-
1
-
-
84864645362
-
Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling
-
Afriat-Jurnou L, Jackson CJ, Tawfik DS. 2012. Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling. Biochemistry 51(31):6047-6055.
-
(2012)
Biochemistry
, vol.51
, Issue.31
, pp. 6047-6055
-
-
Afriat-Jurnou, L.1
Jackson, C.J.2
Tawfik, D.S.3
-
2
-
-
13444254292
-
The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information
-
Arnaud MB, CostanzoMC, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G. 2005. The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. Nucleic Acids Res. 33:D358-D363.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Arnaud, M.B.1
Costanzomc Skrzypek, M.S.2
Binkley, G.3
Lane, C.4
Miyasato, S.R.5
Sherlock, G.6
-
3
-
-
0033555906
-
Tandem repeats finder: A program to analyze DNA sequences
-
Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27(2):573-580.
-
(1999)
Nucleic Acids Res
, vol.27
, Issue.2
, pp. 573-580
-
-
Benson, G.1
-
5
-
-
26844454995
-
Domain rearrangements in protein evolution
-
Björklund AK, Ekman D, Light S, Frey-Skott J, Elofsson A. 2005. Domain rearrangements in protein evolution. J Mol Biol. 353(4):911-923.
-
(2005)
J Mol Biol
, vol.353
, Issue.4
, pp. 911-923
-
-
Björklund, A.K.1
Ekman, D.2
Light, S.3
Frey-Skott, J.4
Elofsson, A.5
-
6
-
-
0036017388
-
Evolutionary rate heterogeneity in proteins with long disordered regions
-
Brown CJ, Takayama S, Campen AM, Vise P, Marshall TW, Oldfield CJ, Williams CJ, Dunker AK. 2002. Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol. 55(1):104-110.
-
(2002)
J Mol Evol
, vol.55
, Issue.1
, pp. 104-110
-
-
Brown, C.J.1
Takayama, S.2
Campen, A.M.3
Vise, P.4
Marshall, T.W.5
Oldfield, C.J.6
Williams, C.J.7
Dunker, A.K.8
-
7
-
-
37549023418
-
DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage
-
de la Chaux N,Messer PW, Arndt PF. 2007. DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage. BMC Evol Biol. 7:191.
-
(2007)
BMC Evol Biol
, vol.7
, pp. 191
-
-
De La Chaux Nmesser, P.W.1
Arndt, P.F.2
-
8
-
-
14844342815
-
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
-
Dosztanyi Z, Csizmok V, Tompa P, Simon I. 2005. The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol. 347: 827-839.
-
(2005)
J Mol Biol
, vol.347
, pp. 827-839
-
-
Dosztanyi, Z.1
Csizmok, V.2
Tompa, P.3
Simon, I.4
-
9
-
-
77950957385
-
Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins
-
Dosztanyi Z, Meszaros B, Simon I. 2010. Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins. Brief Bioinform. 11:225-243.
-
(2010)
Brief Bioinform.
, vol.11
, pp. 225-243
-
-
Dosztanyi, Z.1
Meszaros, B.2
Simon, I.3
-
11
-
-
33745686603
-
What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?
-
Ekman D, Light S, Björklund A, Elofsson A. 2006. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol. 7(6):R45.
-
(2006)
Genome Biol
, vol.7
, Issue.6
-
-
Ekman, D.1
Light, S.2
Björklund, A.3
Elofsson, A.4
-
12
-
-
38049103341
-
Statistical power of phylo-HMM for evolutionarily conserved element detection
-
Fan X, Zhu J, Schadt EE, Liu JS. 2007. Statistical power of phylo-HMM for evolutionarily conserved element detection. BMC Bioinformatics 8:374.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 374
-
-
Fan, X.1
Zhu, J.2
Schadt, E.E.3
Liu, J.S.4
-
13
-
-
79952334224
-
A new repeat-masking method enables specific detection of homologous sequences
-
Frith MC. 2011. A new repeat-masking method enables specific detection of homologous sequences. Nucleic Acids Res. 39(4):e23.
-
(2011)
Nucleic Acids Res.
