-
1
-
-
56749102973
-
Prediction of TF target sites based on atomistic models of protein-DNA complexes
-
Angarica, V.E. et al. (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.E.1
-
2
-
-
67249103597
-
Assessment of the optimization of affinity and specificity at protein-DNA interfaces
-
Ashworth, J. and Baker, D. (2009) Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Nucleic Acids Res., 37, e73.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Ashworth, J.1
Baker, D.2
-
3
-
-
34247098754
-
Multiscale modeling of biomolecular systems: in serial and in parallel
-
DOI 10.1016/j.sbi.2007.03.004, PII S0959440X07000346, Theory and Simulation / Mecromolecular Assemblages
-
Ayton, G.S. et al. (2007) Multiscale modeling of biomolecular systems: in serial and in parallel. Curr. Opin. Struct. Biol., 17, 192-198. (Pubitemid 46584804)
-
(2007)
Current Opinion in Structural Biology
, vol.17
, Issue.2
, pp. 192-198
-
-
Ayton, G.S.1
Noid, W.G.2
Voth, G.A.3
-
4
-
-
2942606066
-
Structure and evolution of transcriptional regulatory networks
-
DOI 10.1016/j.sbi.2004.05.004, PII S0959440X04000788
-
Babu, M.M. et al. (2004) Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol., 14, 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
-
6
-
-
0033954256
-
The protein data bank
-
Berman, H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 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
-
7
-
-
24944493938
-
Biochemistry: Toward high-resolution de novo structure prediction for small proteins
-
DOI 10.1126/science.1113801
-
Bradley, P. et al. (2005) Toward high-resolution de novo structure prediction for small proteins. Science, 309, 1868-1871. (Pubitemid 41325099)
-
(2005)
Science
, vol.309
, Issue.5742
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.S.2
Baker, D.3
-
8
-
-
33745726575
-
Structure prediction of helical transmembrane proteins at two length scales
-
DOI 10.1142/S0219720006001965, PII S0219720006001965
-
Chen, Z. and Xu, Y. (2006) Structure prediction of helical transmembrane proteins at two length scales. J. Bioinform. Comput. Biol., 4, 317-333. (Pubitemid 43997122)
-
(2006)
Journal of Bioinformatics and Computational Biology
, vol.4
, Issue.2
, pp. 317-333
-
-
Chen, Z.1
Xu, Y.2
-
9
-
-
77949358476
-
Comparison of DNA binding across protein superfamilies
-
Contreras-Moreira, B. et al. (2010) Comparison of DNA binding across protein superfamilies. Proteins, 78, 52-62.
-
(2010)
Proteins
, vol.78
, pp. 52-62
-
-
Contreras-Moreira, B.1
-
10
-
-
34047138418
-
Energetics of protein-DNA interactions
-
Donald, J.E. et al. (2007) Energetics of protein-DNA interactions. Nucleic Acids Res., 35, 1039-1047.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 1039-1047
-
-
Donald, J.E.1
-
11
-
-
4544293652
-
Toward an atomistic model for predicting transcription-factor binding sites
-
DOI 10.1002/prot.20199
-
Endres, R.G. et al. (2004) Toward an atomistic model for predicting transcription-factor binding sites. Proteins, 57, 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
-
12
-
-
84865078347
-
Multiscale modeling of macromolecular biosystems
-
Flores, S.C. et al. (2012) Multiscale modeling of macromolecular biosystems. Brief. Bioinform., 13, 395-405.
-
(2012)
Brief. Bioinform
, vol.13
, pp. 395-405
-
-
Flores, S.C.1
-
13
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
DOI 10.1002/prot.340230412
-
Frishman, D. and Argos, P. (1995) Knowledge-based protein secondary structure assignment. Proteins, 23, 566-579. (Pubitemid 26009520)
-
(1995)
Proteins: Structure, Function and Genetics
, vol.23
, Issue.4
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
14
-
-
47249125424
-
DBD-Hunter: A knowledge-based method for the prediction of DNA-protein interactions
-
DOI 10.1093/nar/gkn332
-
Gao, M. and Skolnick, J. (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res., 36, 3978-3992. (Pubitemid 351984814)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.12
, pp. 3978-3992
-
-
Gao, M.1
Skolnick, J.2
-
15
-
-
77951212412
-
PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy
-
Gopal, S.M. et al. (2010) PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy. Proteins, 78, 1266-1281.
