From: Fei Chen (
Date: Wed Mar 05 2008 - 19:48:49 CST

Thank you very much.
As you know, we cannot exactly compute all the force(bond, angle and
dihedral forces, van der Waal forces, etc.), can I take account of some of
them which is the determinant?
Can I segment the protein base on the different force?
Thank you.

On Thu, Mar 6, 2008 at 6:32 AM, Andrew Dalke <>

> On Mar 5, 2008, at 2:53 PM, Fei Chen wrote:
> > I'm not sure whether it's apt to issue the problem here.
> > I assume that there is some forces responsible for the structure or
> > function of a protein.
> > I want to find the main reason that result in the structure or
> > function of a protein.
> > I can compute the bond-force or non-bond force between two atoms in
> > a protein, should some atoms' force be the most important for the
> > structure or function of the protein? Are bond-force and non-bond
> > force adequate? Or should I take other factors for account?
> The answer is "yes to all".
> You asked a question which is almost impossible to answer, because
> there's a basic understanding that seems to be lacking in the question.
> You need to get an understanding of chemistry first, or of physics.
> The forces are that of quantum mechanics, although relativistic
> quantum mechanics is mostly only needed for heavy/metallic atoms.
> The approximation made for more organic systems is that nucleons are
> point charges, electrons are "fast", and that the only force to worry
> about is mediated by photons. That is, electricity and magnetism.
> "bonds" are an approximation for how to think about the quantum
> mechanics. They are useful, but incomplete. Molecular modeling also
> talks about angle and dihedral forces, van der Waal forces, and
> "normal" electrostatic forces. Some people talk about aromatics and
> ring currents. All of these are aspects of the same electromagnetic
> force.
> The way that force is expressed differs for different molecules. All
> molecules have a strong covalent component. That defines the primary
> structure. But there's also additional structures caused by other
> modes, like hydrogen bonds in alpha helices and beta sheets. There's
> a force term caused by the change in entropy around polar proteins,
> which has its own effect.
> So the answer is "yes, there are other factors you'll need to take
> into account." Knowing what those are pretty much describes the
> field of structural biology.
> Andrew

Chen Fei