-
1
-
-
0035931911
-
Chance and necessity: the evolution of morphological complexity and diversity
-
Carroll SB, (2001) Chance and necessity: the evolution of morphological complexity and diversity. Nature 409: 1102-1109.
-
(2001)
Nature
, vol.409
, pp. 1102-1109
-
-
Carroll, S.B.1
-
2
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Consortium TEP, (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Consortium, T.E.P.1
-
3
-
-
77950519937
-
Origins of Specificity in Protein-DNA Recognition
-
Rohs R, Jin X, West SM, Joshi R, Honig B, et al. (2010) Origins of Specificity in Protein-DNA Recognition. Annual Review of Biochemistry 79: 233-269.
-
(2010)
Annual Review of Biochemistry
, vol.79
, pp. 233-269
-
-
Rohs, R.1
Jin, X.2
West, S.M.3
Joshi, R.4
Honig, B.5
-
4
-
-
33845341455
-
Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
-
Elnitski L, Jin VX, Farnham PJ, Jones SJM, (2006) Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques. Genome research 16: 1455-1464.
-
(2006)
Genome Research
, vol.16
, pp. 1455-1464
-
-
Elnitski, L.1
Jin, V.X.2
Farnham, P.J.3
Jones, S.J.M.4
-
5
-
-
70349312354
-
ChIP-seq: advantages and challenges of a maturing technology
-
Park PJ, (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 669-680
-
-
Park, P.J.1
-
6
-
-
33644877699
-
HTPSELEX-a database of high-throughput SELEX libraries for transcription factor binding sites
-
Jagannathan V, Roulet E, Delorenzi M, Bucher P, (2006) HTPSELEX-a database of high-throughput SELEX libraries for transcription factor binding sites. Nucl Acids Res 34: D90-94.
-
(2006)
Nucl Acids Res
, vol.34
-
-
Jagannathan, V.1
Roulet, E.2
Delorenzi, M.3
Bucher, P.4
-
7
-
-
0033977960
-
SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation
-
Ponomarenko JV, Orlova GV, Ponomarenko MP, Lavryushev SV, Frolov AS, et al. (2000) SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. Nucl Acids Res 28: 205-208.
-
(2000)
Nucl Acids Res
, vol.28
, pp. 205-208
-
-
Ponomarenko, J.V.1
Orlova, G.V.2
Ponomarenko, M.P.3
Lavryushev, S.V.4
Frolov, A.S.5
-
8
-
-
78049440479
-
High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions
-
Agius P, Arvey A, Chang W, Noble WS, Leslie C, (2010) High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions. PLoS Comput Biol 6: e1000916.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Agius, P.1
Arvey, A.2
Chang, W.3
Noble, W.S.4
Leslie, C.5
-
9
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Research 28: 235-242.
-
(2000)
Nucleic Acids Research
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
10
-
-
51349134974
-
Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach
-
Zhijie L, Jun-Tao G, Ting L, Ying X, (2008) Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach. Proteins: Structure, Function, and Bioinformatics 72: 1114-1124.
-
(2008)
Proteins: Structure, Function, and Bioinformatics
, vol.72
, pp. 1114-1124
-
-
Zhijie, L.1
Jun-Tao, G.2
Ting, L.3
Ying, X.4
-
11
-
-
56749102973
-
Prediction of TF target sites based on atomistic models of protein-DNA complexes
-
Angarica V, Perez A, Vasconcelos A, Collado-Vides J, Contreras-Moreira B, (2008) Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics 9: 436.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 436
-
-
Angarica, V.1
Perez, A.2
Vasconcelos, A.3
Collado-Vides, J.4
Contreras-Moreira, B.5
-
12
-
-
34047153962
-
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry
-
Siggers TW, Honig B, (2007) Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Research 35: 1085-1097.
-
(2007)
Nucleic Acids Research
, vol.35
, pp. 1085-1097
-
-
Siggers, T.W.1
Honig, B.2
-
13
-
-
33845976703
-
An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure
-
Robertson TA, Varani G, (2007) An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure. Proteins-Structure Function and Bioinformatics 66: 359-374.
-
(2007)
Proteins-Structure Function and Bioinformatics
, vol.66
, pp. 359-374
-
-
Robertson, T.A.1
Varani, G.2
-
14
-
-
0036412071
-
Specificity of protein-DNA recognition revealed by structure-based potentials: Symmetric/asymmetric and cognate/non-cognate binding
-
Selvaraj S, Kono H, Sarai A, (2002) Specificity of protein-DNA recognition revealed by structure-based potentials: Symmetric/asymmetric and cognate/non-cognate binding. Journal of Molecular Biology 322: 907-915.
