PredictProtein Google Group

How to compute SOV?

wanglj...@gmail.com (lijun wang) — Mon, 23 Nov 2009 09:04:11 UT

Hi,all
I am working on protein secondary structure prediction, and i want to
compute SOV(the segmant overlap measurement), But I couldn't find how to
compute it?
Pls help me
Thanks all!

query

ibi2008...@iiita.ac.in (VANDHANA) — Sat, 21 Nov 2009 14:14:53 UT

Hello,

Is it possible to
check docking interaction of a mineral (containing metal ions such as
Ca,P,O,H) with a protein? If yes, kindly suggest how.

Thanks,
Regards,

Determining absolute protein concentration

j.g.m...@durham.ac.uk (MINA J.G.M.) — Fri, 20 Nov 2009 16:15:17 UT

Dear All,

I am working with a trans membrane protein in the form of microsomal membranes preparation.
I can determine the total protein concentration using Lowry Method.
I also have a specific fluoreometric enzyme assay for my protein.

Is there any kinetic/mathematical equation which I can use based on my specific assay to detemine the actual concentration of my active protein in MOLAR CONCENTRATION (c.f titration of the active site)?

structure validation to choose best structure

ibi2008...@iiita.ac.in (VANDHANA) — Sat, 14 Nov 2009 04:57:55 UT

Hello,
Does anyone know the method to predict the best model of
all mod3ls obtained on basis of energy. Kindly respond.
Thank
you

PDB ids for proteins under SCOP family

mystic2psy...@gmail.com (PRASAD BAJAJ) — Sat, 14 Nov 2009 02:31:07 UT

hi
i am new to this field.
so if anyone can tell me how i can get PDB ids for proteins under same SCOP
family and wanted to know same for each family except doing it manually.
i would be really thankful if anyone can help me.
Thanks

enzyme-protein proteolysis

ibi2008...@iiita.ac.in (VANDHANA) — Sat, 07 Nov 2009 02:36:30 UT

Hello all,
Is there any method by which we can show the
interaction of a proteolytic enzyme with a protein insilico ? Kindly do
tell.
Thanks,
Regards

SPDBV script

vikrant_n...@iari.res.in — Fri, 06 Nov 2009 03:57:21 UT

Dear All
I am working on solvent accessable residues on protein surface. I am able
select these residues using SPDBV. Now my problem is that I want a SPDBV
script for that, so that the selected residues with their postion in the
protein sequence can be saved in an output file.
Thanks

Mineral 3D structure database

ibi2008...@iiita.ac.in (VANDHANA) — Mon, 02 Nov 2009 13:12:54 UT

Hello all,
Is there any mineral 3D structure database
from which the coordinates can be obtained as a .mol or .pbd file ? Kindly
respond soon.
Regards,
Vandhana

protein tertiary structure prediction

swatimishr...@gmail.com (swati mishra) — Mon, 02 Nov 2009 10:39:17 UT

Is there any software to predict protein tertiary structure..like the
3D kind,that is available with the PDB site???..from the linear amino
acid sequences....???

hello everybody

suneh...@gmail.com (suneha upadhyay) — Mon, 26 Oct 2009 14:34:01 UT

hello everybody
I am looking for the website providing free domain prediction if only amino
acid sequense of the protein is known.
could anybody help me with it...
thanks a lot
Suneha Upadhyay
Ph.D (Biochemistry)
New Delhi

trasduction mRNA and RNA to aminoacid sequence

fredymetalhe...@gmail.com (realrocker) — Tue, 20 Oct 2009 12:43:51 UT

good day for all, i just want to know names of servers that makes the
trasduction for a sequence of mRNA and RNA

thanks for all

Prediction of side chains in proteins

shahriar.a...@gmail.com (Shahriar) — Sun, 18 Oct 2009 14:44:36 UT

Hi everybody,
I am looking for some great websites providing free
prediction of amino acids side chain.
Could anybody help me with it?
Thanks a lot.
Shahriar

Autodock

eslami_g2...@yahoo.com (gilda eslami) — Sat, 17 Oct 2009 11:59:23 UT

Hi
I would like to use Autodock but Unfortunately, I do not know any about.
Is there anybody know any about Autodock?
I am looking forward to hearing from you soon
regards
Gilda

how to understand the molecular dynamics and simulation of protein in discovery studio

abhishektyagi...@gmail.com (Abhishek Tyagi) — Fri, 16 Oct 2009 11:49:26 UT

i wan to know how to do molecular dynamics and simulation of protein
using Discovery Studio, on the bases of femtoseconds and nenoseconds
level. while using the software some links are given to run simulation
but how to understand the process behind the software and how to
corelate the results.

Hydrogen exchange rates

christoph.go...@uni-graz.at (Christoph Göbl) — Mon, 12 Oct 2009 14:33:59 UT

Dear colleges,
I am searching for a program that can calculate roughly hydrogen exchange rates (from amides) from a .pdb file.
I have experimental NMR data and I'm just curious if a software like this exists?
Thanks in advance,
best regards
Christoph