (2013)
Skwark MJ, Abdel-Rehim A, Elofsson A: PconsC: combination of direct information methods and alignments improves contact prediction. Bioinformatics. 2013, 29 (14): 1815-1816. (10.1093/bioinformatics/btt259) / Bioinformatics by MJ Skwark (2013)
Wang Z, Xu J: Predicting protein contact map using evolutionary and physical constraints by integer programming. Bioinformatics. 2013, 29 (13): i266-i273. (10.1093/bioinformatics/btt211) / Bioinformatics by Z Wang (2013)
Marks DS, Hopf TA, Sander C: Protein structure prediction from sequence variation. Nature biotechnology. 2012, 30 (11): 1072-1080. (10.1038/nbt.2419) / Nature biotechnology by DS Marks (2012)
de Juan D, Pazos F, Valencia A: Emerging methods in protein co-evolution. Nature reviews Genetics. 2013, 14 (4): 249-261. (10.1038/nrg3414) / Nature reviews Genetics by D de Juan (2013)
Przybylski D, Rost B: Alignments grow, secondary structure prediction improves. Proteins. 2002, 46 (2): 197-205. (10.1002/prot.10029) / Proteins by D Przybylski (2002)
Kaján L, Yachdav G, Vicedo E, Steinegger M, Mirdita M, Angermüller C, Böhm A, Domke S, Ertl J, Mertes C, Reisinger E, Staniewski C, Rost B: Cloud prediction of protein structure and function with predict protein for debian. BioMed Research International. 2013, 2013: 6- (10.1155/2013/398968) / BioMed Research International by L Kaján (2013)
Debian - the universal operating system. http://www.debian.org/,
Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992, 89 (22): 10915-10919. (10.1073/pnas.89.22.10915) / Proc Natl Acad Sci U S A by S Henikoff (1992)
OpenMP ARB: OpenMP Application Program Interface V3.0. 2008, OpenMP Architecture Review Board / OpenMP Application Program Interface V3.0 by OpenMP ARB (2008)
Anderson E, Bai Z, Bischof C, Blackford LS, Demmel J, Dongarra JJ, Croz JD, Hammarling S, Greenbaum A, McKenney A, Sorensen D: LAPACK Users’ guide. 1999, Siam, 9: (10.1137/1.9780898719604) / LAPACK Users’ guide by E Anderson (1999)
Mátyás A, Sustik BC: GLASSOFAST: an efficient GLASSO implementation. The University of Texas at Austin UTCS Technical Report. 2012, 1-3. TR-12-29 / The University of Texas at Austin UTCS Technical Report by A Mátyás (2012)
Friedman J, Hastie T, Tibshirani R: Sparse inverse covariance estimation with the graphical lasso. Biostatistics. 2008, 9 (3): 432-441. (10.1093/biostatistics/kxm045) / Biostatistics by J Friedman (2008)
Bash reference manual. http://www.gnu.org/software/bash/manual/bashref.html#Programmable-Completion,
Clint Whaley R, Petitet A, Dongarra JJ: Automated empirical optimizations of software and the ATLAS project. Parallel Comput. 2001, 27 (1): 3-35. (10.1016/S0167-8191(00)00087-9) / Parallel Comput by R Clint Whaley (2001)
Blackford LS, Demmel J, Dongarra J, Duff I, Hammarling S, Henry G, Heroux M, Kaufman L, Lumsdaine A, Petitet A, Pozo R, Remington K, Whaley RC: An updated set of basic linear algebra subprograms (BLAS). ACM Trans Math Softw. 2002, 28 (2): 135-151. (10.1145/567806.567807) / ACM Trans Math Softw by LS Blackford (2002)
GNU General Public License. http://www.gnu.org/licenses/gpl-3.0.html,
Debian derivatives. http://wiki.debian.org/Derivatives,
Field D, Tiwari B, Booth T, Houten S, Swan D, Bertrand N, Thurston M: Open software for biologists: from famine to feast. Nature biotechnology. 2006, 24 (7): 801-803. (10.1038/nbt0706-801) / Nature biotechnology by D Field (2006)
Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, Nelson KE: Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinforma. 2012, 13: 42- (10.1186/1471-2105-13-42) / BMC Bioinforma by K Krampis (2012)
Moller S, Krabbenhoft HN, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C, Holland R, Belhachemi D, Plessy C: Community-driven computational biology with Debian Linux. BMC Bioinforma. 2010, 11 (12): S5- (10.1186/1471-2105-11-S12-S5) / BMC Bioinforma by S Moller (2010)
Debian Med. http://www.debian.org/devel/debian-med/,
FreeContact FTP download. ftp://rostlab.org/free/
Grana O, Baker D, MacCallum RM, Meiler J, Punta M, Rost B, Tress ML, Valencia A: CASP6 assessment of contact prediction. Proteins. 2005, 61 (Suppl 7): 214-224. (10.1002/prot.20739) / Proteins by O Grana (2005)
Kalaš M, Puntervoll P, Joseph A, Bartaševičiūtė E, Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C: BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics. 2010, 26 (18): i540-i546. (10.1093/bioinformatics/btq391) / Bioinformatics by M Kalaš (2010)

Dates

Type	When
Created	11 years, 4 months ago (March 26, 2014, 8:06 a.m.)
