-
1
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
DNA binding sites: representation and discovery. Stormo GD, Bioinformatics (Oxford, England) 2000 16 1 16 23 (Pubitemid 30204197)
-
(2000)
Bioinformatics
, vol.16
, Issue.1
, pp. 16-23
-
-
Stormo, G.D.1
-
3
-
-
75149141847
-
Mechanisms of transcription factor selectivity
-
Mechanisms of transcription factor selectivity. Pan Y, Tsai CJ, Ma B, Nussinov R, Trends Genet 2010 26 2 75 83
-
(2010)
Trends Genet
, vol.26
, Issue.2
, pp. 75-83
-
-
Pan, Y.1
Tsai, C.J.2
Ma, B.3
Nussinov, R.4
-
4
-
-
36849063165
-
Structure and evolution of gene regulatory networks in microbial genomes
-
DOI 10.1016/j.resmic.2007.09.001, PII S0923250807001763, Microbial Genomics
-
Structure and evolution of gene regulatory networks in microbial genomes. Janga SC, Collado-Vides J, Res Microbiol 2007 158 10 787 794 (Pubitemid 350235176)
-
(2007)
Research in Microbiology
, vol.158
, Issue.10
, pp. 787-794
-
-
Janga, S.C.1
Collado-Vides, J.2
-
5
-
-
33744780700
-
Evolution of transcriptional regulatory networks in microbial genomes
-
DOI 10.1016/j.sbi.2006.04.001, PII S0959440X06000650
-
Evolution of transcriptional regulatory networks in microbial genomes. Gelfand MS, Current opinion in structural biology 2006 16 3 420 429 (Pubitemid 43831639)
-
(2006)
Current Opinion in Structural Biology
, vol.16
, Issue.3
, pp. 420-429
-
-
Gelfand, M.S.1
-
6
-
-
77957277053
-
Early Career Research Award Lecture. Structure, evolution and dynamics of transcriptional regulatory networks
-
Early Career Research Award Lecture. Structure, evolution and dynamics of transcriptional regulatory networks. Babu MM, Biochem Soc Trans 2010 38 5 1155 1178
-
(2010)
Biochem Soc Trans
, vol.38
, Issue.5
, pp. 1155-1178
-
-
Babu, M.M.1
-
7
-
-
2942606066
-
Structure and evolution of transcriptional regulatory networks
-
DOI 10.1016/j.sbi.2004.05.004, PII S0959440X04000788
-
Structure and evolution of transcriptional regulatory networks. Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA, Current opinion in structural biology 2004 14 3 283 291 (Pubitemid 38749055)
-
(2004)
Current Opinion in Structural Biology
, vol.14
, Issue.3
, pp. 283-291
-
-
Babu, M.M.1
Luscombe, N.M.2
Aravind, L.3
Gerstein, M.4
Teichmann, S.A.5
-
8
-
-
0742306815
-
Computational prediction of transcription-factor binding site locations
-
Computational prediction of transcription-factor binding site locations. Bulyk ML, Genome biology 2003 5 1 201
-
(2003)
Genome Biology
, vol.5
, Issue.1
, pp. 201
-
-
Bulyk, M.L.1
-
9
-
-
49349114121
-
Computational approaches to study transcriptional regulation
-
Computational approaches to study transcriptional regulation. Babu MM, Biochem Soc Trans 2008 36 Pt 4 758 765
-
(2008)
Biochem Soc Trans
, vol.36
, Issue.PART 4
, pp. 758-765
-
-
Babu, M.M.1
-
10
-
-
4544293652
-
Toward an atomistic model for predicting transcription-factor binding sites
-
DOI 10.1002/prot.20199
-
Toward an atomistic model for predicting transcription-factor binding sites. Endres RG, Schulthess TC, Wingreen NS, Proteins 2004 57 2 262 268 (Pubitemid 39223731)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.57
, Issue.2
, pp. 262-268
-
-
Endres, R.G.1
Schulthess, T.C.2
Wingreen, N.S.3
-
11
-
-
29444434700
-
Ab initio prediction of transcription factor targets using structural knowledge
-
Ab initio prediction of transcription factor targets using structural knowledge. Kaplan T, Friedman N, Margalit H, PLoS computational biology 2005 1 1 1
-
(2005)
PLoS Computational Biology
, vol.1
, Issue.1
, pp. 51
-
-
Kaplan, T.1
Friedman, N.2
Margalit, H.3
-
12
-
-
34047153962
-
2 zinc-finger binding specificity: Sensitivity to docking geometry