, vol.39
, Issue.4
-
-
Frith, M.C.1
-
14
-
-
33846840904
-
The conversion of 30 UTRs into coding regions
-
Giacomelli MG, Hancock AS, Masel J. 2007. The conversion of 30 UTRs into coding regions. Mol Biol Evol. 24(2):457-464.
-
(2007)
Mol Biol Evol
, vol.24
, Issue.2
, pp. 457-464
-
-
Giacomelli, M.G.1
Hancock, A.S.2
Masel, J.3
-
15
-
-
84866916321
-
Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication
-
Guo B, Zou M, Wagner A. 2012. Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication. Mol Biol Evol. 29)10):3005-3022.
-
(2012)
Mol Biol Evol.
, vol.29
, Issue.10
, pp. 3005-3022
-
-
Guo, B.1
Zou, M.2
Wagner, A.3
-
16
-
-
79952351014
-
Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder
-
Hegyi H, Kalmar L, Horvath T, Tompa P. 2011. Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder. Nucleic Acids Res. 39(4): 1208-1219.
-
(2011)
Nucleic Acids Res.
, vol.39
, Issue.4
, pp. 1208-1219
-
-
Hegyi, H.1
Kalmar, L.2
Horvath, T.3
Tompa, P.4
-
17
-
-
0033578684
-
Protein secondary structure prediction based on positionspecific scoring matrices
-
Jones D. 1999. Protein secondary structure prediction based on positionspecific scoring matrices. J Mol Biol. 292(2):195-202.
-
(1999)
J Mol Biol
, vol.292
, Issue.2
, pp. 195-202
-
-
Jones, D.1
-
18
-
-
0242362157
-
Prediction of disordered regions in proteins from position specific score matrices
-
Jones D, Ward J. 2003. Prediction of disordered regions in proteins from position specific score matrices. Proteins 53(Suppl 6), 573-578.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL.6
, pp. 573-578
-
-
Jones, D.1
Ward, J.2
-
19
-
-
77952850689
-
Quality assessment of protein modelstructures using evolutionary conservation
-
Kalman M, Ben-Tal N. 2010. Quality assessment of protein modelstructures using evolutionary conservation. Bioinformatics 26(10):1299-1307.
-
(2010)
Bioinformatics
, vol.26
, Issue.10
, pp. 1299-1307
-
-
Kalman, M.1
Ben-Tal, N.2
-
20
-
-
77955103653
-
Systematic analysis of short internal indels and their impact on protein folding
-
Kim R, Guo JT. 2010. Systematic analysis of short internal indels and their impact on protein folding. BMC Struct Biol. 10:24.
-
(2010)
BMC Struct Biol.
, vol.10
, pp. 24
-
-
Kim, R.1
Guo, J.T.2
-
21
-
-
0043123037
-
Mreps: Efficient and flexible detection of tandem repeats in DNA
-
Kolpakov R, Bana G, Kucherov G. 2003. mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res. 31(13):3672-3678.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3672-3678
-
-
Kolpakov, R.1
Bana, G.2
Kucherov, G.3
-
22
-
-
0023256559
-
Slipped-strand mispairing: A major mechanism for DNA sequence evolution
-
Levinson G, Gutman G. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol. 4(3):203-221.
-
(1987)
Mol Biol Evol
, vol.4
, Issue.3
, pp. 203-221
-
-
Levinson, G.1
Gutman, G.2
-
23
-
-
84876290145
-
Long indels are disordered: A study of disorder and indels in homologous eukaryotic proteins
-
Light S, Sagit R, Ekman D, Qin J, Elofsson A. 2013. Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins. Biochim Biophys Acta. 1834:890-897.
-
(1834)
Biochim Biophys Acta
, pp. 890-897
-
-
Light, S.1
Sagit, R.2
Ekman, D.3
Qin, J.4
Elofsson, A.5
-
24
-
-
0242458482
-
Protein disorder prediction: Implications for structural proteomics
-
Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. 2003. Protein disorder prediction: implications for structural proteomics. Structure 11(11):1453-1459.
