Document (#30259)

Author
Artymiuk, P.J.
Spriggs, R.V.
Willett, P.
Title
Graph theoretic methods for the analysis of structural relationships in biological macromolecules
Source
Journal of the American Society for Information Science and Technology. 56(2005) no.5, S.518-528
Year
2005
Abstract
Subgraph isomorphism and maximum common subgraph isomorphism algorithms from graph theory provide an effective and an efficient way of identifying structural relationships between biological macromolecules. They thus provide a natural complement to the pattern matching algorithms that are used in bioinformatics to identify sequence relationships. Examples are provided of the use of graph theory to analyze proteins for which three-dimensional crystallographic or NMR structures are available, focusing on the use of the Bron-Kerbosch clique detection algorithm to identify common folding motifs and of the Ullmann subgraph isomorphism algorithm to identify patterns of amino acid residues. Our methods are also applicable to other types of biological macromolecule, such as carbohydrate and nucleic acid structures.
Footnote
Beitrag in einem special issue on bioinformatics

Similar documents (author)

  1. Willett, P.: Recent trends in hierarchic document clustering : a critical review (1988) 5.02
    5.020828 = sum of:
      5.020828 = weight(author_txt:willett in 2604) [ClassicSimilarity], result of:
        5.020828 = score(doc=2604,freq=1.0), product of:
          0.99999994 = queryWeight, product of:
            8.033325 = idf(docFreq=38, maxDocs=44218)
            0.12448145 = queryNorm
          5.0208282 = fieldWeight in 2604, product of:
            1.0 = tf(freq=1.0), with freq of:
              1.0 = termFreq=1.0
            8.033325 = idf(docFreq=38, maxDocs=44218)
            0.625 = fieldNorm(doc=2604)
    
  2. Willett, P.: Best-match text retrieval (1993) 5.02
    5.020828 = sum of:
      5.020828 = weight(author_txt:willett in 7818) [ClassicSimilarity], result of:
        5.020828 = score(doc=7818,freq=1.0), product of:
          0.99999994 = queryWeight, product of:
            8.033325 = idf(docFreq=38, maxDocs=44218)
            0.12448145 = queryNorm
          5.0208282 = fieldWeight in 7818, product of:
            1.0 = tf(freq=1.0), with freq of:
              1.0 = termFreq=1.0
            8.033325 = idf(docFreq=38, maxDocs=44218)
            0.625 = fieldNorm(doc=7818)
    
  3. Willett, P.: From chemical documentation to chemoinformatics : 50 years of chemical information science (2009) 5.02
    5.020828 = sum of:
      5.020828 = weight(author_txt:willett in 3656) [ClassicSimilarity], result of:
        5.020828 = score(doc=3656,freq=1.0), product of:
          0.99999994 = queryWeight, product of:
            8.033325 = idf(docFreq=38, maxDocs=44218)
            0.12448145 = queryNorm
          5.0208282 = fieldWeight in 3656, product of:
            1.0 = tf(freq=1.0), with freq of:
              1.0 = termFreq=1.0
            8.033325 = idf(docFreq=38, maxDocs=44218)
            0.625 = fieldNorm(doc=3656)
    
  4. Perry, R.; Willett, P.: ¬A revies of the use of inverted files for best match searching in information retrieval systems (1983) 4.02
    4.016662 = sum of:
      4.016662 = weight(author_txt:willett in 2701) [ClassicSimilarity], result of:
        4.016662 = score(doc=2701,freq=1.0), product of:
          0.99999994 = queryWeight, product of:
            8.033325 = idf(docFreq=38, maxDocs=44218)
            0.12448145 = queryNorm
          4.0166626 = fieldWeight in 2701, product of:
            1.0 = tf(freq=1.0), with freq of:
              1.0 = termFreq=1.0
            8.033325 = idf(docFreq=38, maxDocs=44218)
            0.5 = fieldNorm(doc=2701)
    
  5. Robertson, A.M.; Willett, P.: Retrieval techniques for historical English text : searching the sixteenth and seventeenth century titles in the Catalogue of Caterbury Cathedral Library using spelling-correction methods (1992) 4.02
    4.016662 = sum of:
      4.016662 = weight(author_txt:willett in 4209) [ClassicSimilarity], result of:
        4.016662 = score(doc=4209,freq=1.0), product of:
          0.99999994 = queryWeight, product of:
            8.033325 = idf(docFreq=38, maxDocs=44218)
            0.12448145 = queryNorm
          4.0166626 = fieldWeight in 4209, product of:
            1.0 = tf(freq=1.0), with freq of:
              1.0 = termFreq=1.0
            8.033325 = idf(docFreq=38, maxDocs=44218)
            0.5 = fieldNorm(doc=4209)
    