-
DOI 10.1093/nar/gkl1155
-
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Siggers TW, Honig B, Nucleic Acids Res 2007 35 4 1085 1097 (Pubitemid 46522964)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.4
, pp. 1085-1097
-
-
Siggers, T.W.1
Honig, B.2
-
13
-
-
51349134974
-
Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach
-
Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach. Liu Z, Guo JT, Li T, Xu Y, Proteins 2008 72 4 1114 1124
-
(2008)
Proteins
, vol.72
, Issue.4
, pp. 1114-1124
-
-
Liu, Z.1
Guo, J.T.2
Li, T.3
Xu, Y.4
-
14
-
-
56749102973
-
Prediction of TF target sites based on atomistic models of protein-DNA complexes
-
Prediction of TF target sites based on atomistic models of protein-DNA complexes. Angarica VE, Perez AG, Vasconcelos AT, Collado-Vides J, Contreras-Moreira B, BMC Bioinformatics 2008 9 436
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 436
-
-
Angarica, V.E.1
Perez, A.G.2
Vasconcelos, A.T.3
Collado-Vides, J.4
Contreras-Moreira, B.5
-
15
-
-
68049118950
-
An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles
-
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, Proteins 2009 76 3 718 730
-
(2009)
Proteins
, vol.76
, Issue.3
, pp. 718-730
-
-
Xu, B.1
Yang, Y.2
Liang, H.3
Zhou, Y.4
-
16
-
-
66249112873
-
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions
-
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. Gao M, Skolnick J, PLoS Comput Biol 2009 5 3 1000341
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.3
, pp. 51000341
-
-
Gao, M.1
Skolnick, J.2
-
17
-
-
47249125424
-
DBD-Hunter: A knowledge-based method for the prediction of DNA-protein interactions
-
DOI 10.1093/nar/gkn332
-
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Gao M, Skolnick J, Nucleic Acids Res 2008 36 12 3978 3992 (Pubitemid 351984814)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.12
, pp. 3978-3992
-
-
Gao, M.1
Skolnick, J.2
-
18
-
-
0033954256
-
The Protein Data Bank
-
The Protein Data Bank. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE, Nucleic Acids Res 2000 28 1 235 242 (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
19
-
-
33646472024
-
High-resolution protein-protein docking
-
High-resolution protein-protein docking. Gray JJ, Curr Opin Struct Biol 2006 16 2 183 193
-
(2006)
Curr Opin Struct Biol
, vol.16
, Issue.2
, pp. 183-193
-
-
Gray, J.J.1
-
20
-
-
44949117092
-
A combination of rescoring and refinement significantly improves protein docking performance
-
DOI 10.1002/prot.21920
-
A combination of rescoring and refinement significantly improves protein docking performance. Pierce B, Weng Z, Proteins 2008 72 1 270 279 (Pubitemid 351809165)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.72
, Issue.1
, pp. 270-279
-
-
Pierce, B.1
Weng, Z.2
-
21
-
-
77949382951
-
Present and future challenges and limitations in protein-protein docking
-
Present and future challenges and limitations in protein-protein docking. Pons C, Grosdidier S, Solernou A, Perez-Cano L, Fernandez-Recio J, Proteins 2010 78 1 95 108
-
(2010)
Proteins
, vol.78
, Issue.1
, pp. 95-108
-
-
Pons, C.1
Grosdidier, S.2
Solernou, A.3
Perez-Cano, L.4
Fernandez-Recio, J.5
-
22
-
-
70349768241
-
Docking and chemoinformatic screens for new ligands and targets
-
Docking and chemoinformatic screens for new ligands and targets. Kolb P, Ferreira RS, Irwin JJ, Shoichet BK, Curr Opin Biotechnol 2009 20 4 429 436
-
(2009)
Curr Opin Biotechnol
, vol.20
, Issue.4
, pp. 429-436
-
-
Kolb, P.1
Ferreira, R.S.2
Irwin, J.J.3
Shoichet, B.K.4
-
23
-
-
33746285812
-
Information-driven protein-DNA docking using HADDOCK: It is a matter of flexibility