Deposited	3 years, 11 months ago (Sept. 1, 2021, 11:33 p.m.)
Indexed	3 months ago (May 20, 2025, 6:39 a.m.)
Issued	11 years, 4 months ago (March 26, 2014)
Published	11 years, 4 months ago (March 26, 2014)
Published Online	11 years, 4 months ago (March 26, 2014)
Published Print	10 years, 8 months ago (Dec. 1, 2014)

Funders 0

None

BibTeX

@article{Kaj_n_2014, title={FreeContact: fast and free software for protein contact prediction from residue co-evolution}, volume={15}, ISSN={1471-2105}, url={http://dx.doi.org/10.1186/1471-2105-15-85}, DOI={10.1186/1471-2105-15-85}, number={1}, journal={BMC Bioinformatics}, publisher={Springer Science and Business Media LLC}, author={Kaján, László and Hopf, Thomas A and Kalaš, Matúš and Marks, Debora S and Rost, Burkhard}, year={2014}, month=mar }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        5,
        20
      ]
    ],
    "date-time": "2025-05-20T10:39:05Z",
    "timestamp": 1747737545054
  },
  "reference-count": 36,
  "publisher": "Springer Science and Business Media LLC",
  "issue": "1",
  "content-domain": {
    "domain": [
      "link.springer.com"
    ],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2014,
        12
      ]
    ]
  },
  "DOI": "10.1186/1471-2105-15-85",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2014,
        3,
        26
      ]
    ],
    "date-time": "2014-03-26T12:06:29Z",
    "timestamp": 1395835589000
  },
  "update-policy": "http://dx.doi.org/10.1007/springer_crossmark_policy",
  "source": "Crossref",
  "is-referenced-by-count": 148,
  "title": "FreeContact: fast and free software for protein contact prediction from residue co-evolution",
  "prefix": "10.1186",
  "volume": "15",
  "author": [
    {
      "given": "L\u00e1szl\u00f3",
      "family": "Kaj\u00e1n",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Thomas A",
      "family": "Hopf",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Mat\u00fa\u0161",
      "family": "Kala\u0161",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Debora S",
      "family": "Marks",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Burkhard",
      "family": "Rost",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "297",
  "published-online": {
    "date-parts": [
      [
        2014,
        3,
        26
      ]
    ]
  },
  "reference": [
    {
      "issue": "1",
      "key": "6340_CR1",
      "doi-asserted-by": "publisher",
      "first-page": "235",
      "DOI": "10.1093/nar/28.1.235",
      "volume": "28",
      "author": "HM Berman",
      "year": "2000",
      "unstructured": "Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The protein data bank. Nucleic Acids Res. 2000, 28 (1): 235-242.",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "key": "6340_CR2",
      "doi-asserted-by": "publisher",
      "first-page": "bar009",
      "DOI": "10.1093/database/bar009",
      "volume": "2011",
      "author": "M Magrane",
      "year": "2011",
      "unstructured": "Magrane M, Consortium U: UniProt knowledgebase: a hub of integrated protein data. Database: the journal of biological databases and curation. 2011, 2011: bar009-",
      "journal-title": "Database: the journal of biological databases and curation"
    },
    {
      "key": "6340_CR3",
      "doi-asserted-by": "publisher",
      "first-page": "113",
      "DOI": "10.1146/annurev.bb.25.060196.000553",
      "volume": "25",
      "author": "B Rost",
      "year": "1996",
      "unstructured": "Rost B, Sander C: Bridging the protein sequence-structure gap by structure predictions. Annual review of biophysics and biomolecular structure. 1996, 25: 113-136.",
