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| Author(s): |
Marta Maria Cassiano
Total Authors: 1
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| Document type: | Doctoral Thesis |
| Press: | São Paulo. |
| Institution: | Universidade de São Paulo (USP). Instituto de Física (IF/SBI) |
| Defense date: | 1998-04-29 |
| Examining board members: |
Paulo Mascarello Bisch;
Jose Alfredo Gomes Areas;
Luiz Carlos Gomide Freitas;
Isabelle Ortmans;
José Roberto Ruggiero
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| Advisor: | Paulo Mascarello Bisch; Amando Siuiti Ito |
| Abstract | |
The computational package THOR for molecular mechanic and dynamics simulation was improved by the introduction of techniques for modeling of biomolecular systems with explicit representation of solvent molecules. Those techniques include the application of periodic boundary conditions, the use of a cut-off sphere for the potential, with modifications in the electrostatic potential, and the utilization of the method shake to impose distance constraints. Furthermore, a neighbours list was implemented, due to the high number of atoms to be dealt with when the solvent is explicity represented. Simulations were performed on some systems of biological interest, and the influence of the solvent on their conformational properties was analysed. The results are in good agreement with theoretical previsions and experimental data. (AU) | |