Similar documents (content)

  1. Rodríguez, A.; Carazo, J.M.; Trelles-Salazar, O.: Mining association rules from biological databases (2005) 0.19
    0.18857546 = sum of:
      0.18857546 = product of:
        0.6734838 = sum of:
          0.03541509 = weight(abstract_txt:pattern in 5261) [ClassicSimilarity], result of:
            0.03541509 = score(doc=5261,freq=1.0), product of:
              0.090722896 = queryWeight, product of:
                1.0794592 = boost
                6.2458487 = idf(docFreq=232, maxDocs=44218)
                0.013456101 = queryNorm
              0.39036554 = fieldWeight in 5261, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                6.2458487 = idf(docFreq=232, maxDocs=44218)
                0.0625 = fieldNorm(doc=5261)
          0.06525368 = weight(abstract_txt:sequence in 5261) [ClassicSimilarity], result of:
            0.06525368 = score(doc=5261,freq=2.0), product of:
              0.10822261 = queryWeight, product of:
                1.178981 = boost
                6.82169 = idf(docFreq=130, maxDocs=44218)
                0.013456101 = queryNorm
              0.6029579 = fieldWeight in 5261, product of:
                1.4142135 = tf(freq=2.0), with freq of:
                  2.0 = termFreq=2.0
                6.82169 = idf(docFreq=130, maxDocs=44218)
                0.0625 = fieldNorm(doc=5261)
          0.12899186 = weight(abstract_txt:bioinformatics in 5261) [ClassicSimilarity], result of:
            0.12899186 = score(doc=5261,freq=2.0), product of:
              0.17046015 = queryWeight, product of:
                1.4796507 = boost
                8.561393 = idf(docFreq=22, maxDocs=44218)
                0.013456101 = queryNorm
              0.75672734 = fieldWeight in 5261, product of:
                1.4142135 = tf(freq=2.0), with freq of:
                  2.0 = termFreq=2.0
                8.561393 = idf(docFreq=22, maxDocs=44218)
                0.0625 = fieldNorm(doc=5261)
          0.09351217 = weight(abstract_txt:algorithm in 5261) [ClassicSimilarity], result of:
            0.09351217 = score(doc=5261,freq=3.0), product of:
              0.15140481 = queryWeight, product of:
                1.9721167 = boost
                5.705423 = idf(docFreq=399, maxDocs=44218)
                0.013456101 = queryNorm
              0.6176301 = fieldWeight in 5261, product of:
                1.7320508 = tf(freq=3.0), with freq of:
                  3.0 = termFreq=3.0
                5.705423 = idf(docFreq=399, maxDocs=44218)
                0.0625 = fieldNorm(doc=5261)
          0.054060366 = weight(abstract_txt:algorithms in 5261) [ClassicSimilarity], result of:
            0.054060366 = score(doc=5261,freq=1.0), product of:
              0.15153769 = queryWeight, product of:
                1.9729819 = boost
                5.707926 = idf(docFreq=398, maxDocs=44218)
                0.013456101 = queryNorm
              0.35674536 = fieldWeight in 5261, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                5.707926 = idf(docFreq=398, maxDocs=44218)
                0.0625 = fieldNorm(doc=5261)
          0.048443757 = weight(abstract_txt:relationships in 5261) [ClassicSimilarity], result of:
            0.048443757 = score(doc=5261,freq=1.0), product of:
              0.16123413 = queryWeight, product of:
                2.4925098 = boost
                4.807296 = idf(docFreq=981, maxDocs=44218)
                0.013456101 = queryNorm
              0.300456 = fieldWeight in 5261, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                4.807296 = idf(docFreq=981, maxDocs=44218)
                0.0625 = fieldNorm(doc=5261)
          0.24780685 = weight(abstract_txt:biological in 5261) [ClassicSimilarity], result of:
            0.24780685 = score(doc=5261,freq=2.0), product of:
              0.37992448 = queryWeight, product of:
                3.8261065 = boost
                7.3793993 = idf(docFreq=74, maxDocs=44218)
                0.013456101 = queryNorm
              0.6522529 = fieldWeight in 5261, product of:
                1.4142135 = tf(freq=2.0), with freq of:
                  2.0 = termFreq=2.0
                7.3793993 = idf(docFreq=74, maxDocs=44218)
                0.0625 = fieldNorm(doc=5261)
        0.28 = coord(7/25)
    