-
(2010)
Proteins
, vol.78
, pp. 1266-1281
-
-
Gopal, S.M.1
-
16
-
-
36849063165
-
Structure and evolution of gene regulatory networks in microbial genomes
-
DOI 10.1016/j.resmic.2007.09.001, PII S0923250807001763, Microbial Genomics
-
Janga, S.C. and Collado-Vides, J. (2007) Structure and evolution of gene regulatory networks in microbial genomes. Res. Microbiol., 158, 787-794. (Pubitemid 350235176)
-
(2007)
Research in Microbiology
, vol.158
, Issue.10
, pp. 787-794
-
-
Janga, S.C.1
Collado-Vides, J.2
-
17
-
-
29444434700
-
Ab initio prediction of transcription factor targets using structural knowledge
-
Kaplan, T. et al. (2005) Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput. Biol., 1, e1.
-
(2005)
PLoS Comput. Biol
, vol.1
-
-
Kaplan, T.1
-
18
-
-
67650403798
-
PDA: An automatic and comprehensive analysis program for protein-DNA complex structures
-
Kim, R. and Guo, J.T. (2009) PDA: an automatic and comprehensive analysis program for protein-DNA complex structures. BMC Genom., 10 (Suppl. 1), S13.
-
(2009)
BMC Genom
, vol.10
, Issue.SUPPL. 1
-
-
Kim, R.1
Guo, J.T.2
-
19
-
-
37549009571
-
Coarse-grained models for simulations of multiprotein complexes: Application to ubiquitin binding
-
Kim, Y.C. and Hummer, G. (2008) Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J. Mol. Biol., 375, 1416-1433.
-
(2008)
J. Mol. Biol
, vol.375
, pp. 1416-1433
-
-
Kim, Y.C.1
Hummer, G.2
-
20
-
-
80055047271
-
Benchmarks for flexible and rigid transcription factor-DNA docking
-
Kim, R. et al. (2011) Benchmarks for flexible and rigid transcription factor-DNA docking. BMC Struct. Biol., 11, 45.
-
(2011)
BMC Struct. Biol
, vol.11
, pp. 45
-
-
Kim, R.1
-
21
-
-
0033120215
-
Structure-based prediction of DNA target sites by regulatory proteins
-
DOI 10.1002/(SICI)1097-0134(19990401)35:1<114::AID-PROT11>3.0.CO;2- T
-
Kono, H. and Sarai, A. (1999) Structure-based prediction of DNA target sites by regulatory proteins. Proteins, 35, 114-131. (Pubitemid 29128158)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.35
, Issue.1
, pp. 114-131
-
-
Kono, H.1
Sarai, A.2
-
22
-
-
13744259639
-
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential
-
DOI 10.1093/nar/gki204
-
Liu, Z. et al. (2005) Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential. Nucleic Acids Res., 33, 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
-
23
-
-
51349134974
-
Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach
-
Liu, Z. et al. (2008) Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach. Proteins, 72, 1114-1124.
-
(2008)
Proteins
, vol.72
, pp. 1114-1124
-
-
Liu, Z.1
-
24
-
-
0036074510
-
Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
-
DOI 10.1016/S0022-2836(02)00571-5
-
Luscombe, N.M. and Thornton, J.M. (2002) Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J. Mol. Biol., 320, 991-1009. (Pubitemid 34808820)
-
(2002)
Journal of Molecular Biology
, vol.320
, Issue.5
, pp. 991-1009
-
-
Luscombe, N.M.1
Thornton, J.M.2
-
25
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
-
Luscombe, N.M. et al. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874. (Pubitemid 32685051)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.13
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
26
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal-structures-quasi-chemical approximation
-
Miyazawa, S. and Jernigan, R.L. (1985) Estimation of effective interresidue contact energies from protein crystal-structures-quasi-chemical approximation. Macromolecules, 18, 534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
27
-
-
0344980720
-
Combination of scoring functions improves discrimination in protein-protein docking
-
DOI 10.1002/prot.10473
-
Murphy, J. et al. (2003) Combination of scoring functions improves discrimination in protein-protein docking. Proteins, 53, 840-854. (Pubitemid 37490437)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.53
, Issue.4
, pp. 840-854
-
-
Murphy, J.1
Gatchell, D.W.2
Prasad, J.C.3
Vajda, S.4
-
28
-
-
80052583392
-
(Compressed) sensing and sensibility
-
Pande, V.S. (2011) (Compressed) sensing and sensibility. Proc. Natl Acad. Sci. USA, 108, 14713-14714.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 14713-14714
-
-
Pande, V.S.1
-
29
-
-
17044403057
-
Type II restriction endonucleases: Structure and mechanism
-
Pingoud, A. et al. (2005) Type II restriction endonucleases: structure and mechanism. Cell. Mol. Life Sci., 62, 685-707.
