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Volumn 104, Issue 43, 2000, Pages 10092-10099

Free-energy perturbation calculations of DNA destabilization by base substitutions: The effect of neutral guanine·thymine, adenine·cytosine and adenine·difluorotoluene mismatches

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CRYSTAL DEFECTS; FLUORINE; FREE ENERGY; NUCLEATION; PERTURBATION TECHNIQUES; SUBSTITUTION REACTIONS; TOLUENE; X RAY CRYSTALLOGRAPHY;

EID: 0034320964     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp001760z     Document Type: Article
Times cited : (57)

References (55)
  • 23
    • 84983715113 scopus 로고    scopus 로고
    • Tripos Inc., 1699 South Hanley Rd., St. Louis, Missouri, 63144
    • SYBYL 6.6; Tripos Inc., 1699 South Hanley Rd., St. Louis, Missouri, 63144.
    • SYBYL 6.6
  • 29
    • 0032342086 scopus 로고    scopus 로고
    • Lipkowitz, K. B., Boyd, D. B.,Eds.; Wiley-VCH: New York
    • Meirovitch, H. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B.,Eds.; Wiley-VCH: New York, 1998; Vol. 12; pp 1.
    • (1998) Reviews in Computational Chemistry , vol.12 , pp. 1
    • Meirovitch, H.1
  • 36
    • 33645930898 scopus 로고    scopus 로고
    • note
    • One should realize, however, that a complete exploration of the available configuration space or a "complete" convergence is an unrealistic goal for any current simulation method because of computer time limitations. A realistic goal is to obtain sufficient convergence in the quantity under consideration without running infinitely long trajectories. This is why we have developped the SCAAS and LRF methods, which attempt to obtain reasonable convergence in electrostatic energies. As with any related scientific problem it is essential to examine whether one could reproduce the relevant observed quantity, while realizing that no simulation is perfect. In doing so, it is much more important to examine sensitivity to different boundary conditions and long-range treatments than to run one very long trajectory.
  • 49
    • 85088174716 scopus 로고    scopus 로고
    • note
    • 25 (TG/AC step) = -0.26-0.14 + 1.12 + 1.72 = 2.4 ± 0.4 kcal/mol. The error range was estimated by assuming 0.1 kcal/mol uncertainty for each nearest neighbor parameter.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.