-
(2002)
Journal of Molecular Biology
, vol.322
, pp. 907-915
-
-
Selvaraj, S.1
Kono, H.2
Sarai, A.3
-
16
-
-
0035221367
-
A structure-based approach for prediction of protein binding sites in gene upstream regions
-
Mandel-Gutfreund Y, Baron A, Margalit H, (2001) A structure-based approach for prediction of protein binding sites in gene upstream regions. Pac Symp Biocomput pp. 139-150.
-
(2001)
Pac Symp Biocomput
, pp. 139-150
-
-
Mandel-Gutfreund, Y.1
Baron, A.2
Margalit, H.3
-
17
-
-
0033120215
-
Structure-based prediction of DNA target sites by regulatory proteins
-
Kono H, Sarai A, (1999) Structure-based prediction of DNA target sites by regulatory proteins. Proteins-Structure Function and Genetics 35: 114-131.
-
(1999)
Proteins-Structure Function and Genetics
, vol.35
, pp. 114-131
-
-
Kono, H.1
Sarai, A.2
-
18
-
-
1642534609
-
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
-
Zhang C, Liu S, Zhou HY, Zhou YQ, (2004) An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Science 13: 400-411.
-
(2004)
Protein Science
, vol.13
, pp. 400-411
-
-
Zhang, C.1
Liu, S.2
Zhou, H.Y.3
Zhou, Y.Q.4
-
19
-
-
0035393302
-
Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level
-
Luscombe NM, Laskowski RA, Thornton JM, (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucl Acids Res 29: 2860-2874.
-
(2001)
Nucl Acids Res
, vol.29
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
20
-
-
67650403798
-
PDA: an automatic and comprehensive analysis program for protein-DNA complex structures
-
Kim R, Guo J-T, (2009) PDA: an automatic and comprehensive analysis program for protein-DNA complex structures. BMC Genomics 10: S13.
-
(2009)
BMC Genomics
, vol.10
-
-
Kim, R.1
Guo, J.-T.2
-
21
-
-
66249112873
-
From Nonspecific DNA-Protein Encounter Complexes to the Prediction of DNA-Protein Interactions
-
Gao M, Skolnick J, (2009) From Nonspecific DNA-Protein Encounter Complexes to the Prediction of DNA-Protein Interactions. PLoS Comput Biol 5: e1000341.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Gao, M.1
Skolnick, J.2
-
22
-
-
66249122733
-
A generalized knowledge-based discriminatory function for biomolecular interactions
-
Brady B, Ram S, (2009) A generalized knowledge-based discriminatory function for biomolecular interactions. Proteins: Structure, Function, and Bioinformatics 76: 115-128.
-
(2009)
Proteins: Structure, Function, and Bioinformatics
, vol.76
, pp. 115-128
-
-
Brady, B.1
Ram, S.2
-
23
-
-
47249125424
-
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions
-
Gao M, Skolnick J, (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucl Acids Res 36: 3978-3992.
-
(2008)
Nucl Acids Res
, vol.36
, pp. 3978-3992
-
-
Gao, M.1
Skolnick, J.2
-
24
-
-
33846803179
-
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces
-
Tjong H, Zhou HX, (2007) DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Research 35: 1465-1477.
-
(2007)
Nucleic Acids Research
, vol.35
, pp. 1465-1477
-
-
Tjong, H.1
Zhou, H.X.2
-
25
-
-
27244460904
-
Protein-DNA binding specificity predictions with structural models
-
Morozov AV, Havranek JJ, Baker D, Siggia ED, (2005) Protein-DNA binding specificity predictions with structural models. Nucleic Acids Research 33: 5781-5798.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 5781-5798
-
-
Morozov, A.V.1
Havranek, J.J.2
Baker, D.3
Siggia, E.D.4
-
26
-
-
11844279783
-
Structural alignment of protein-DNA interfaces: Insights into the determinants of binding specificity
-
Siggers TW, Silkov A, Honig B, (2005) Structural alignment of protein-DNA interfaces: Insights into the determinants of binding specificity. Journal of Molecular Biology 345: 1027-1045.
-
(2005)
Journal of Molecular Biology
, vol.345
, pp. 1027-1045
-
-
Siggers, T.W.1
Silkov, A.2
Honig, B.3
-
27
-
-
77955668141
-
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies
-
Alamanova D, Stegmaier P, Kel A, (2010) Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. BMC bioinformatics 11: 225.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 225
-
-
Alamanova, D.1
Stegmaier, P.2
Kel, A.3
-
28
-
-
77955034560
-
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function
-
Zhao H, Yang Y, Zhou Y, (2010) Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinformatics.