-
Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. van Dijk M, van Dijk AD, Hsu V, Boelens R, Bonvin AM, Nucleic Acids Res 2006 34 11 3317 3325
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.11
, pp. 3317-3325
-
-
Van Dijk, M.1
Van Dijk, A.D.2
Hsu, V.3
Boelens, R.4
Bonvin, A.M.5
-
24
-
-
77957242417
-
Pushing the limits of what is achievable in protein-DNA docking: Benchmarking HADDOCK's performance
-
Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance. van Dijk M, Bonvin AM, Nucleic Acids Res 2010 38 17 5634 5647
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.17
, pp. 5634-5647
-
-
Van Dijk, M.1
Bonvin, A.M.2
-
25
-
-
0028140592
-
MONTY: A Monte Carlo approach to protein-DNA recognition
-
MONTY: a Monte Carlo approach to protein-DNA recognition. Knegtel RM, Antoon J, Rullmann C, Boelens R, Kaptein R, J Mol Biol 1994 235 1 318 324 (Pubitemid 24049516)
-
(1994)
Journal of Molecular Biology
, vol.235
, Issue.1
, pp. 318-324
-
-
Knegtel, R.M.A.1
Antoon, J.2
Rullmann, C.3
Boelens, R.4
Kaptein, R.5
-
26
-
-
0030310317
-
Assessing the performance of fold recognition methods by means of a comprehensive benchmark
-
Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Fischer D, Elofsson A, Rice D, Eisenberg D, Pac Symp Biocomput 1996 300 318
-
(1996)
Pac Symp Biocomput
, pp. 300-318
-
-
Fischer, D.1
Elofsson, A.2
Rice, D.3
Eisenberg, D.4
-
27
-
-
0035014847
-
Multi-class protein fold recognition using support vector machines and neural networks
-
Multi-class protein fold recognition using support vector machines and neural networks. Ding CH, Dubchak I, Bioinformatics 2001 17 4 349 358 (Pubitemid 32421929)
-
(2001)
Bioinformatics
, vol.17
, Issue.4
, pp. 349-358
-
-
Ding, C.H.Q.1
Dubchak, I.2
-
28
-
-
4544367743
-
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
-
DOI 10.1002/prot.20149
-
Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Kellenberger E, Rodrigo J, Muller P, Rognan D, Proteins 2004 57 2 225 242 (Pubitemid 39223729)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.57
, Issue.2
, pp. 225-242
-
-
Kellenberger, E.1
Rodrigo, J.2
Muller, P.3
Rognan, D.4
-
29
-
-
0038187615
-
A protein-protein docking benchmark
-
DOI 10.1002/prot.10390
-
A protein-protein docking benchmark. Chen R, Mintseris J, Janin J, Weng Z, Proteins 2003 52 1 88 91 (Pubitemid 36648855)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.52
, Issue.1
, pp. 88-91
-
-
Chen, R.1
Mintseris, J.2
Janin, J.3
Weng, Z.4
-
30
-
-
77957944014
-
Protein-protein docking benchmark version 4.0
-
Protein-protein docking benchmark version 4.0. Hwang H, Vreven T, Janin J, Weng Z, Proteins 2010 78 15 3111 3114
-
(2010)
Proteins
, vol.78
, Issue.15
, pp. 3111-3114
-
-
Hwang, H.1
Vreven, T.2
Janin, J.3
Weng, Z.4
-
31
-
-
78649828754
-
Issues in bioinformatics benchmarking: The case study of multiple sequence alignment
-
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Aniba MR, Poch O, Thompson JD, Nucleic Acids Res 2010 38 21 7353 7363
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.21
, pp. 7353-7363
-
-
Aniba, M.R.1
Poch, O.2
Thompson, J.D.3
-
33
-
-
0041828241
-
Scaling laws in the functional content of genomes
-
DOI 10.1016/S0168-9525(03)00203-8
-
Scaling laws in the functional content of genomes. van Nimwegen E, Trends in genetics: TIG 2003 19 9 479 484 (Pubitemid 37101085)
-
(2003)
Trends in Genetics
, vol.19
, Issue.9
, pp. 479-484
-
-
Van Nimwegen, E.1
-
34
-
-
33746748243
-
An overview of the structures of protein-DNA complexes
-
An overview of the structures of protein-DNA complexes. Luscombe NM, Austin SE, Berman HM, Thornton JM, Genome Biol 2000 1 1 EVIEWS001
