DOI: 10.1002/pro.5560040318. Transmembrane helices predicted at 95% accuracy

Transmembrane helices predicted at 95% accuracy

10.1002/pro.5560040318

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractWe describe a neural network system that predicts the locations of transmembrane helices in integral membrane proteins. By using evolutionary information as input to the network system, the method significantly improved on a previously published neural network prediction method that had been based on single sequence information. The input data were derived from multiple alignments for each position in a window of 13 adjacent residues: amino acid frequency, conservation weights, number of insertions and deletions, and position of the window with respect to the ends of the protein chain. Additional input was the amino acid composition and length of the whole protein. A rigorous cross‐validation test on 69 proteins with experimentally determined locations of transmembrane segments yielded an overall two‐state per‐residue accuracy of 95%. About 94% of all segments were predicted correctly. When applied to known globular proteins as a negative control, the network system incorrectly predicted fewer than 5% of globular proteins as having transmembrane helices. The method was applied to all 269 open reading frames from the complete yeast VIII chromosome. For 59 of these, at least two transmembrane helices were predicted. Thus, the prediction is that about one‐fourth of all proteins from yeast VIII contain one transmembrane helix, and some 20%, more than one.

Bibliography

Rost, B., Sander, C., Casadio, R., & Fariselli, P. (1995). Transmembrane helices predicted at 95% accuracy. Protein Science, 4(3), 521â533. Portico.

Authors 4

Burkhard Rost (first)
Chris Sander (additional)
Rita Casadio (additional)
Piero Fariselli (additional)

References 49 Referenced 541

10.1111/j.1432-1033.1982.tb07002.x
10.1093/nar/22.17.3626
10.1002/j.1460-2075.1993.tb05814.x
10.1016/S0022-2836(77)80200-3
10.1016/0022-2836(87)90189-6
10.1126/science.8178151
10.1111/j.1432-1033.1990.tb15566.x
10.1038/318618a0
10.1006/jmbi.1993.1375
10.1016/0022-2836(84)90309-7
10.1073/pnas.81.1.140
10.1146/annurev.bb.15.060186.001541
10.1007/BF00205811
10.1016/S0022-2836(05)80271-2
10.1126/science.8091229
{'key': 'e_1_2_1_17_1', 'first-page': '275', 'article-title': 'The rapid generation of mutation data matrices from protein sequences', 'volume': '5', 'author': 'Jones DT', 'year': '1992', 'journal-title': 'CABIOS'} / CABIOS / The rapid generation of mutation data matrices from protein sequences by Jones DT (1992)
10.1021/bi00176a037
10.1002/bip.360221211
10.1038/367614a0
10.1016/0022-2836(82)90515-0
10.1006/jmbi.1993.1066
10.1002/prot.340180203
10.1126/science.3529391
10.1016/0005-2795(75)90109-9
10.1016/0014-5793(92)80506-C
10.1016/0896-6273(93)90269-W
10.1038/357038a0
10.1073/pnas.85.8.2444
10.1016/0076-6879(92)10029-D
10.1006/jmbi.1994.1220
10.1073/pnas.90.16.7558
10.1006/jmbi.1993.1413
10.1093/protein/6.8.831
10.1002/prot.340190108
10.1002/prot.340200303
10.1016/0968-0004(93)90017-H
10.1016/S0022-2836(05)80007-5
10.1038/323533a0
10.1002/prot.340090107
{'key': 'e_1_2_1_41_1', 'first-page': '3597', 'article-title': 'The HSSP database of protein structure‐sequence alignments', 'volume': '22', 'author': 'Sander C', 'year': '1994', 'journal-title': 'Nucleic Acids Res'} / Nucleic Acids Res / The HSSP database of protein structure‐sequence alignments by Sander C (1994)
10.1111/j.1432-1033.1993.tb17885.x
10.1002/prot.340180309
10.1111/j.1432-1033.1981.tb05700.x
10.1093/nar/14.11.4683
10.1111/j.1432-1033.1991.tb16117.x
10.1016/0022-2836(92)90934-C
10.1111/j.1432-1033.1988.tb14150.x
10.1002/j.1460-2075.1993.tb05876.x
10.1016/0022-2836(92)90903-W