      "journal-title": "Annual review of biophysics and biomolecular structure"
    },
    {
      "issue": "Database issue",
      "key": "6340_CR4",
      "doi-asserted-by": "publisher",
      "first-page": "D387",
      "DOI": "10.1093/nar/gkn750",
      "volume": "37",
      "author": "F Kiefer",
      "year": "2009",
      "unstructured": "Kiefer F, Arnold K, Kunzli M, Bordoli L, Schwede T: The SWISS-MODEL repository and associated resources. Nucleic Acids Res. 2009, 37 (Database issue): D387-392.",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "issue": "Database issue",
      "key": "6340_CR5",
      "doi-asserted-by": "publisher",
      "first-page": "D465",
      "DOI": "10.1093/nar/gkq1091",
      "volume": "39",
      "author": "U Pieper",
      "year": "2011",
      "unstructured": "Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sj\u00f6lander K, Ferrin TE, Burley SK, Sali A: ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2011, 39 (Database issue): D465-474.",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "issue": "2",
      "key": "6340_CR6",
      "doi-asserted-by": "publisher",
      "first-page": "188",
      "DOI": "10.1002/prot.20012",
      "volume": "56",
      "author": "J Liu",
      "year": "2004",
      "unstructured": "Liu J, Hegyi H, Acton TB, Montelione GT, Rost B: Automatic target selection for structural genomics on eukaryotes. Proteins. 2004, 56 (2): 188-200.",
      "journal-title": "Proteins"
    },
    {
      "issue": "7",
      "key": "6340_CR7",
      "doi-asserted-by": "publisher",
      "first-page": "1607",
      "DOI": "10.1016/j.cell.2012.04.012",
      "volume": "149",
      "author": "TA Hopf",
      "year": "2012",
      "unstructured": "Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS: Three-dimensional structures of membrane proteins from genomic sequencing. Cell. 2012, 149 (7): 1607-1621.",
      "journal-title": "Cell"
    },
    {
      "issue": "12",
      "key": "6340_CR8",
      "doi-asserted-by": "publisher",
      "first-page": "e28766",
      "DOI": "10.1371/journal.pone.0028766",
      "volume": "6",
      "author": "DS Marks",
      "year": "2011",
      "unstructured": "Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C: Protein 3D structure computed from evolutionary sequence variation. PLoS ONE. 2011, 6 (12): e28766-",
      "journal-title": "PLoS ONE"
    },
    {
      "key": "6340_CR9",
      "unstructured": "EVcouplings and EVfold. http://evfold.org/evfold-web/evfold.do,"
    },
    {
      "issue": "49",
      "key": "6340_CR10",
      "doi-asserted-by": "publisher",
      "first-page": "E1293",
      "DOI": "10.1073/pnas.1111471108",
      "volume": "108",
      "author": "F Morcos",
      "year": "2011",
      "unstructured": "Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M: Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A. 2011, 108 (49): E1293-1301.",
      "journal-title": "Proc Natl Acad Sci U S A"
    },
    {
      "issue": "2",
      "key": "6340_CR11",
      "doi-asserted-by": "publisher",
      "first-page": "184",
      "DOI": "10.1093/bioinformatics/btr638",
      "volume": "28",
      "author": "DT Jones",
      "year": "2012",
      "unstructured": "Jones DT, Buchan DW, Cozzetto D, Pontil M: PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics. 2012, 28 (2): 184-190.",
      "journal-title": "Bioinformatics"
    },
    {
      "issue": "1\u20131",
      "key": "6340_CR12",
      "doi-asserted-by": "publisher",
      "first-page": "012707",
      "DOI": "10.1103/PhysRevE.87.012707",
      "volume": "87",
      "author": "M Ekeberg",
      "year": "2013",