-
(2000)
Genome Biol
, vol.1
, Issue.1
-
-
Luscombe, N.M.1
Austin, S.E.2
Berman, H.M.3
Thornton, J.M.4
-
35
-
-
0036074510
-
Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
-
DOI 10.1016/S0022-2836(02)00571-5
-
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. Luscombe NM, Thornton JM, J Mol Biol 2002 320 5 991 1009 (Pubitemid 34808820)
-
(2002)
Journal of Molecular Biology
, vol.320
, Issue.5
, pp. 991-1009
-
-
Luscombe, N.M.1
Thornton, J.M.2
-
36
-
-
67249103597
-
Assessment of the optimization of affinity and specificity at protein-DNA interfaces
-
Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Ashworth J, Baker D, Nucleic Acids Res 2009 37 10 73
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.10
, pp. 573
-
-
Ashworth, J.1
Baker, D.2
-
37
-
-
67650403798
-
PDA: An automatic and comprehensive analysis program for protein-DNA complex structures
-
PDA: an automatic and comprehensive analysis program for protein-DNA complex structures. Kim R, Guo JT, BMC Genomics 2009 10 Suppl 1 13
-
(2009)
BMC Genomics
, vol.10
, Issue.SUPPL. 1
, pp. 1913
-
-
Kim, R.1
Guo, J.T.2
-
39
-
-
0033574510
-
Protein-DNA interactions: A structural analysis
-
DOI 10.1006/jmbi.1999.2659
-
Protein-DNA interactions: A structural analysis. Jones S, van Heyningen P, Berman HM, Thornton JM, J Mol Biol 1999 287 5 877 896 (Pubitemid 29188875)
-
(1999)
Journal of Molecular Biology
, vol.287
, Issue.5
, pp. 877-896
-
-
Jones, S.1
Van Heyningen, P.2
Berman, H.M.3
Thornton, J.M.4
-
40
-
-
77949358476
-
Comparison of DNA binding across protein superfamilies
-
Comparison of DNA binding across protein superfamilies. Contreras-Moreira B, Sancho J, Angarica VE, Proteins 2010 78 1 52 62
-
(2010)
Proteins
, vol.78
, Issue.1
, pp. 52-62
-
-
Contreras-Moreira, B.1
Sancho, J.2
Angarica, V.E.3
-
41
-
-
33748290192
-
Classification of Protein-DNA Complexes Based on Structural Descriptors
-
DOI 10.1016/j.str.2006.06.018, PII S0969212606003029
-
Classification of protein-DNA complexes based on structural descriptors. Prabakaran P, Siebers JG, Ahmad S, Gromiha MM, Singarayan MG, Sarai A, Structure 2006 14 9 1355 1367 (Pubitemid 44331615)
-
(2006)
Structure
, vol.14
, Issue.9
, pp. 1355-1367
-
-
Prabakaran, P.1
Siebers, J.G.2
Ahmad, S.3
Gromiha, M.M.4
Singarayan, M.G.5
Sarai, A.6
-
42
-
-
70350686719
-
The role of DNA shape in protein-DNA recognition
-
The role of DNA shape in protein-DNA recognition. Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B, Nature 2009 461 7268 1248 1253
-
(2009)
Nature
, vol.461
, Issue.7268
, pp. 1248-1253
-
-
Rohs, R.1
West, S.M.2
Sosinsky, A.3
Liu, P.4
Mann, R.S.5
Honig, B.6
-
43
-
-
75549088300
-
3D-footprint: A database for the structural analysis of protein-DNA complexes
-
Database
-
3D-footprint: a database for the structural analysis of protein-DNA complexes. Contreras-Moreira B, Nucleic Acids Research 2010 38 Database 91 97
-
(2010)
Nucleic Acids Research
, Issue.38
, pp. 491-97
-
-
Contreras-Moreira, B.1
-
44
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures. Murzin AG, Brenner SE, Hubbard T, Chothia C, J Mol Biol 1995 247 4 536 540
-
(1995)
J Mol Biol
, vol.247
, Issue.4
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
45
-
-
0032400516
-
Modelling repressor proteins docking to DNA
-
DOI 10.1002/(SICI)1097-0134(19981201)33:4<535::AID-PROT6>3.0.CO;2-D
-
Modelling repressor proteins docking to DNA. Aloy P, Moont G, Gabb HA, Querol E, Aviles FX, Sternberg MJ, Proteins 1998 33 4 535 549 (Pubitemid 28565736)
-
(1998)
Proteins: Structure, Function and Genetics
, vol.33
, Issue.4
, pp. 535-549
-
-
Aloy, P.1
Moont, G.2
Gabb, H.A.3
Querol, E.4
Aviles, F.X.5
