-
1
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB, (1973) Principles that govern the folding of protein chains. Science 181: 223-230.
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
2
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 253-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 242-253
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
4
-
-
0037079055
-
The language of genes
-
Searls DB, (2002) The language of genes. Nature 420: 211-217.
-
(2002)
Nature
, vol.420
, pp. 211-217
-
-
Searls, D.B.1
-
5
-
-
0030821916
-
Linguistic approaches to biological sequences
-
Searls DB, (1997) Linguistic approaches to biological sequences. Comput Appl Biosci 13: 333-344.
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 333-344
-
-
Searls, D.B.1
-
6
-
-
33745603223
-
Grammatical representations of macromolecular structure
-
Chiang D, Joshi AK, Searls DB, (2006) Grammatical representations of macromolecular structure. J Comput Biol 13: 1077-1100.
-
(2006)
J Comput Biol
, vol.13
, pp. 1077-1100
-
-
Chiang, D.1
Joshi, A.K.2
Searls, D.B.3
-
7
-
-
79955605443
-
TMBHMM: a frequency profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane domains
-
Singh NK, Goodman A, Walter P, Helms V, Hayat S, (2011) TMBHMM: a frequency profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane domains. Biochim Biophys Acta 1814: 664-670.
-
(2011)
Biochim Biophys Acta
, vol.1814
, pp. 664-670
-
-
Singh, N.K.1
Goodman, A.2
Walter, P.3
Helms, V.4
Hayat, S.5
-
8
-
-
79959254306
-
A network of SCOP hidden Markov models and its analysis
-
Zhang L, Watson LT, Heath LS, (2011) A network of SCOP hidden Markov models and its analysis. BMC Bioinformatics 12: 191.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 191
-
-
Zhang, L.1
Watson, L.T.2
Heath, L.S.3
-
9
-
-
0031269127
-
Predicting protein secondary structure using stochastic tree grammars
-
Abe N, Mamitsuka H, (1997) Predicting protein secondary structure using stochastic tree grammars. Machine Learn 29: 275-301.
-
(1997)
Machine Learn
, vol.29
, pp. 275-301
-
-
Abe, N.1
Mamitsuka, H.2
-
11
-
-
77952007362
-
Secondary structure characterization based on amino acid composition and availability in proteins
-
Otaki JM, Tsutsumi M, Gotoh T, Yamamoto H, (2010) Secondary structure characterization based on amino acid composition and availability in proteins. J Chem Inf Model 50: 690-700.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 690-700
-
-
Otaki, J.M.1
Tsutsumi, M.2
Gotoh, T.3
Yamamoto, H.4
-
12
-
-
79959728388
-
Parallel and antiparallel β-strands differ in amino acid composition and availability of short constituent sequences
-
Tsutsumi M, Otaki JM, (2011) Parallel and antiparallel β-strands differ in amino acid composition and availability of short constituent sequences. J Chem Inf Model 50: 1457-1464.
-
(2011)
J Chem Inf Model
, vol.50
, pp. 1457-1464
-
-
Tsutsumi, M.1
Otaki, J.M.2
-
13
-
-
0023045765
-
Heuristic information analysis of sequences
-
Claverie J-M, Bougueleret L, (1986) Heuristic information analysis of sequences. Nucl Acid Res 14: 179-196.
-
(1986)
Nucl Acid Res
, vol.14
, pp. 179-196
-
-
Claverie, J.-M.1
Bougueleret, L.2
-
14
-
-
0037342499
-
Alignment-free sequence comparison - a review
-
Vinga S, Almeida JS, (2003) Alignment-free sequence comparison - a review. Bioinformatics 19: 513-523.
-
(2003)
Bioinformatics
, vol.19
, pp. 513-523
-
-
Vinga, S.1
Almeida, J.S.2
-
15
-
-
1042269469
-
Comparative evaluation of word composition distances for the recognition of SCOP relationships
-
Vinga S, Gouveia-Oliveira R, Almeida JS, (2004) Comparative evaluation of word composition distances for the recognition of SCOP relationships. Bioinformatics 20: 206-215.
-
(2004)
Bioinformatics
, vol.20
, pp. 206-215
-
-
Vinga, S.1
Gouveia-Oliveira, R.2
Almeida, J.S.3
-
16
-
-
80054875426
-
A mathematical consideration of the word-composition vector method in comparison of biological sequences
-
Aita T, Husimi Y, Nishigaki K, (2011) A mathematical consideration of the word-composition vector method in comparison of biological sequences. BioSystems 106: 67-75.
-
(2011)
BioSystems
, vol.106
, pp. 67-75
-
-
Aita, T.1
Husimi, Y.2
Nishigaki, K.3
-
17
-
-
33846300700
-
Primary sequences of proteins from complete genomes display a singular periodicity: alignment-free n-gram analysis
-
Radomski JP, Slonimski PP, (2007) Primary sequences of proteins from complete genomes display a singular periodicity: alignment-free n-gram analysis. C R Biol 330: 33-48.
