3D-lattice protein
Rafael N Szeinfeld
szeinfel at FOX.CCE.USP.BR
Thu Mar 10 15:07:33 EST 1994
On 10 Mar 1994, Sam Rushing wrote:
> In article <Pine.3.85.9403081855.A15756-0100000 at fox.cce.usp.br>, szeinfel at FOX.CCE.USP.BR (Rafael N Szeinfeld) says:
> >
> >
> > Hi Netter's
> > I would like to know if there is any program that takes as input
> >a pdb file with atomic coordinates of a protein (let's say from Brokheaven
> >protein databank) and inserts it in a cubic lattice (you define the
> >dimensions of the unit cell) so that as output you have a matrix M(AxBxC)
> >where each element of the matrix M(i,j,k)=1 if the this unit cell is
> >ocuppied by one or more atoms or M(i,j,k)=0 if this unit cell is empty.
> >By adjusting the dimension(l, where V(volume)=l^3) you can select how
> >accurate is your lattice model if your unit cell have the dimensions of
> >an atom, your lattice model will be equal to the atomic coordinates file.
> >I'm not sure if I expressed well my idea but I'll appreciate any comment.
> >
> > Rafael Najmanovich
> >
> >
> very good idea and it's new, so I think you won't have chance to find out an
> existing program.
>
> however since you've got such a clear idea, it wouldn't take long for people who
> has experience to build such a one from sratch.
>
> best wishes!
>
> Chuck An
>
> ps. I'm not sure what you are going to do with this arigorithm. but would you
> agree that, since a protein is almost as compact as any crystalls, there won't be
> so many zeros in the matrix? regardless what kind of cordinates you are going
> to make use of.
>
>
I'm confused about who sent this messsage (Chuck or Sam) anyway,
I think this idea is not new since there's a paper (Yuzo Ueda,
Hiroshi Taketomi and Nobuhiro Go from Kyushu University, Japan.
Biopolymers 17:1531-1548(1978).) where they do these or something
aproximate with lysozyme. You're right about the ssmall number of zeros
but the inportant is that as you know where's the N-terminus and the
C-terminus, this representation is good to perform simulations. By the
way, if someone knows the e-mail adress of any autor of the above
mentioned paper please let me know.
Rafael Najmanovich
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