Sternberg, M.J.E.6
-
46
-
-
58149191270
-
The Universal Protein Resource (UniProt) 2009
-
Database
-
The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 2009 37 Database 169 174
-
(2009)
Nucleic Acids Res
, Issue.37
, pp. 4169-174
-
-
-
47
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
DOI 10.1038/75556
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Nat Genet 2000 25 1 25 29 (Pubitemid 30257031)
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
48
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
DOI 10.1093/nar/gki524
-
TM-align: a protein structure alignment algorithm based on the TM-score. Zhang Y, Skolnick J, Nucleic Acids Res 2005 33 7 2302 2309 (Pubitemid 41439897)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.7
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
49
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
DOI 10.1002/prot.20264
-
Scoring function for automated assessment of protein structure template quality. Zhang Y, Skolnick J, Proteins 2004 57 4 702 710 (Pubitemid 39626992)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.57
, Issue.4
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
50
-
-
0034201441
-
EMBOSS: The European Molecular Biology Open Software Suite
-
EMBOSS: the European Molecular Biology Open Software Suite. Rice P, Longden I, Bleasby A, Trends Genet 2000 16 6 276 277
-
(2000)
Trends Genet
, vol.16
, Issue.6
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
51
-
-
0036639910
-
Parameter optimized surfaces (POPS): Analysis of key interactions and conformational changes in the ribosome
-
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome. Fraternali F, Cavallo L, Nucleic Acids Res 2002 30 13 2950 2960 (Pubitemid 34790204)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.13
, pp. 2950-2960
-
-
Fraternali, F.1
Cavallo, L.2
-
52
-
-
0043180474
-
PISCES: A protein sequence culling server
-
DOI 10.1093/bioinformatics/btg224
-
PISCES: a protein sequence culling server. Wang G, Dunbrack RL Jr, Bioinformatics 2003 19 12 1589 1591 (Pubitemid 37038881)
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
53
-
-
0025183708
-
Basic local alignment search tool
-
Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, J Mol Biol 1990 215 3 403 410
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
54
-
-
13744259639
-
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential
-
DOI 10.1093/nar/gki204
-
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential. Liu Z, Mao F, Guo JT, Yan B, Wang P, Qu Y, Xu Y, Nucleic Acids Res 2005 33 2 546 558 (Pubitemid 40360984)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.2
, pp. 546-558
-
-
Liu, Z.1
Mao, F.2
Guo, J.-T.3
Yan, B.4
Wang, P.5
Qu, Y.6
Xu, Y.7
-
55
-
-
17144383951
-
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
-
DOI 10.1021/jm049314d
-
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. Zhang C, Liu S, Zhu Q, Zhou Y, J Med Chem 2005 48 7 2325 2335 (Pubitemid 40516427)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.7
, pp. 2325-2335
-
-
Zhang, C.1
Liu, S.2
Zhu, Q.3
Zhou, Y.4
-
57
-
-
0035369335
-
Nuclear-receptor interactions on DNA-response elements
-
DOI 10.1016/S0968-0004(01)01800-X, PII S096800040101800X
-
Nuclear-receptor interactions on DNA-response elements. Khorasanizadeh S, Rastinejad F, Trends Biochem Sci 2001 26 6 384 390 (Pubitemid 32530657)
-
(2001)
Trends in Biochemical Sciences
, vol.26
, Issue.6
, pp. 384-390
-
-
Khorasanizadeh, S.1
Rastinejad, F.2
-
58
-
-
0035980235
-
DNA deformability as a recognition feature in the RevErb response Element
-
DOI 10.1021/bi011086r
-