-
(2007)
C R Biol
, vol.330
, pp. 33-48
-
-
Radomski, J.P.1
Slonimski, P.P.2
-
18
-
-
34548752832
-
The relationship between n-gram patterns and protein secondary structure
-
Vries JK, Liu X, Bahar I, (2007) The relationship between n-gram patterns and protein secondary structure. Proteins 68: 830-838.
-
(2007)
Proteins
, vol.68
, pp. 830-838
-
-
Vries, J.K.1
Liu, X.2
Bahar, I.3
-
19
-
-
40749141222
-
Subfamily specific conservation profiles for proteins based on n-gram patterns
-
Vries JK, Liu X, (2008) Subfamily specific conservation profiles for proteins based on n-gram patterns. BMC Bioinformatics 9: 72.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 72
-
-
Vries, J.K.1
Liu, X.2
-
20
-
-
78649774404
-
Improving protein secondary structure prediction based on short subsequences with local structure similarity
-
Lin HN, Sung TY, Ho SY, Hsu WL, (2010) Improving protein secondary structure prediction based on short subsequences with local structure similarity. BMC Genomics 11Suppl 4: S4.
-
(2010)
BMC Genomics
, vol.11
-
-
Lin, H.N.1
Sung, T.Y.2
Ho, S.Y.3
Hsu, W.L.4
-
21
-
-
78650997356
-
N-gram analysis of 970 microbial organisms reveals presence of biological language models
-
Osmanbeyoglu HU, Ganapathiraju MK, (2011) N-gram analysis of 970 microbial organisms reveals presence of biological language models. BMC Bioinformatics 12: 12.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 12
-
-
Osmanbeyoglu, H.U.1
Ganapathiraju, M.K.2
-
24
-
-
0037417789
-
Least effort and the origin of scaling in human language
-
Ferrer i Cancho R, Solé RV, (2003) Least effort and the origin of scaling in human language. Proc Natl Acad Sci USA 100: 788-791.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 788-791
-
-
Ferrer i Cancho, R.1
Solé, R.V.2
-
25
-
-
14144249883
-
Frequency distribution of the number of amino acid triplets in the non-redundant protein database
-
Otaki JM, Gotoh T, Yamamoto H, (2003) Frequency distribution of the number of amino acid triplets in the non-redundant protein database. J Jpn Soc Inf Knowledge 13: 25-38.
-
(2003)
J Jpn Soc Inf Knowledge
, vol.13
, pp. 25-38
-
-
Otaki, J.M.1
Gotoh, T.2
Yamamoto, H.3
-
26
-
-
14144250991
-
Availability of short amino acid sequences in proteins
-
Otaki JM, Ienaka S, Gotoh T, Yamamoto H, (2005) Availability of short amino acid sequences in proteins. Protein Sci 14: 617-625.
-
(2005)
Protein Sci
, vol.14
, pp. 617-625
-
-
Otaki, J.M.1
Ienaka, S.2
Gotoh, T.3
Yamamoto, H.4
-
27
-
-
46149083265
-
Potential implications of availability of short amino acid sequences in proteins: an old and new approach to protein decoding and design
-
Otaki JM, Gotoh T, Yamamoto H, (2008) Potential implications of availability of short amino acid sequences in proteins: an old and new approach to protein decoding and design. Biotechnol Annu Rev 14: 109-141.
-
(2008)
Biotechnol Annu Rev
, vol.14
, pp. 109-141
-
-
Otaki, J.M.1
Gotoh, T.2
Yamamoto, H.3
-
28
-
-
0035172128
-
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank
-
Noguchi T, Matsuda H, Akiyama Y, (2001) PDB-REPRDB: a database of representative protein chains from the Protein Data Bank. Nucleic Acids Res 29: 219-220.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 219-220
-
-
Noguchi, T.1
Matsuda, H.2
Akiyama, Y.3
-
29
-
-
84856991721
-
Critical truth about power laws
-
Stumpf MPH, Porter MA, (2012) Critical truth about power laws. Science 335: 665-666.
-
(2012)
Science
, vol.335
, pp. 665-666
-
-
Stumpf, M.P.H.1
Porter, M.A.2
-
32
-
-
79957545106
-
Statistical analyses support power law distributions found in neuronal avalanches
-
Klaus A, Yu S, Plenz D, (2011) Statistical analyses support power law distributions found in neuronal avalanches. PLoS ONE 6: e19779.