  2. Sebastian, Y.: Literature-based discovery by learning heterogeneous bibliographic information networks (2017) 0.12
    0.11575103 = sum of:
      0.11575103 = product of:
        0.41339654 = sum of:
          0.024636427 = weight(abstract_txt:efficient in 535) [ClassicSimilarity], result of:
            0.024636427 = score(doc=535,freq=1.0), product of:
              0.07785822 = queryWeight, product of:
                5.7860904 = idf(docFreq=368, maxDocs=44218)
                0.013456101 = queryNorm
              0.3164268 = fieldWeight in 535, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                5.7860904 = idf(docFreq=368, maxDocs=44218)
                0.0546875 = fieldNorm(doc=535)
          0.016501134 = weight(abstract_txt:provide in 535) [ClassicSimilarity], result of:
            0.016501134 = score(doc=535,freq=1.0), product of:
              0.075093985 = queryWeight, product of:
                1.388882 = boost
                4.0180984 = idf(docFreq=2161, maxDocs=44218)
                0.013456101 = queryNorm
              0.21973975 = fieldWeight in 535, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                4.0180984 = idf(docFreq=2161, maxDocs=44218)
                0.0546875 = fieldNorm(doc=535)
          0.02565023 = weight(abstract_txt:methods in 535) [ClassicSimilarity], result of:
            0.02565023 = score(doc=535,freq=2.0), product of:
              0.07997976 = queryWeight, product of:
                1.4333519 = boost
                4.146752 = idf(docFreq=1900, maxDocs=44218)
                0.013456101 = queryNorm
              0.320709 = fieldWeight in 535, product of:
                1.4142135 = tf(freq=2.0), with freq of:
                  2.0 = termFreq=2.0
                4.146752 = idf(docFreq=1900, maxDocs=44218)
                0.0546875 = fieldNorm(doc=535)
          0.048214234 = weight(abstract_txt:structures in 535) [ClassicSimilarity], result of:
            0.048214234 = score(doc=535,freq=2.0), product of:
              0.12181557 = queryWeight, product of:
                1.7689444 = boost
                5.117636 = idf(docFreq=719, maxDocs=44218)
                0.013456101 = queryNorm
              0.39579698 = fieldWeight in 535, product of:
                1.4142135 = tf(freq=2.0), with freq of:
                  2.0 = termFreq=2.0
                5.117636 = idf(docFreq=719, maxDocs=44218)
                0.0546875 = fieldNorm(doc=535)
          0.050784983 = weight(abstract_txt:structural in 535) [ClassicSimilarity], result of:
            0.050784983 = score(doc=535,freq=1.0), product of:
              0.1588862 = queryWeight, product of:
                2.0202534 = boost
                5.8446846 = idf(docFreq=347, maxDocs=44218)
                0.013456101 = queryNorm
              0.3196312 = fieldWeight in 535, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                5.8446846 = idf(docFreq=347, maxDocs=44218)
                0.0546875 = fieldNorm(doc=535)
          0.059946094 = weight(abstract_txt:relationships in 535) [ClassicSimilarity], result of:
            0.059946094 = score(doc=535,freq=2.0), product of:
              0.16123413 = queryWeight, product of:
                2.4925098 = boost
                4.807296 = idf(docFreq=981, maxDocs=44218)
                0.013456101 = queryNorm
              0.37179533 = fieldWeight in 535, product of:
                1.4142135 = tf(freq=2.0), with freq of:
                  2.0 = termFreq=2.0
                4.807296 = idf(docFreq=981, maxDocs=44218)
                0.0546875 = fieldNorm(doc=535)
          0.18766342 = weight(abstract_txt:graph in 535) [ClassicSimilarity], result of:
            0.18766342 = score(doc=535,freq=3.0), product of:
              0.3014202 = queryWeight, product of:
                3.407961 = boost
                6.572923 = idf(docFreq=167, maxDocs=44218)
                0.013456101 = queryNorm
              0.62259734 = fieldWeight in 535, product of:
                1.7320508 = tf(freq=3.0), with freq of:
                  3.0 = termFreq=3.0
                6.572923 = idf(docFreq=167, maxDocs=44218)
                0.0546875 = fieldNorm(doc=535)
        0.28 = coord(7/25)
    
