Molecular medicine for the 21. century: A computational basis for design and critique of vaccines and therapeutics
- Los Alamos National Lab., NM (United States). Theoretical Div.
This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The kissing-loop RNA motif is thought to modulate different steps in the retroviral life cycle. Using an RNA folding protocol developed under this project, the authors are studying the folding of the potential kissing-loop motif in HIV. Using only limited information on base-springs, and the constraints based on the connectivities, they are modeling the structure and the flexibility of this particular structural motif and have developed three predicted structures with low conformational energy. Following on the earlier work which analyzed correlated mutations in the V3 loop of HIV, they have developed an evolutionary model which incorporates non-independent mutations at different sequence positions in model sequences. This model takes into account the effects of the phylogenetic tree on the analysis of mutations, and shows a higher correspondence of correlated positions with structurally adjacent positions in the model than previous analyses. Additional research under this project has dealt with analyzing the dynamics of HIV in vivo. Using some simple models and patient data, they were able to establish for the first time some quantitative estimates of HIV dynamics in vivo.
- Research Organization:
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Sponsoring Organization:
- USDOE Assistant Secretary for Human Resources and Administration, Washington, DC (United States)
- DOE Contract Number:
- W-7405-ENG-36
- OSTI ID:
- 515543
- Report Number(s):
- LA-UR-97-2568; ON: DE97008683; TRN: AHC29718%%58
- Resource Relation:
- Other Information: PBD: [1997]
- Country of Publication:
- United States
- Language:
- English
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