Subject: Protein structures

From: "Victor Anisimov" <[email-masked]>
Date: Mon, 28 May 2001 13:23:37 +0200

Dear netters,

Can someone advise me on the following topic:

Applying quantum chemical calculations to proteins I always
spend a lot of my time on mechanical preliminary purification
of the protein structures setting hydrogen atoms in proper positions
and checking the structure errors.

The software that can automate this process is usually not
enough reliable and requires a posteriori expert's check. The
manual correction is tremendously impractical for hundreds of
proteins with thousands of residues that I need to submit for QM
calculation.

Could you please share with me your experience what software you
consider as the most trustworthy or may be there is some
free or commercially available database of proteins with correct
hydrogen atoms already assigned. What would be your normal
procedure if you would need to submit 50000 atoms' protein for
QM calculation taking the structure from the PDB database?

My second question is related to protein structure correction
feature of graphical applications that goes beyond adding
hydrogen atoms.
There are many graphical applications that can advise a user to
correct some part of the molecule. To best of my knowledge all
of them are based on the Lewis structure rules. As PDB structures
not always obeying Lewis principles and valence rules the result
of the automatic correction is not reliable enough.

Could you please recommend me a software free or commercial
if it exists that can safely repair protein structure or can check it
and graphically select those parts of the protein that require
human expertise for correction. Once the user qualified the fragment
as valid the next time check should not suggest this fragment for
correction.

Thanks for your help,
Victor.

==================================================
Victor Anisimov, PhD,
Senior Software Researcher - Computational Chemist
FQS Poland, a Fujitsu company
ul. Starowislna 13-15, 31-038 Krakow, Poland
Email: [email-masked]
Tel.(+48 12) 429-4345  Fax(+48 12) 429-6124
==================================================

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From: Lev Gorenstein <[email-masked]>
Date: Mon, 28 May 2001 21:05:41 -0500

Dear netters,

On Mon, 28 May 2001, Victor Anisimov wrote:

VA> What would be your normal procedure if you would need to
VA> submit 50000 atoms' protein for QM calculation

Which made me think of a question: what are current "limits" (due
to RAM/performance/time requirements/cost/etc.) for QM calculations
of large molecules?  What's the largest peptide that can be dealt
with on an ab initio level (insert your favorite basis set here) in
a reasonable time?  What's the similar state of the art protein for
semiempirical methods?  And, for comparison sake, what's the state
of the art for molecular mechanics?

Can anyone suggest any references or data for such comparison?

Regards,
	Lev

-- 
Daddy, why doesn't this magnet pick up this floppy disk?