And go for some conformation corresponding to local minimum?
Dear Anjani,
Determination of global minimum is a demanding task. optimization is a method for finding minima of a multidimensional function. Also, the number of minima for a function grows exponentially!!!!. The more a function has variables, the more it has minima. So, finding of global minima between all the minima is a difficult task, because it needs all the minima to be determined., hence nearest minimum, based on initial variable is sufficient. for instance imagine an alkane which has 18 carbon atoms. Finding global minimum which is corresponds to the lowest conformer takes near 6 months. Do you understand why?. :)
Is the same reason you gave ? I mean there are multiple variables to consider while determining/ predicting the minima or to say overall minima.
Can you suggest me a book which can introduce me to all these concepts. I mean beginning from Bioactive molecule to identification of Leads to constructing a QSAR model ?
Dear Anjani,
I could not understand what you mean. Please, give me more detail?
Im sorry for being ambiguous.
I meant Which book shall I begin with, when my aim is to know the definite workflow of Pharmacophore based drug design?
Anjani,
Why do you think you need the global minimum structure in the first place? What use does it have?
The bound conformation for any ligand is NEVER the global minimum, though it may be close in either geometry or energy you will never know if advance how different. If you want the global minimum to understand the stability of a bound conformation (energy gap between bound conformation and global minimum) you are asking the wrong question. The global minimum energy conformation of any molecule is a computational curiosity, nothing more; it has no actual utility.
If books on pharmacophore-based drug design are your goal, have you asked Google? Google knows much :-).
Yes I realised it later in lectures that however it is a global minimum its not as important as bound conformation. Bound conformation has some forces acting on it and would not be a global minimum anyway.
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