protein structure prediction and recognition

[no_on...@yahoo.com]

Hi all, I am a new student in the field of protein structure prediction
and I get confused with protein structure prediction and recognition. I
want to know what are the differences between them. Thank you.

[Nonappa B]

Hi,
I suggest u to go to biochemistry online where u will find aonline
book and get all the information. What u can do is that first go to
google and then give biochemistry online search. If u don't get in i
have a link in my web papge u just go to
www.geocities.com/nonappa/nona_org

all the best

--
Nonappa
Research Scholar
Department of Organic Chemistry
Indian Institute of Science
Bangalore -560012
Ph: +919880276516
email: no...@students.orgchem.iisc.ernet.in
non...@yahoo.com
non...@gmail.com

[fayyaz]

hi ,
see man these are two different things with almost similar purposes ,
the prediction is made on the basis of the similarities with other
protein residues ,
in this regard we see
1 the position of the hydrophobic and the hydrophilic residues in
different regions,
2 how the alpha and b chain formed by the arranging the which residues
, how many can b formed ,
prediction is for the new proteins and recognition is for determined
protein structures
but i cannt understand urs problem wheather u want to know about the
difference or ways how the protein are predicted or recognized
--
biochemi

[no_on...@yahoo.com]

Thank you very much.
I am a computer science student and I am doing my PhD. my interset is
Parallel and Distriubuted computing. My supervisour asks me to read
about the protein tertiary structure prediction and come out with a
topic form my PhD.
The research area are is very wide and I get confused. I am now
consetrating on ab initio methods.
I want to know how to predict the protein tertiary structure using ab
initio methods?
How to strat from protein sequence to get the 3D structure? I mean how
to determine first the representation of the protein. then the
poteintial function and the conformation search method.

Please help me to narrow my research area.

Thank you.

[fayyaz]

hi
see if u dont have the background about the biochemistry and about the
protein, u need to study some basics
as
1 the properties of the aminoacids constituting the proteins
2 what are the primary , secondry , tertiay structures of proteins ,
3 then there are lot of software available , free on net for 3 d
modeling , first u study the prerequirments then i will tell u , how
to interpret all theseinformation into yours work ,
i will give u the adresses of protein data banks, and same softwares
and few instructions to make your work easy

fayyaz
MSc hons biochemistry
BSc hons biochemistry
Institue of biochemistry and biotechnolgy
university of the punjab
lahore , pakistan
+923004474407

[William Knight]

I agree with fayyaz that there is a lot of background material that is
needed by someone in computer science who would like to get into
computational biology. Once you get the background, then you can best
learn about protein folding through scientific journals such as the
Journal of Computational Chemistry. However, to get started, I would
reccommend an introductory book on molecular modeling such as
"Molecular Modeling and Simulation", by T. Schlick. It has a good
introduction to molecular mechanics and molecular dynamics, but it
doesn't cover ab initio methods. However, the simpler molecular
mechanics approach might be a better way for you to get started because
it could give you a more intuitive feel for what is going on with
molecules. Starting off with the more rigourous QM methods might be
biting off more than you can swallow. Buying an introductory book may
cost you some money up front, but it can save you a lot of time by
giving some clear explanations of the basic concepts, which is
sometimes harder to find from just reading journal articles.