      "unstructured": "Ekeberg M, Lovkvist C, Lan Y, Weigt M, Aurell E: Improved contact prediction in proteins: using pseudolikelihoods to infer potts models. Physical review E, Statistical, nonlinear, and soft matter physics. 2013, 87 (1\u20131): 012707-",
      "journal-title": "Physical review E, Statistical, nonlinear, and soft matter physics"
    },
    {
      "issue": "14",
      "key": "6340_CR13",
      "doi-asserted-by": "publisher",
      "first-page": "1815",
      "DOI": "10.1093/bioinformatics/btt259",
      "volume": "29",
      "author": "MJ Skwark",
      "year": "2013",
      "unstructured": "Skwark MJ, Abdel-Rehim A, Elofsson A: PconsC: combination of direct information methods and alignments improves contact prediction. Bioinformatics. 2013, 29 (14): 1815-1816.",
      "journal-title": "Bioinformatics"
    },
    {
      "issue": "13",
      "key": "6340_CR14",
      "doi-asserted-by": "publisher",
      "first-page": "i266",
      "DOI": "10.1093/bioinformatics/btt211",
      "volume": "29",
      "author": "Z Wang",
      "year": "2013",
      "unstructured": "Wang Z, Xu J: Predicting protein contact map using evolutionary and physical constraints by integer programming. Bioinformatics. 2013, 29 (13): i266-i273.",
      "journal-title": "Bioinformatics"
    },
    {
      "issue": "11",
      "key": "6340_CR15",
      "doi-asserted-by": "publisher",
      "first-page": "1072",
      "DOI": "10.1038/nbt.2419",
      "volume": "30",
      "author": "DS Marks",
      "year": "2012",
      "unstructured": "Marks DS, Hopf TA, Sander C: Protein structure prediction from sequence variation. Nature biotechnology. 2012, 30 (11): 1072-1080.",
      "journal-title": "Nature biotechnology"
    },
    {
      "issue": "4",
      "key": "6340_CR16",
      "doi-asserted-by": "publisher",
      "first-page": "249",
      "DOI": "10.1038/nrg3414",
      "volume": "14",
      "author": "D de Juan",
      "year": "2013",
      "unstructured": "de Juan D, Pazos F, Valencia A: Emerging methods in protein co-evolution. Nature reviews Genetics. 2013, 14 (4): 249-261.",
      "journal-title": "Nature reviews Genetics"
    },
    {
      "issue": "2",
      "key": "6340_CR17",
      "doi-asserted-by": "publisher",
      "first-page": "197",
      "DOI": "10.1002/prot.10029",
      "volume": "46",
      "author": "D Przybylski",
      "year": "2002",
      "unstructured": "Przybylski D, Rost B: Alignments grow, secondary structure prediction improves. Proteins. 2002, 46 (2): 197-205.",
      "journal-title": "Proteins"
    },
    {
      "key": "6340_CR18",
      "doi-asserted-by": "publisher",
      "first-page": "6",
      "DOI": "10.1155/2013/398968",
      "volume": "2013",
      "author": "L Kaj\u00e1n",
      "year": "2013",
      "unstructured": "Kaj\u00e1n L, Yachdav G, Vicedo E, Steinegger M, Mirdita M, Angerm\u00fcller C, B\u00f6hm A, Domke S, Ertl J, Mertes C, Reisinger E, Staniewski C, Rost B: Cloud prediction of protein structure and function with predict protein for debian. BioMed Research International. 2013, 2013: 6-",
      "journal-title": "BioMed Research International"
    },
    {
      "key": "6340_CR19",
      "unstructured": "Debian - the universal operating system. http://www.debian.org/,"
    },
    {
      "issue": "22",
      "key": "6340_CR20",
      "doi-asserted-by": "publisher",
      "first-page": "10915",
      "DOI": "10.1073/pnas.89.22.10915",
      "volume": "89",
      "author": "S Henikoff",
      "year": "1992",
      "unstructured": "Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992, 89 (22): 10915-10919.",
      "journal-title": "Proc Natl Acad Sci U S A"