-
(2003)
Structure
, vol.11
, Issue.11
, pp. 1453-1459
-
-
Linding, R.1
Jensen, L.J.2
Diella, F.3
Bork, P.4
Gibson, T.J.5
Russell, R.B.6
-
26
-
-
79959807202
-
Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences
-
McDonald MJ, Wang W-C, Huang H-D, Leu J-Y. 2011. Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. PLoS Biol. 9(6):e1000622.
-
(2011)
PLoS Biol.
, vol.9
, Issue.6
-
-
Mc Donald, M.J.1
Wang, W.-C.2
Huang, H.-D.3
Leu, J.-Y.4
-
27
-
-
77957092799
-
From the Cover: Charge interactions can dominate the dimensions of intrinsically disordered proteins
-
Müller-Späth S, Soranno A, Hirschfeld V, Hofmann H, Rüegger S, Reymond L, Nettels D, Schuler B. 2010. From the Cover: charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc Natl Acad Sci USA. 107(33):14609-14614.
-
(2010)
Proc Natl Acad Sci USA.
, vol.107
, Issue.33
, pp. 14609-14614
-
-
Müller-Späth, S.1
Soranno, A.2
Hirschfeld, V.3
Hofmann, H.4
Rüegger, S.5
Reymond, L.6
Nettels, D.7
Schuler, B.8
-
28
-
-
75549086594
-
InParanoid 7: New algorithms and tools for eukaryotic orthology analysis
-
(Database issue)
-
Ostlund G, Schmitt T, Forslund K, Kostler T, Messina DN, Roopra S, Frings O, Sonnhammer EL. 2010. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 38(Database issue):196-203.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 196-203
-
-
Ostlund, G.1
Schmitt, T.2
Forslund, K.3
Kostler, T.4
Messina, D.N.5
Roopra, S.6
Frings, O.7
Sonnhammer, E.L.8
-
29
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm M, Storm CE, Sonnhammer EL. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol. 314(5):1041-1052.
-
(2001)
J Mol Biol
, vol.314
, Issue.5
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.2
Sonnhammer, E.L.3
-
30
-
-
34547599318
-
Natively unstructured loops differ from other loops
-
Schlessinger A, Liu J, Rost B. 2007. Natively unstructured loops differ from other loops. PLoS Comput Biol. 3(7):e140.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.7
-
-
Schlessinger, A.1
Liu, J.2
Rost, B.3
-
31
-
-
34548750953
-
Natively unstructured regions in proteins identified from contact predictions
-
Schlessinger A, Punta M, Rost B. 2007. Natively unstructured regions in proteins identified from contact predictions. Bioinformatics 23(18):2376-2384.
-
(2007)
Bioinformatics
, vol.23
, Issue.18
, pp. 2376-2384
-
-
Schlessinger, A.1
Punta, M.2
Rost, B.3
-
32
-
-
84885949386
-
Improved disorder prediction by combination of orthogonal approaches
-
Schlessinger A, Punta M, Yachdav G, Kajan L, Rost B. 2009. Improved disorder prediction by combination of orthogonal approaches. PLoS One 4(2):e4433.
-
(2009)
PLoS One
, vol.4
, Issue.2
-
-
Schlessinger, A.1
Punta, M.2
Yachdav, G.3
Kajan, L.4
Rost, B.5
-
33
-
-
33645288849
-
PROFbval: Predict flexible and rigid residues in proteins
-
Schlessinger A, Yachdav G, Rost B. 2006. PROFbval: predict flexible and rigid residues in proteins. Bioinformatics 22(7):891-893.
-
(2006)
Bioinformatics
, vol.22
, Issue.7
, pp. 891-893
-
-
Schlessinger, A.1
Yachdav, G.2
Rost, B.3
-
34
-
-
0036205377
-
TREEPUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREEPUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
Von Haeseler, A.4
-
35
-
-
49549122021
-
-
SGD Project [cited 2013 Sep 24] Available from
-
SGD Project. 2011. Saccharomyces genome database. [cited 2013 Sep 24]. Available from: http://www.yeastgenome.org/.