-
(2010)
Bioinformatics
-
-
Zhao, H.1
Yang, Y.2
Zhou, Y.3
-
29
-
-
84856424317
-
Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures
-
Chen C-Y, Chien T-Y, Lin C-K, Lin C-W, Weng Y-Z, et al. (2012) Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures. PLoS ONE 7: e30446.
-
(2012)
PLoS ONE
, vol.7
-
-
Chen, C.-Y.1
Chien, T.-Y.2
Lin, C.-K.3
Lin, C.-W.4
Weng, Y.-Z.5
-
31
-
-
1642452665
-
Analyzing protein-DNA recognition mechanisms
-
Paillard G, Lavery R, (2004) Analyzing protein-DNA recognition mechanisms. Structure 12: 113-122.
-
(2004)
Structure
, vol.12
, pp. 113-122
-
-
Paillard, G.1
Lavery, R.2
-
32
-
-
9644255719
-
Specificity in protein-DNA interactions: Energetic recognition by the (cytosine-C5)-methyltransferase from HhaI
-
Huang N, MacKerell AD, (2005) Specificity in protein-DNA interactions: Energetic recognition by the (cytosine-C5)-methyltransferase from HhaI. Journal of Molecular Biology 345: 265-274.
-
(2005)
Journal of Molecular Biology
, vol.345
, pp. 265-274
-
-
Huang, N.1
MacKerell, A.D.2
-
34
-
-
84870013758
-
Molecular Dynamics Study of the Role of the Spine of Hydration in DNA A-Tracts in Determining Nucleosome Occupancy
-
Zhu X, Schatz GC, (2012) Molecular Dynamics Study of the Role of the Spine of Hydration in DNA A-Tracts in Determining Nucleosome Occupancy. The Journal of Physical Chemistry B.
-
(2012)
The Journal of Physical Chemistry B
-
-
Zhu, X.1
Schatz, G.C.2
-
35
-
-
13744259639
-
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential
-
Liu Z, Mao F, Guo J-T, Yan B, Wang P, et al. (2005) Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential. Nucl Acids Res 33: 546-558.
-
(2005)
Nucl Acids Res
, vol.33
, pp. 546-558
-
-
Liu, Z.1
Mao, F.2
Guo, J.-T.3
Yan, B.4
Wang, P.5
-
36
-
-
17144383951
-
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
-
Zhang C, Liu S, Zhu QQ, Zhou YQ, (2005) A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. Journal of Medicinal Chemistry 48: 2325-2335.
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, pp. 2325-2335
-
-
Zhang, C.1
Liu, S.2
Zhu, Q.Q.3
Zhou, Y.Q.4
-
37
-
-
33646011728
-
In quest of an empirical potential for protein structure prediction
-
Skolnick J, (2006) In quest of an empirical potential for protein structure prediction. Current Opinion in Structural Biology 16: 166-171.
-
(2006)
Current Opinion in Structural Biology
, vol.16
, pp. 166-171
-
-
Skolnick, J.1
-
38
-
-
0041509110
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction (vol 11, pg 2714, 2002)
-
Zhou HY, Zhou YQ, (2003) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction (vol 11, pg 2714, 2002). Protein Science 12: 2121-2121.
-
(2003)
Protein Science
, vol.12
, pp. 2121
-
-
Zhou, H.Y.1
Zhou, Y.Q.2
-
39
-
-
68049118950
-
An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles
-
Xu B, Yang Y, Liang H, Zhou Y, (2009) An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles. Proteins: Structure, Function, and Bioinformatics 76: 718-730.
-
(2009)
Proteins: Structure, Function, and Bioinformatics
, vol.76
, pp. 718-730
-
-
Xu, B.1
Yang, Y.2
Liang, H.3
Zhou, Y.4
-
40
-
-
0037208166
-
TRANSFAC(R): transcriptional regulation, from patterns to profiles
-
Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, et al. (2003) TRANSFAC(R): transcriptional regulation, from patterns to profiles. Nucl Acids Res 31: 374-378.
-
(2003)
Nucl Acids Res
, vol.31
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gossling, E.4
Haubrock, M.5
-
41
-
-
0032861774
-
SCPD: a Promoter Database of the Yeast Saccharomyces cerevisiae
-
Zhu J, Zhang MQ, (1999) SCPD: a Promoter Database of the Yeast Saccharomyces cerevisiae. Bioinformatics 15: 607-611.
-
(1999)
Bioinformatics
, vol.15
, pp. 607-611
-
-
Zhu, J.1
Zhang, M.Q.2
-
42
-
-
0030831182
-
Genetic and physical maps of Saccharomyces cerevisiae
-
Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, et al. (1997) Genetic and physical maps of Saccharomyces cerevisiae. Nature 387: 67.