    },
    {
      "key": "6340_CR21",
      "volume-title": "OpenMP Application Program Interface V3.0",
      "author": "OpenMP ARB",
      "year": "2008",
      "unstructured": "OpenMP ARB: OpenMP Application Program Interface V3.0. 2008, OpenMP Architecture Review Board"
    },
    {
      "key": "6340_CR22",
      "doi-asserted-by": "publisher",
      "DOI": "10.1137/1.9780898719604",
      "volume-title": "LAPACK Users\u2019 guide",
      "author": "E Anderson",
      "year": "1999",
      "unstructured": "Anderson E, Bai Z, Bischof C, Blackford LS, Demmel J, Dongarra JJ, Croz JD, Hammarling S, Greenbaum A, McKenney A, Sorensen D: LAPACK Users\u2019 guide. 1999, Siam, 9:"
    },
    {
      "key": "6340_CR23",
      "first-page": "1",
      "volume-title": "The University of Texas at Austin UTCS Technical Report",
      "author": "A M\u00e1ty\u00e1s",
      "year": "2012",
      "unstructured": "M\u00e1ty\u00e1s A, Sustik BC: GLASSOFAST: an efficient GLASSO implementation. The University of Texas at Austin UTCS Technical Report. 2012, 1-3. TR-12-29"
    },
    {
      "issue": "3",
      "key": "6340_CR24",
      "doi-asserted-by": "publisher",
      "first-page": "432",
      "DOI": "10.1093/biostatistics/kxm045",
      "volume": "9",
      "author": "J Friedman",
      "year": "2008",
      "unstructured": "Friedman J, Hastie T, Tibshirani R: Sparse inverse covariance estimation with the graphical lasso. Biostatistics. 2008, 9 (3): 432-441.",
      "journal-title": "Biostatistics"
    },
    {
      "key": "6340_CR25",
      "unstructured": "Bash reference manual. http://www.gnu.org/software/bash/manual/bashref.html#Programmable-Completion,"
    },
    {
      "issue": "1",
      "key": "6340_CR26",
      "doi-asserted-by": "publisher",
      "first-page": "3",
      "DOI": "10.1016/S0167-8191(00)00087-9",
      "volume": "27",
      "author": "R Clint Whaley",
      "year": "2001",
      "unstructured": "Clint Whaley R, Petitet A, Dongarra JJ: Automated empirical optimizations of software and the ATLAS project. Parallel Comput. 2001, 27 (1): 3-35.",
      "journal-title": "Parallel Comput"
    },
    {
      "issue": "2",
      "key": "6340_CR27",
      "doi-asserted-by": "publisher",
      "first-page": "135",
      "DOI": "10.1145/567806.567807",
      "volume": "28",
      "author": "LS Blackford",
      "year": "2002",
      "unstructured": "Blackford LS, Demmel J, Dongarra J, Duff I, Hammarling S, Henry G, Heroux M, Kaufman L, Lumsdaine A, Petitet A, Pozo R, Remington K, Whaley RC: An updated set of basic linear algebra subprograms (BLAS). ACM Trans Math Softw. 2002, 28 (2): 135-151.",
      "journal-title": "ACM Trans Math Softw"
    },
    {
      "key": "6340_CR28",
      "unstructured": "GNU General Public License. http://www.gnu.org/licenses/gpl-3.0.html,"
    },
    {
      "key": "6340_CR29",
      "unstructured": "Debian derivatives. http://wiki.debian.org/Derivatives,"
    },
    {
      "issue": "7",
      "key": "6340_CR30",
      "doi-asserted-by": "publisher",
      "first-page": "801",
      "DOI": "10.1038/nbt0706-801",
      "volume": "24",
      "author": "D Field",
      "year": "2006",
      "unstructured": "Field D, Tiwari B, Booth T, Houten S, Swan D, Bertrand N, Thurston M: Open software for biologists: from famine to feast. Nature biotechnology. 2006, 24 (7): 801-803.",
      "journal-title": "Nature biotechnology"
    },
    {
      "key": "6340_CR31",
      "doi-asserted-by": "publisher",
      "first-page": "42",
      "DOI": "10.1186/1471-2105-13-42",
      "volume": "13",
      "author": "K Krampis",
      "year": "2012",
