Paper Citing NAMD - Abstract
Monajjemi, M.; Sabaghzadeh, R.; Ilkhani, A. R.; Mollaamin, F.
Nano-modeling of insulin-like growth factor 1 (IGF-1) by computational methods
AFRICAN JOURNAL OF MICROBIOLOGY RESEARCH, 5:2895-2905, SEP 23 2011
The empirical force fields have great difficulty in simulating folding of insulin-like growth factor 1 (IGF-1). In an effort to understand the conformational preferences that may be attributed to stereoelectronic effects, a number of computational studies are carried out. Monte Carlo, molecular dynamics and Langevin simulation methods by MM+, amber and optimized potential for liquid simulations (OPLS) force fields of calculations have been performed on IGF-1 as growth factor. The parameters of minimized structure of IGF-1, calculated potential energy for important dihedral angles and the effect of temperature on geometry of optimized structure have been calculated. In this work, we have used different temperatures at gas and water media and we have seen that in simulation approaches, scaling up the interaction energy has a similar effect to lowering temperature. This study has demonstrated that the simple model including an approximate average solvent effect can simulate the qualitative feature of the IGF-1. The key research was to find dynamics of biomolecular structure and an appropriate effective stabilized energy.