-
(2011)
Saccharomyces Genome Database
-
-
-
36
-
-
80054078476
-
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
-
(12 co-authors)
-
Sievers F, Wilm A, Dineen D, et al. (12 co-authors). 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 7:539.
-
(2011)
Mol Syst Biol.
, vol.7
, pp. 539
-
-
Sievers, F.1
Wilm, A.2
Dineen, D.3
-
37
-
-
67650868984
-
Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins
-
Simon M, Hancock JM. 2009. Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. Genome Biol. 10(6):R59.
-
(2009)
Genome Biol
, vol.10
, Issue.6
-
-
Simon, M.1
Hancock, J.M.2
-
38
-
-
1842717956
-
Occurrence and consequences of coding sequence insertions and deletions in mammalian genomes
-
Taylor MS, Ponting CP, Copley RR. 2004. Occurrence and consequences of coding sequence insertions and deletions in mammalian genomes. Genome Res. 14(4):555-566.
-
(2004)
Genome Res
, vol.14
, Issue.4
, pp. 555-566
-
-
Taylor, M.S.1
Ponting, C.P.2
Copley, R.R.3
-
39
-
-
51349155028
-
Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
-
Tian D, Wang Q, Zhang P, Araki H, Yang S, Kreitman M, Nagylaki T, Hudson R, Bergelson J, Chen J-Q. 2008. Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature 455(7209):105-108.
-
(2008)
Nature
, vol.455
, Issue.7209
, pp. 105-108
-
-
Tian, D.1
Wang, Q.2
Zhang, P.3
Araki, H.4
Yang, S.5
Kreitman, M.6
Nagylaki, T.7
Hudson, R.8
Bergelson, J.9
Chen, J.-Q.10
-
40
-
-
0042819915
-
Intrinsically unstructured proteins evolve by repeat expansion
-
Tompa P. 2003. Intrinsically unstructured proteins evolve by repeat expansion. Bioessays 25(9):847-855.
-
(2003)
Bioessays
, vol.25
, Issue.9
, pp. 847-855
-
-
Tompa, P.1
-
42
-
-
84875601072
-
Protein insertions and deletions enabled by neutral roaming in sequence space
-
Toth-Petroczy A, Tawfik DS. 2013. Protein insertions and deletions enabled by neutral roaming in sequence space. Mol Biol Evol. 30(4):761-771.
-
(2013)
Mol Biol Evol.
, vol.30
, Issue.4
, pp. 761-771
-
-
Toth-Petroczy, A.1
Tawfik, D.S.2
-
43
-
-
1542358787
-
Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
-
Ward JJ, Sodhi JS,McGuffin LJ, Buxton BF, Jones DT. 2004. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol. 337:635-645.
-
(2004)
J Mol Biol
, vol.337
, pp. 635-645
-
-
Ward, J.J.1
Sodhi, J.S.2
McGuffin, L.J.3
Buxton, B.F.4
Jones, D.T.5
-
44
-
-
0028501914
-
Non-globular domains in protein sequences: Automated segmentation using complexity measures
-
Wootton J. 1994. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem. 18(3):269-285.
-
(1994)
Comput Chem
, vol.18
, Issue.3
, pp. 269-285
-
-
Wootton, J.1
-
45
-
-
84859701551
-
Orderly order in protein intrinsic disorder distribution: Disorder in 3500 proteomes from viruses and the three domains of life
-
Xue B, Dunker AK, Uversky VN. 2012. Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life. J Biomol Struct Dyn. 30(2):137-149.
-
(2012)
J Biomol Struct Dyn.
, vol.30
, Issue.2
, pp. 137-149
-
-
Xue, B.1
Dunker, A.K.2
Uversky, V.N.3
-
46
-
-
20744437001
-
RONN: The bio-basis function neural network technique applied to the detection of natively disordered regions in proteins
-
Yang ZR, Thomson R, McNeil P, Esnouf RM. 2005. RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21:3369-3376.
-
(2005)
Bioinformatics
, vol.21
, pp. 3369-3376
-
-
Yang, Z.R.1
Thomson, R.2
McNeil, P.3
Esnouf, R.M.4
|