-
(1997)
Nature
, vol.387
, pp. 67
-
-
Cherry, J.M.1
Ball, C.2
Weng, S.3
Juvik, G.4
Schmidt, R.5
-
43
-
-
0036226603
-
BLAT The BLAST-Like Alignment Tool
-
Kent WJ, (2002) BLAT The BLAST-Like Alignment Tool. Genome research 12: 656-664.
-
(2002)
Genome Research
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
44
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
Tompa M, Li N, Bailey TL, Church GM, De Moor B, et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nature biotechnology 23: 137-144.
-
(2005)
Nature Biotechnology
, vol.23
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
de Moor, B.5
-
45
-
-
84857675809
-
On Docking, Scoring and Assessing Protein-DNA Complexes in a Rigid-Body Framework
-
Parisien M, Freed KF, Sosnick TR, (2012) On Docking, Scoring and Assessing Protein-DNA Complexes in a Rigid-Body Framework. PLoS ONE 7: e32647.
-
(2012)
PLoS ONE
, vol.7
-
-
Parisien, M.1
Freed, K.F.2
Sosnick, T.R.3
-
46
-
-
23144438711
-
PISCES: recent improvements to a PDB sequence culling server
-
Wang G, Dunbrack RL Jr, (2005) PISCES: recent improvements to a PDB sequence culling server. Nucl Acids Res 33: W94-98.
-
(2005)
Nucl Acids Res
, vol.33
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
48
-
-
0034628901
-
Computational identification of Cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
Hughes JD, Estep PW, Tavazoie S, Church GM, (2000) Computational identification of Cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. Journal of Molecular Biology 296: 1205-1214.
-
(2000)
Journal of Molecular Biology
, vol.296
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
49
-
-
0035228215
-
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
-
Liu X, Brutlag DL, Liu JS, (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput pp. 127-138.
-
(2001)
Pac Symp Biocomput
, pp. 127-138
-
-
Liu, X.1
Brutlag, D.L.2
Liu, J.S.3
-
50
-
-
33644875782
-
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles
-
Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, et al. (2006) A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucl Acids Res 34: D95-97.
-
(2006)
Nucl Acids Res
, vol.34
-
-
Vlieghe, D.1
Sandelin, A.2
de Bleser, P.J.3
Vleminckx, K.4
Wasserman, W.W.5
-
51
-
-
0023147228
-
Selection of DNA binding sites by regulatory proteins.Statistical-mechanical theory and application to operators and promoters
-
Berg OG, von Hippel PH, (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol 193: 723-750.
-
(1987)
J Mol Biol
, vol.193
, pp. 723-750
-
-
Berg, O.G.1
von Hippel, P.H.2
-
52
-
-
34548179533
-
TFIIA Changes the Conformation of the DNA in TBP/TATA Complexes and Increases their Kinetic Stability
-
Hieb AR, Halsey WA, Betterton MD, Perkins TT, Kugel JF, et al. (2007) TFIIA Changes the Conformation of the DNA in TBP/TATA Complexes and Increases their Kinetic Stability. Journal of Molecular Biology 372: 619-632.
-
(2007)
Journal of Molecular Biology
, vol.372
, pp. 619-632
-
-
Hieb, A.R.1
Halsey, W.A.2
Betterton, M.D.3
Perkins, T.T.4
Kugel, J.F.5
-
53
-
-
33749234779
-
What is a desirable statistical energy function for proteins and how can it be obtained?
-
Zhou Y, Zhou HY, Zhang C, Liu S, (2006) What is a desirable statistical energy function for proteins and how can it be obtained? Cell Biochemistry and Biophysics 46: 165-174.
-
(2006)
Cell Biochemistry and Biophysics
, vol.46
, pp. 165-174
-
-
Zhou, Y.1
Zhou, H.Y.2
Zhang, C.3
Liu, S.4
-
55
-
-
40649107189
-
Discovering gapped binding sites of yeast transcription factors
-
Chen C-Y, Tsai H-K, Hsu C-M, May Chen M-J, Hung H-G, et al. (2008) Discovering gapped binding sites of yeast transcription factors. Proceedings of the National Academy of Sciences of the United States of America 105: 2527-2532.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, pp. 2527-2532
-
-
Chen, C.-Y.1
Tsai, H.-K.2
Hsu, C.-M.3
May Chen, M.-J.4
Hung, H.-G.5
-
56
-
-
2142738304
-
WebLogo: a sequence logo generator
-
Crooks G, Hon G, Chandonia J, Brenner S, (2004) WebLogo: a sequence logo generator. Genome research 14: 1188.
-
(2004)
Genome Research
, vol.14
, pp. 1188
-
-
Crooks, G.1
Hon, G.2
Chandonia, J.3
Brenner, S.4
|