-
(2005)
Cell. Mol. Life Sci
, vol.62
, pp. 685-707
-
-
Pingoud, A.1
-
30
-
-
55349123996
-
Insights on protein-DNA recognition by coarse grain modelling
-
Poulain, P. et al. (2008) Insights on protein-DNA recognition by coarse grain modelling. J. Comput. Chem., 29, 2582-2592.
-
(2008)
J. Comput. Chem
, vol.29
, pp. 2582-2592
-
-
Poulain, P.1
-
31
-
-
33748290192
-
Classification of protein-dna complexes based on structural descriptors
-
DOI 10.1016/j.str.2006.06.018, PII S0969212606003029
-
Prabakaran, P. et al. (2006) Classification of protein-DNA complexes based on structural descriptors. Structure, 14, 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
-
32
-
-
33845976703
-
An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure
-
DOI 10.1002/prot.21162
-
Robertson, T.A. and Varani, G. (2007) An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure. Proteins, 66, 359-374. (Pubitemid 46053467)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.66
, Issue.2
, pp. 359-374
-
-
Robertson, T.A.1
Varani, G.2
-
33
-
-
34047153962
-
2 zinc-finger binding specificity: Sensitivity to docking geometry
-
DOI 10.1093/nar/gkl1155
-
Siggers, T.W. and Honig, B. (2007) Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res., 35, 1085-1097. (Pubitemid 46522964)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.4
, pp. 1085-1097
-
-
Siggers, T.W.1
Honig, B.2
-
34
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl, M.J. (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol., 213, 859-883. (Pubitemid 20213222)
-
(1990)
Journal of Molecular Biology
, vol.213
, Issue.4
, pp. 859-883
-
-
Sippl, M.J.1
-
35
-
-
0029000696
-
Knowledge-based potentials for proteins
-
Sippl, M.J. (1995) Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol., 5, 229-235.
-
(1995)
Curr. Opin. Struct. Biol
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
36
-
-
77957242417
-
Pushing the limits of what is achievable in protein-DNA docking: Benchmarking HADDOCK's performance
-
van Dijk, M. and Bonvin, A.M. (2010) Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance. Nucleic Acids Res., 38, 5634-5647.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 5634-5647
-
-
Van Dijk, M.1
Bonvin, A.M.2
-
37
-
-
33746285812
-
Information-driven protein-DNA docking using HADDOCK: It is a matter of flexibility
-
van Dijk, M. et al. (2006) Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Res., 34, 3317-3325.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3317-3325
-
-
Van Dijk, M.1
-
38
-
-
84860388898
-
Integrating atom-based and residue-based scoring functions for protein-protein docking
-
Vreven, T. et al. (2011) Integrating atom-based and residue-based scoring functions for protein-protein docking. Protein Sci., 20, 1576-1586.
-
(2011)
Protein Sci
, vol.20
, pp. 1576-1586
-
-
Vreven, T.1
-
39
-
-
0027510004
-
Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds
-
DOI 10.1021/jm00053a019
-
Wade, R.C. and Goodford, P.J. (1993) Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds. J. Med. Chem., 36, 148-156. (Pubitemid 23040156)
-
(1993)
Journal of Medicinal Chemistry
, vol.36
, Issue.1
, pp. 148-156
-
-
Wade, R.C.1
Goodford, P.J.2
-
40
-
-
84962704372
-
High performance transcription factor-DNA docking with GPU computing
-
Wu, J. et al. (2012) High performance transcription factor-DNA docking with GPU computing. Proteome Sci., 10 (Suppl. 1), S17.
-
(2012)
Proteome Sci
, vol.10
, Issue.SUPPL. 1
-
-
Wu, J.1
-
41
-
-
68049118950
-
An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles
-
Xu, B. et al. (2009) An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles. Proteins, 76, 718-730.
-
(2009)
Proteins
, vol.76
, pp. 718-730
-
-
Xu, B.1
-
42
-
-
17144383951
-
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
-
DOI 10.1021/jm049314d
-
Zhang, C. et al. (2005) A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J. Med. Chem., 48, 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
-
43
-
-
77955034560
-
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function
-
Zhao, H. et al. (2010) Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinformatics, 26, 1857-1863.
-
(2010)
Bioinformatics
, vol.26
, pp. 1857-1863
-
-
Zhao, H.1
-
44
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
DOI 10.1110/ps.0217002
-
Zhou, H. and Zhou, Y. (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci., 11, 2714-2726. (Pubitemid 35191145)
-
(2002)
Protein Science
, vol.11
, Issue.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
|