Dates

Type	When
Created	15 years, 1 month ago (June 29, 2010, 4:44 a.m.)
Deposited	1 year, 9 months ago (Oct. 25, 2023, 11:45 p.m.)
Indexed	2 weeks, 1 day ago (Aug. 6, 2025, 8:58 a.m.)
Issued	30 years, 5 months ago (March 1, 1995)
Published	30 years, 5 months ago (March 1, 1995)
Published Online	16 years, 7 months ago (Dec. 24, 2008)
Published Print	30 years, 5 months ago (March 1, 1995)

Funders 0

None

BibTeX

@article{Rost_1995, title={Transmembrane helices predicted at 95% accuracy}, volume={4}, ISSN={1469-896X}, url={http://dx.doi.org/10.1002/pro.5560040318}, DOI={10.1002/pro.5560040318}, number={3}, journal={Protein Science}, publisher={Wiley}, author={Rost, Burkhard and Sander, Chris and Casadio, Rita and Fariselli, Piero}, year={1995}, month=mar, pages={521–533} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        6
      ]
    ],
    "date-time": "2025-08-06T12:58:28Z",
    "timestamp": 1754485108008
  },
  "reference-count": 49,
  "publisher": "Wiley",
  "issue": "3",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2008,
            12,
            24
          ]
        ],
        "date-time": "2008-12-24T00:00:00Z",
        "timestamp": 1230076800000
      },
      "content-version": "vor",
      "delay-in-days": 5047,
      "URL": "http://onlinelibrary.wiley.com/termsAndConditions#vor"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        1995,
        3
      ]
    ]
  },
  "abstract": "<jats:title>Abstract</jats:title><jats:p>We describe a neural network system that predicts the locations of transmembrane helices in integral membrane proteins. By using evolutionary information as input to the network system, the method significantly improved on a previously published neural network prediction method that had been based on single sequence information. The input data were derived from multiple alignments for each position in a window of 13 adjacent residues: amino acid frequency, conservation weights, number of insertions and deletions, and position of the window with respect to the ends of the protein chain. Additional input was the amino acid composition and length of the whole protein. A rigorous cross\u2010validation test on 69 proteins with experimentally determined locations of transmembrane segments yielded an overall two\u2010state per\u2010residue accuracy of 95%. About 94% of all segments were predicted correctly. When applied to known globular proteins as a negative control, the network system incorrectly predicted fewer than 5% of globular proteins as having transmembrane helices. The method was applied to all 269 open reading frames from the complete yeast VIII chromosome. For 59 of these, at least two transmembrane helices were predicted. Thus, the prediction is that about one\u2010fourth of all proteins from yeast VIII contain one transmembrane helix, and some 20%, more than one.</jats:p>",
  "DOI": "10.1002/pro.5560040318",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2010,
        6,
        29
      ]
    ],
    "date-time": "2010-06-29T08:44:40Z",
    "timestamp": 1277801080000
  },
  "page": "521-533",
  "source": "Crossref",
  "is-referenced-by-count": 541,
  "title": "Transmembrane helices predicted at 95% accuracy",
  "prefix": "10.1002",
  "volume": "4",
  "author": [
    {
      "given": "Burkhard",
      "family": "Rost",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Chris",
      "family": "Sander",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Rita",
      "family": "Casadio",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Piero",
      "family": "Fariselli",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "311",
  "published-online": {
    "date-parts": [
      [
        2008,
        12,
        24
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_2_1_2_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1111/j.1432-1033.1982.tb07002.x"
    },
    {
      "key": "e_1_2_1_3_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/22.17.3626"
    },
    {
      "key": "e_1_2_1_4_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/j.1460-2075.1993.tb05814.x"
    },
    {
      "key": "e_1_2_1_5_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(77)80200-3"
    },
    {
      "key": "e_1_2_1_6_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(87)90189-6"
    },
    {
      "key": "e_1_2_1_7_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.8178151"
    },
    {
      "key": "e_1_2_1_8_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1111/j.1432-1033.1990.tb15566.x"
    },
    {
      "key": "e_1_2_1_9_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/318618a0"
    },
    {
      "key": "e_1_2_1_10_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1993.1375"
    },
    {
      "key": "e_1_2_1_11_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(84)90309-7"
    },
    {
      "key": "e_1_2_1_12_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.81.1.140"
    },
    {
      "key": "e_1_2_1_13_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1146/annurev.bb.15.060186.001541"
    },
    {
      "key": "e_1_2_1_14_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/BF00205811"
    },
    {
