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Volumn 16, Issue 3, 1998, Pages 487-509

Molecular dynamic simulations of environment and sequence dependent dna conformations: The development of the bms nucleic acid force field and comparison with experimental results

Author keywords

[No Author keywords available]

Indexed keywords

CYCLOPENTANE; TETRAHYDROFURAN;

EID: 0032459726     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1998.10508265     Document Type: Article
Times cited : (107)

References (99)
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    • (1988) DNA Bending and Curvature , pp. 191
    • Lavery, R.1
  • 32
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    • This work was carried out over the past few years and has been the basis for the following pre sentations: Parameterization for Nucleic Acids and Molecular Dynamic Simulations; MSI Life Science Symposia, Boston, MA, 1995. Parameterization for Nucleic Acids and Molecular Dynamic Simulations; 212th ACS National Meeting, Orlando, FL, 1996. Environmentally Dependent Molecular Dynamic Simulations of DNA Using the BMS Nucleic Acid Force Field; 213th ACS National Meeting, San Francisco, CA
    • 1997. This work was carried out over the past few years and has been the basis for the following pre sentations:Parameterization for Nucleic Acids and Molecular Dynamic Simulations; MSI Life Science Symposia, Boston, MA, 1995. Parameterization for Nucleic Acids and Molecular Dynamic Simulations; 212th ACS National Meeting, Orlando, FL, 1996. Environmentally Dependent Molecular Dynamic Simulations of DNA Using the BMS Nucleic Acid Force Field; 213th ACS National Meeting, San Francisco, CA
    • (1997)
  • 43
    • 85023956468 scopus 로고    scopus 로고
    • Charmm Formated Cornell force field (CFC), http://www.amber.ucsf.edu/amber/ff94/charmm94.html
  • 46
    • 85023945878 scopus 로고    scopus 로고
    • 2 in 4M NaCl and 75% ethanol solutions
    • 2 in 4M NaCl and 75% ethanol solutions
    • (1998)
  • 47
    • 85023917148 scopus 로고    scopus 로고
    • Force-Fields: The BMS, a CHARMM formated version of the Cornell (CFC), and a modified version of the Cornell force fields are available upon request
    • Force-Fields:The BMS, a CHARMM formated version of the Cornell (CFC), and a modified version of the Cornell force fields are available upon request, david@viper.wfd.pri.bms.com
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    • Gaussian, v94, Gaussian Inc., 4415 Fifth Avenue, Pittsburgh, PA 15213
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    • 85023901606 scopus 로고    scopus 로고
    • QUANTA, v4.1, MSI, 9685 Scranton Road, San Diego, CA 92121
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    • Attempts to adjust the torsion angle parameters so that the C3′-endo conformation is less favored resulted in large barrier height energies between the C2′- and C3′-endo sugar conformation. Interestingly, if the the RESP charge model is used with the CHARMM23 parameters the C2′-endo conformation is preferred. Analyzing the two charge models suggests that moving some of the negative charge off of N1 (pyrimidine) and N9 (purine) may be needed in the development of a better CHARMM23 force field
    • Attempts to adjust the torsion angle parameters so that the C3′-endo conformation is less favored resulted in large barrier height energies between the C2′- and C3′-endo sugar conformation. Interestingly, if the the RESP charge model is used with the CHARMM23 parameters the C2′-endo conformation is preferred. Analyzing the two charge models suggests that moving some of the negative charge off of N1 (pyrimidine) and N9 (purine) may be needed in the development of a better CHARMM23 force field
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    • the low water activity environment simulations hydrogen bond constrains were used on the terminal base pair where end fraying occurred. The hydrogen bond constraints were left on to the end of the simulation or until the ions dissociated to greater than two water layer from the edge of the base pair
    • In the low water activity environment simulations hydrogen bond constrains were used on the terminal base pair where end fraying occurred. The hydrogen bond constraints were left on to the end of the simulation or until the ions dissociated to greater than two water layer from the edge of the base pair


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.