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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