      "key": "e_1_2_1_15_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(05)80271-2"
    },
    {
      "key": "e_1_2_1_16_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.8091229"
    },
    {
      "key": "e_1_2_1_17_1",
      "first-page": "275",
      "article-title": "The rapid generation of mutation data matrices from protein sequences",
      "volume": "5",
      "author": "Jones DT",
      "year": "1992",
      "journal-title": "CABIOS"
    },
    {
      "key": "e_1_2_1_18_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi00176a037"
    },
    {
      "key": "e_1_2_1_19_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/bip.360221211"
    },
    {
      "key": "e_1_2_1_20_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/367614a0"
    },
    {
      "key": "e_1_2_1_21_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(82)90515-0"
    },
    {
      "key": "e_1_2_1_22_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1993.1066"
    },
    {
      "key": "e_1_2_1_23_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.340180203"
    },
    {
      "key": "e_1_2_1_24_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.3529391"
    },
    {
      "key": "e_1_2_1_25_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0005-2795(75)90109-9"
    },
    {
      "key": "e_1_2_1_26_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0014-5793(92)80506-C"
    },
    {
      "key": "e_1_2_1_27_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0896-6273(93)90269-W"
    },
    {
      "key": "e_1_2_1_28_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/357038a0"
    },
    {
      "key": "e_1_2_1_29_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.85.8.2444"
    },
    {
      "key": "e_1_2_1_30_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0076-6879(92)10029-D"
    },
    {
      "key": "e_1_2_1_31_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1994.1220"
    },
    {
      "key": "e_1_2_1_32_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.90.16.7558"
    },
    {
      "key": "e_1_2_1_33_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1993.1413"
    },
    {
      "key": "e_1_2_1_34_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/protein/6.8.831"
    },
    {
      "key": "e_1_2_1_35_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.340190108"
    },
    {
      "key": "e_1_2_1_36_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.340200303"
    },
    {
      "key": "e_1_2_1_37_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0968-0004(93)90017-H"
    },
    {
      "key": "e_1_2_1_38_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(05)80007-5"
    },
    {
      "key": "e_1_2_1_39_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/323533a0"
    },
    {
      "key": "e_1_2_1_40_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.340090107"
    },
    {
      "key": "e_1_2_1_41_1",
      "first-page": "3597",
      "article-title": "The HSSP database of protein structure\u2010sequence alignments",
      "volume": "22",
      "author": "Sander C",
      "year": "1994",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "key": "e_1_2_1_42_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1111/j.1432-1033.1993.tb17885.x"
    },
    {
      "key": "e_1_2_1_43_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.340180309"
    },
    {
      "key": "e_1_2_1_44_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1111/j.1432-1033.1981.tb05700.x"
    },
    {
      "key": "e_1_2_1_45_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/14.11.4683"
    },
    {
      "key": "e_1_2_1_46_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1111/j.1432-1033.1991.tb16117.x"
    },
    {
      "key": "e_1_2_1_47_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(92)90934-C"
    },
    {
      "key": "e_1_2_1_48_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1111/j.1432-1033.1988.tb14150.x"
    },
    {
      "key": "e_1_2_1_49_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/j.1460-2075.1993.tb05876.x"
    },
    {
      "key": "e_1_2_1_50_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(92)90903-W"
    }
  ],
  "container-title": "Protein Science",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fpro.5560040318",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.5560040318",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        10,
        26
      ]
    ],
    "date-time": "2023-10-26T03:45:36Z",
    "timestamp": 1698291936000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://onlinelibrary.wiley.com/doi/10.1002/pro.5560040318"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        1995,
        3
      ]
    ]
  },
  "references-count": 49,
  "journal-issue": {
    "issue": "3",
    "published-print": {
      "date-parts": [
        [
          1995,
          3
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1002/pro.5560040318"
  ],
  "URL": "http://dx.doi.org/10.1002/pro.5560040318",
  "relation": {},
  "ISSN": [
    "0961-8368",
    "1469-896X"
  ],
  "subject": [],
  "container-title-short": "Protein Science",
  "published": {
    "date-parts": [
      [
        1995,
        3
      ]
    ]
  }
}