      "unstructured": "Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, Nelson KE: Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinforma. 2012, 13: 42-",
      "journal-title": "BMC Bioinforma"
    },
    {
      "issue": "12",
      "key": "6340_CR32",
      "doi-asserted-by": "publisher",
      "first-page": "S5",
      "DOI": "10.1186/1471-2105-11-S12-S5",
      "volume": "11",
      "author": "S Moller",
      "year": "2010",
      "unstructured": "Moller S, Krabbenhoft HN, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C, Holland R, Belhachemi D, Plessy C: Community-driven computational biology with Debian Linux. BMC Bioinforma. 2010, 11 (12): S5-",
      "journal-title": "BMC Bioinforma"
    },
    {
      "key": "6340_CR33",
      "unstructured": "Debian Med. http://www.debian.org/devel/debian-med/,"
    },
    {
      "key": "6340_CR34",
      "unstructured": "FreeContact FTP download. ftp://rostlab.org/free/"
    },
    {
      "issue": "Suppl 7",
      "key": "6340_CR35",
      "doi-asserted-by": "publisher",
      "first-page": "214",
      "DOI": "10.1002/prot.20739",
      "volume": "61",
      "author": "O Grana",
      "year": "2005",
      "unstructured": "Grana O, Baker D, MacCallum RM, Meiler J, Punta M, Rost B, Tress ML, Valencia A: CASP6 assessment of contact prediction. Proteins. 2005, 61 (Suppl 7): 214-224.",
      "journal-title": "Proteins"
    },
    {
      "issue": "18",
      "key": "6340_CR36",
      "doi-asserted-by": "publisher",
      "first-page": "i540",
      "DOI": "10.1093/bioinformatics/btq391",
      "volume": "26",
      "author": "M Kala\u0161",
      "year": "2010",
      "unstructured": "Kala\u0161 M, Puntervoll P, Joseph A, Barta\u0161evi\u010di\u016bt\u0117 E, T\u00f6pfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C: BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics. 2010, 26 (18): i540-i546.",
      "journal-title": "Bioinformatics"
    }
  ],
  "container-title": "BMC Bioinformatics",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://link.springer.com/content/pdf/10.1186/1471-2105-15-85.pdf",
      "content-type": "application/pdf",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2021,
        9,
        2
      ]
    ],
    "date-time": "2021-09-02T03:33:22Z",
    "timestamp": 1630553602000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-85"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2014,
        3,
        26
      ]
    ]
  },
  "references-count": 36,
  "journal-issue": {
    "issue": "1",
    "published-print": {
      "date-parts": [
        [
          2014,
          12
        ]
      ]
    }
  },
  "alternative-id": [
    "6340"
  ],
  "URL": "http://dx.doi.org/10.1186/1471-2105-15-85",
  "relation": {},
  "ISSN": [
    "1471-2105"
  ],
  "subject": [],
  "container-title-short": "BMC Bioinformatics",
  "published": {
    "date-parts": [
      [
        2014,
        3,
        26
      ]
    ]
  },
  "assertion": [
    {
      "value": "30 September 2013",
      "order": 1,
      "name": "received",
      "label": "Received",
      "group": {
        "name": "ArticleHistory",
        "label": "Article History"
      }
    },
    {
      "value": "18 March 2014",
      "order": 2,
      "name": "accepted",
      "label": "Accepted",
      "group": {
        "name": "ArticleHistory",
        "label": "Article History"
      }
    },
    {
      "value": "26 March 2014",
      "order": 3,
      "name": "first_online",
      "label": "First Online",
      "group": {
        "name": "ArticleHistory",
        "label": "Article History"
      }
    }
  ],
  "article-number": "85"
}