DNA deformability as a recognition feature in the reverb response element. Sierk ML, Zhao Q, Rastinejad F, Biochemistry 2001 40 43 12833 12843 (Pubitemid 33026630)
-
(2001)
Biochemistry
, vol.40
, Issue.43
, pp. 12833-12843
-
-
Sierk, M.L.1
Zhao, Q.2
Rastinejad, F.3
-
59
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Diversity and complexity in DNA recognition by transcription factors. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, et al. Science 2009 324 5935 1720 1723
-
(2009)
Science
, vol.324
, Issue.5935
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
Talukder, S.4
Gehrke, A.R.5
Jaeger, S.A.6
Chan, E.T.7
Metzler, G.8
Vedenko, A.9
Chen, X.10
-
60
-
-
0023649686
-
Yeast HAP1 activator binds to two upstream activation sites of different sequence
-
Yeast HAP1 activator binds to two upstream activation sites of different sequence. Pfeifer K, Prezant T, Guarente L, Cell 1987 49 1 19 27
-
(1987)
Cell
, vol.49
, Issue.1
, pp. 19-27
-
-
Pfeifer, K.1
Prezant, T.2
Guarente, L.3
-
61
-
-
77957885770
-
Transcription factor binding variation in the evolution of gene regulation
-
Transcription factor binding variation in the evolution of gene regulation. Dowell RD, Trends Genet 2010 26 11 468 475
-
(2010)
Trends Genet
, vol.26
, Issue.11
, pp. 468-475
-
-
Dowell, R.D.1
-
62
-
-
21644458102
-
Classification of protein complexes based on docking difficulty
-
DOI 10.1002/prot.20554
-
Classification of protein complexes based on docking difficulty. Vajda S, Proteins 2005 60 2 176 180 (Pubitemid 40934883)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.60
, Issue.2
, pp. 176-180
-
-
Vajda, S.1
-
63
-
-
76749123486
-
Conformational transitions upon ligand binding: Holo-structure prediction from apo conformations
-
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. Seeliger D, de Groot BL, PLoS Comput Biol 2010 6 1 1000634.
-
(2010)
PLoS Comput Biol
, vol.6
, Issue.1
, pp. 51000634
-
-
Seeliger, D.1
De Groot, B.L.2
-
64
-
-
0024294634
-
Crystal structure of trp repressor/operator complex at atomic resolution
-
Crystal structure of trp repressor/operator complex at atomic resolution. Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB, Nature 1988 335 6188 321 329
-
(1988)
Nature
, vol.335
, Issue.6188
, pp. 321-329
-
-
Otwinowski, Z.1
Schevitz, R.W.2
Zhang, R.G.3
Lawson, C.L.4
Joachimiak, A.5
Marmorstein, R.Q.6
Luisi, B.F.7
Sigler, P.B.8
-
65
-
-
0027451092
-
The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state
-
The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state. Lazazzera BA, Bates DM, Kiley PJ, Genes Dev 1993 7 10 1993 2005 (Pubitemid 23312951)
-
(1993)
Genes and Development
, vol.7
, Issue.10
, pp. 1993-2005
-
-
Lazazzera, B.A.1
Bates, D.M.2
Kiley, P.J.3
-
66
-
-
0030953793
-
The DNA binding pattern of the retinoid X receptor is regulated by ligand-dependent modulation of its oligomeric state
-
DOI 10.1074/jbc.272.19.12771
-
The DNA binding pattern of the retinoid × receptor is regulated by ligand-dependent modulation of its oligomeric state. Kersten S, Gronemeyer H, Noy N, J Biol Chem 1997 272 19 12771 12777 (Pubitemid 27203377)
-
(1997)
Journal of Biological Chemistry
, vol.272
, Issue.19
, pp. 12771-12777
-
-
Kersten, S.1
Gronemeyer, H.2
Noy, N.3
-
67
-
-
79956121416
-
The oligomeric state of CtBP determines its role as a transcriptional co-activator and co-repressor of Wingless targets
-
The oligomeric state of CtBP determines its role as a transcriptional co-activator and co-repressor of Wingless targets. Bhambhani C, Chang JL, Akey DL, Cadigan KM, Embo J 2011 30 10 2031 2043
-
(2011)
Embo J
, vol.30
, Issue.10
, pp. 2031-2043
-
-
Bhambhani, C.1
Chang, J.L.2
Akey, D.L.3
Cadigan, K.M.4
|