107 related articles for article (PubMed ID: 11754342)
1. ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences.
Lafontaine I; Lavery R
Biopolymers; 2000-2001; 56(4):292-310. PubMed ID: 11754342
[TBL] [Abstract][Full Text] [Related]
2. Dynamic simulations of 13 TATA variants refine kinetic hypotheses of sequence/activity relationships.
Qian X; Strahs D; Schlick T
J Mol Biol; 2001 May; 308(4):681-703. PubMed ID: 11350169
[TBL] [Abstract][Full Text] [Related]
3. Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies.
Zakrzewska K; Bouvier B; Michon A; Blanchet C; Lavery R
Phys Chem Chem Phys; 2009 Dec; 11(45):10712-21. PubMed ID: 20145815
[TBL] [Abstract][Full Text] [Related]
4. Molecular modelling methods for prediction of sequence-selectivity in DNA recognition.
Wang H; Laughton CA
Methods; 2007 Jun; 42(2):196-203. PubMed ID: 17472901
[TBL] [Abstract][Full Text] [Related]
5. Minimum sequence requirements for selective RNA-ligand binding: a molecular mechanics algorithm using molecular dynamics and free-energy techniques.
Anderson PC; Mecozzi S
J Comput Chem; 2006 Nov; 27(14):1631-40. PubMed ID: 16900493
[TBL] [Abstract][Full Text] [Related]
6. Optimization of nucleic acid sequences.
Lafontaine I; Lavery R
Biophys J; 2000 Aug; 79(2):680-5. PubMed ID: 10920002
[TBL] [Abstract][Full Text] [Related]
7. High-speed molecular mechanics searches for optimal DNA interaction sites.
Lafontaine I; Lavery R
Comb Chem High Throughput Screen; 2001 Dec; 4(8):707-17. PubMed ID: 11812263
[TBL] [Abstract][Full Text] [Related]
8. [The role of weak specific and nonspecific interactions in recognition and conversation by enzymes of long DNA].
Nevinskiĭ GA
Mol Biol (Mosk); 2004; 38(5):756-85. PubMed ID: 15554181
[TBL] [Abstract][Full Text] [Related]
9. An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure.
Robertson TA; Varani G
Proteins; 2007 Feb; 66(2):359-74. PubMed ID: 17078093
[TBL] [Abstract][Full Text] [Related]
10. Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition.
Miller JC; Pabo CO
J Mol Biol; 2001 Oct; 313(2):309-15. PubMed ID: 11800559
[TBL] [Abstract][Full Text] [Related]
11. Sequence-dependent solution structure and motions of 13 TATA/TBP (TATA-box binding protein) complexes.
Strahs D; Barash D; Qian X; Schlick T
Biopolymers; 2003 Jun; 69(2):216-43. PubMed ID: 12767124
[TBL] [Abstract][Full Text] [Related]
12. The mechanics of minor groove width variation in DNA, and its implications for the accommodation of ligands.
Laughton C; Luisi B
J Mol Biol; 1999 May; 288(5):953-63. PubMed ID: 10329191
[TBL] [Abstract][Full Text] [Related]
13. DNA flexibility as a function of allomorphic conformation and of base sequence.
Poncin M; Piazzola D; Lavery R
Biopolymers; 1992 Aug; 32(8):1077-103. PubMed ID: 1420973
[TBL] [Abstract][Full Text] [Related]
14. Characterization of nonspecific protein-DNA interactions by 1H paramagnetic relaxation enhancement.
Iwahara J; Schwieters CD; Clore GM
J Am Chem Soc; 2004 Oct; 126(40):12800-8. PubMed ID: 15469275
[TBL] [Abstract][Full Text] [Related]
15. Ligands recognizing the minor groove of DNA: development and applications.
Wemmer DE
Biopolymers; 1999-2000; 52(4):197-211. PubMed ID: 11295751
[TBL] [Abstract][Full Text] [Related]
16. A simple physical model for the prediction and design of protein-DNA interactions.
Havranek JJ; Duarte CM; Baker D
J Mol Biol; 2004 Nov; 344(1):59-70. PubMed ID: 15504402
[TBL] [Abstract][Full Text] [Related]
17. Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition.
Araúzo-Bravo MJ; Fujii S; Kono H; Ahmad S; Sarai A
J Am Chem Soc; 2005 Nov; 127(46):16074-89. PubMed ID: 16287294
[TBL] [Abstract][Full Text] [Related]
18. Prediction of atomic structure from sequence for double helical DNA oligomers.
Farwer J; Packer MJ; Hunter CA
Biopolymers; 2006 Jan; 81(1):51-61. PubMed ID: 16184626
[TBL] [Abstract][Full Text] [Related]
19. Crystal structure of a ternary SAP-1/SRF/c-fos SRE DNA complex.
Mo Y; Ho W; Johnston K; Marmorstein R
J Mol Biol; 2001 Nov; 314(3):495-506. PubMed ID: 11846562
[TBL] [Abstract][Full Text] [Related]
20. Binding of netropsin to several DNA constructs: evidence for at least two different 1:1 complexes formed from an -AATT-containing ds-DNA construct and a single minor groove binding ligand.
Freyer MW; Buscaglia R; Cashman D; Hyslop S; Wilson WD; Chaires JB; Lewis EA
Biophys Chem; 2007 Mar; 126(1-3):186-96. PubMed ID: 16837123
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]