  3. Arnopoulos, P.: ¬A SUM of science : the taxonomy and methodology of sociophysics (1993) 0.12
    0.11555063 = sum of:
      0.11555063 = product of:
        0.5777531 = sum of:
          0.042082224 = weight(abstract_txt:applicable in 5877) [ClassicSimilarity], result of:
            0.042082224 = score(doc=5877,freq=1.0), product of:
              0.10177875 = queryWeight, product of:
                1.1433425 = boost
                6.615483 = idf(docFreq=160, maxDocs=44218)
                0.013456101 = queryNorm
              0.41346768 = fieldWeight in 5877, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                6.615483 = idf(docFreq=160, maxDocs=44218)
                0.0625 = fieldNorm(doc=5877)
          0.038369842 = weight(abstract_txt:theory in 5877) [ClassicSimilarity], result of:
            0.038369842 = score(doc=5877,freq=2.0), product of:
              0.09570134 = queryWeight, product of:
                1.5679123 = boost
                4.5360413 = idf(docFreq=1287, maxDocs=44218)
                0.013456101 = queryNorm
              0.40093318 = fieldWeight in 5877, product of:
                1.4142135 = tf(freq=2.0), with freq of:
                  2.0 = termFreq=2.0
                4.5360413 = idf(docFreq=1287, maxDocs=44218)
                0.0625 = fieldNorm(doc=5877)
          0.038962986 = weight(abstract_txt:structures in 5877) [ClassicSimilarity], result of:
            0.038962986 = score(doc=5877,freq=1.0), product of:
              0.12181557 = queryWeight, product of:
                1.7689444 = boost
                5.117636 = idf(docFreq=719, maxDocs=44218)
                0.013456101 = queryNorm
              0.31985226 = fieldWeight in 5877, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                5.117636 = idf(docFreq=719, maxDocs=44218)
                0.0625 = fieldNorm(doc=5877)
          0.054060366 = weight(abstract_txt:algorithms in 5877) [ClassicSimilarity], result of:
            0.054060366 = score(doc=5877,freq=1.0), product of:
              0.15153769 = queryWeight, product of:
                1.9729819 = boost
                5.707926 = idf(docFreq=398, maxDocs=44218)
                0.013456101 = queryNorm
              0.35674536 = fieldWeight in 5877, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                5.707926 = idf(docFreq=398, maxDocs=44218)
                0.0625 = fieldNorm(doc=5877)
          0.4042777 = weight(abstract_txt:isomorphism in 5877) [ClassicSimilarity], result of:
            0.4042777 = score(doc=5877,freq=1.0), product of:
              0.6633636 = queryWeight, product of:
                5.055734 = boost
                9.7509775 = idf(docFreq=6, maxDocs=44218)
                0.013456101 = queryNorm
              0.6094361 = fieldWeight in 5877, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                9.7509775 = idf(docFreq=6, maxDocs=44218)
                0.0625 = fieldNorm(doc=5877)
        0.2 = coord(5/25)
    