-
(2011)
PLoS ONE
, vol.6
-
-
Klaus, A.1
Yu, S.2
Plenz, D.3
-
33
-
-
75549087533
-
PROSITE, a protein domain database for functional characterization and annotation
-
Sigrist CJA, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, et al. (2010) PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res 38: D161-D166.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Sigrist, C.J.A.1
Cerutti, L.2
de Castro, E.3
Langendijk-Genevaux, P.S.4
Bulliard, V.5
-
34
-
-
79952221890
-
Wikipedia information flow analysis reveals the scale-free architecture of the semantic space
-
Masucci AP, Kalampokis A, Eguíluz VM, Hernández-García E, (2011) Wikipedia information flow analysis reveals the scale-free architecture of the semantic space. PLoS One 6: e17333.
-
(2011)
PLoS One
, vol.6
-
-
Masucci, A.P.1
Kalampokis, A.2
Eguíluz, V.M.3
Hernández-García, E.4
-
36
-
-
0030782481
-
How are model protein structures distributed in sequence space?
-
Bornberg-Bauer E, (1997) How are model protein structures distributed in sequence space? Biophys J 73: 2393-2403.
-
(1997)
Biophys J
, vol.73
, pp. 2393-2403
-
-
Bornberg-Bauer, E.1
-
37
-
-
0036434526
-
Zipf's law in importance of genes for cancer classification using microarray data
-
Li W, Yang Y, (2002) Zipf's law in importance of genes for cancer classification using microarray data. J Theor Biol 219: 539-551.
-
(2002)
J Theor Biol
, vol.219
, pp. 539-551
-
-
Li, W.1
Yang, Y.2
-
38
-
-
0345860861
-
Zipf's law and human transcriptomes: an explanation with an evolutionary model
-
Ogasawara O, Kawamoto S, Okubo K, (2003) Zipf's law and human transcriptomes: an explanation with an evolutionary model. C R Biol 326: 1097-1101.
-
(2003)
C R Biol
, vol.326
, pp. 1097-1101
-
-
Ogasawara, O.1
Kawamoto, S.2
Okubo, K.3
-
39
-
-
0037471175
-
Zipf's law in gene expression
-
Furusawa C, Kaneko K, (2003) Zipf's law in gene expression. Phys Rev Lett 90: 088102.
-
(2003)
Phys Rev Lett
, vol.90
, pp. 088102
-
-
Furusawa, C.1
Kaneko, K.2
-
40
-
-
33749867157
-
Analyzing proteome topology and function by automated multidimensional fluorescence microscopy
-
Schubert W, Bonnekoh B, Pommer AJ, Philipsen L, Böckelmann R, et al. (2006) Analyzing proteome topology and function by automated multidimensional fluorescence microscopy. Nat Biotechnol 24: 1270-1278.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1270-1278
-
-
Schubert, W.1
Bonnekoh, B.2
Pommer, A.J.3
Philipsen, L.4
Böckelmann, R.5
-
42
-
-
0026953429
-
Random texts exhibit Zipf's-law-like word frequency distribution
-
Li W, (1992) Random texts exhibit Zipf's-law-like word frequency distribution. IEEE T Inform Theory 38: 1842-1845.
-
(1992)
IEEE T Inform Theory
, vol.38
, pp. 1842-1845
-
-
Li, W.1
-
43
-
-
24744469980
-
Power laws, Pareto distributions and Zipf's law
-
MEJ Newman, (2005) Power laws, Pareto distributions and Zipf's law. Contemporary Phys 46: 323-351.
-
(2005)
Contemporary Phys
, vol.46
, pp. 323-351
-
-
Newman, M.E.J.1
-
44
-
-
34547890729
-
Parameter estimation for power-law distributions by maximum likelihood methods
-
Bauke H, (2007) Parameter estimation for power-law distributions by maximum likelihood methods. Eur Phys J B 58: 167-173.
-
(2007)
Eur Phys J B
, vol.58
, pp. 167-173
-
-
Bauke, H.1
-
45
-
-
77949686094
-
Random texts do not exhibit the real Zipf's law-like rank distribution
-
Ferrer-i-Cancho R, Elvevåg B, (2010) Random texts do not exhibit the real Zipf's law-like rank distribution. PLoS One 5: e9411.
-
(2010)
PLoS One
, vol.5
-
-
Ferrer-i-Cancho, R.1
Elvevåg, B.2
-
47
-
-
0030064378
-
Linguistic complexity of protein sequences as compared to texts of human languages
-
Popov O, Segal DM, Trifonov EN, (1996) Linguistic complexity of protein sequences as compared to texts of human languages. BioSystems 38: 65-74.
-
(1996)
BioSystems
, vol.38
, pp. 65-74
-
-
Popov, O.1
Segal, D.M.2
Trifonov, E.N.3
-
48
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte J, Doolittle RF, (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
-
(1982)
J Mol Biol
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
49
-
-
33746837770
-
Structural diversity of protein segments follows a power-law distribution
-
Sawada Y, Honda S, (2006) Structural diversity of protein segments follows a power-law distribution. Biophys J 91: 1213-1223.
-
(2006)
Biophys J
, vol.91
, pp. 1213-1223
-
-
Sawada, Y.1
Honda, S.2
|