  4. Ito, J.: Bibliographic structure : a frame of reference for bibliographic relationships (1994) 0.11
    0.110636145 = sum of:
      0.110636145 = product of:
        0.46098393 = sum of:
          0.042654663 = weight(abstract_txt:focusing in 3085) [ClassicSimilarity], result of:
            0.042654663 = score(doc=3085,freq=1.0), product of:
              0.078374505 = queryWeight, product of:
                1.0033101 = boost
                5.805243 = idf(docFreq=361, maxDocs=44218)
                0.013456101 = queryNorm
              0.54424155 = fieldWeight in 3085, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                5.805243 = idf(docFreq=361, maxDocs=44218)
                0.09375 = fieldNorm(doc=3085)
          0.053122636 = weight(abstract_txt:pattern in 3085) [ClassicSimilarity], result of:
            0.053122636 = score(doc=3085,freq=1.0), product of:
              0.090722896 = queryWeight, product of:
                1.0794592 = boost
                6.2458487 = idf(docFreq=232, maxDocs=44218)
                0.013456101 = queryNorm
              0.5855483 = fieldWeight in 3085, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                6.2458487 = idf(docFreq=232, maxDocs=44218)
                0.09375 = fieldNorm(doc=3085)
          0.028287657 = weight(abstract_txt:provide in 3085) [ClassicSimilarity], result of:
            0.028287657 = score(doc=3085,freq=1.0), product of:
              0.075093985 = queryWeight, product of:
                1.388882 = boost
                4.0180984 = idf(docFreq=2161, maxDocs=44218)
                0.013456101 = queryNorm
              0.3766967 = fieldWeight in 3085, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                4.0180984 = idf(docFreq=2161, maxDocs=44218)
                0.09375 = fieldNorm(doc=3085)
          0.06846632 = weight(abstract_txt:common in 3085) [ClassicSimilarity], result of:
            0.06846632 = score(doc=3085,freq=2.0), product of:
              0.107443914 = queryWeight, product of:
                1.6613215 = boost
                4.806278 = idf(docFreq=982, maxDocs=44218)
                0.013456101 = queryNorm
              0.6372285 = fieldWeight in 3085, product of:
                1.4142135 = tf(freq=2.0), with freq of:
                  2.0 = termFreq=2.0
                4.806278 = idf(docFreq=982, maxDocs=44218)
                0.09375 = fieldNorm(doc=3085)
          0.12312138 = weight(abstract_txt:structural in 3085) [ClassicSimilarity], result of:
            0.12312138 = score(doc=3085,freq=2.0), product of:
              0.1588862 = queryWeight, product of:
                2.0202534 = boost
                5.8446846 = idf(docFreq=347, maxDocs=44218)
                0.013456101 = queryNorm
              0.77490294 = fieldWeight in 3085, product of:
                1.4142135 = tf(freq=2.0), with freq of:
                  2.0 = termFreq=2.0
                5.8446846 = idf(docFreq=347, maxDocs=44218)
                0.09375 = fieldNorm(doc=3085)
          0.14533128 = weight(abstract_txt:relationships in 3085) [ClassicSimilarity], result of:
            0.14533128 = score(doc=3085,freq=4.0), product of:
              0.16123413 = queryWeight, product of:
                2.4925098 = boost
                4.807296 = idf(docFreq=981, maxDocs=44218)
                0.013456101 = queryNorm
              0.90136796 = fieldWeight in 3085, product of:
                2.0 = tf(freq=4.0), with freq of:
                  4.0 = termFreq=4.0
                4.807296 = idf(docFreq=981, maxDocs=44218)
                0.09375 = fieldNorm(doc=3085)
        0.24 = coord(6/25)
    
  5. Meng, K.; Ba, Z.; Ma, Y.; Li, G.: ¬A network coupling approach to detecting hierarchical linkages between science and technology (2024) 0.09
    0.092701115 = sum of:
      0.092701115 = product of:
        0.579382 = sum of:
          0.038962986 = weight(abstract_txt:structures in 1205) [ClassicSimilarity], result of:
            0.038962986 = score(doc=1205,freq=1.0), product of:
              0.12181557 = queryWeight, product of:
                1.7689444 = boost
                5.117636 = idf(docFreq=719, maxDocs=44218)
                0.013456101 = queryNorm
              0.31985226 = fieldWeight in 1205, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                5.117636 = idf(docFreq=719, maxDocs=44218)
                0.0625 = fieldNorm(doc=1205)
          0.054060366 = weight(abstract_txt:algorithms in 1205) [ClassicSimilarity], result of:
            0.054060366 = score(doc=1205,freq=1.0), product of:
              0.15153769 = queryWeight, product of:
                1.9729819 = boost
                5.707926 = idf(docFreq=398, maxDocs=44218)
                0.013456101 = queryNorm
              0.35674536 = fieldWeight in 1205, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                5.707926 = idf(docFreq=398, maxDocs=44218)
                0.0625 = fieldNorm(doc=1205)
          0.08208092 = weight(abstract_txt:structural in 1205) [ClassicSimilarity], result of:
            0.08208092 = score(doc=1205,freq=2.0), product of:
              0.1588862 = queryWeight, product of:
                2.0202534 = boost
                5.8446846 = idf(docFreq=347, maxDocs=44218)
                0.013456101 = queryNorm
              0.516602 = fieldWeight in 1205, product of:
                1.4142135 = tf(freq=2.0), with freq of:
                  2.0 = termFreq=2.0
                5.8446846 = idf(docFreq=347, maxDocs=44218)
                0.0625 = fieldNorm(doc=1205)
          0.4042777 = weight(abstract_txt:isomorphism in 1205) [ClassicSimilarity], result of:
            0.4042777 = score(doc=1205,freq=1.0), product of:
              0.6633636 = queryWeight, product of:
                5.055734 = boost
                9.7509775 = idf(docFreq=6, maxDocs=44218)
                0.013456101 = queryNorm
              0.6094361 = fieldWeight in 1205, product of:
                1.0 = tf(freq=1.0), with freq of:
                  1.0 = termFreq=1.0
                9.7509775 = idf(docFreq=6, maxDocs=44218)
                0.0625 = fieldNorm(doc=1205)
        0.16 = coord(4/25)