Dear Amit,
I don’t think that PROCHECK is the right tool for assessing the quality of a
comparative model. It was revolutionary in its time, but the criteria it looks
at can mostly be satisfied by energy minimisation even of an incorrect model,
especially if you don’t have to simultaneously sa
Hi All,
I am trying to generate a model using comparative modeling. Can
anybody suggest the quality of the model based on procheck summary.
+--<<< P R O C H E C K S U M M A R Y >>>--+
|
Have you tried with Interactome3D?
http://interactome3d.irbbarcelona.org
Best,
Roberto
: [ccp4bb] homology modeling of dimeric proteins
Dear All,
Could annyone please suggest me any program or server that can build homology
based models of dimeric/oligomeric proteins? Previously I have used many
software/servers which can build the monomer of my target proteins but not the
dimers
Dear All,
Could annyone please suggest me any program or server that can build
homology based models of dimeric/oligomeric proteins? Previously I have
used many software/servers which can build the monomer of my target
proteins but not the dimers. Self docking of homology based monomer is not
work
Dear Paul!
you might want to have a look at http://salilab.org/modeller/ . The
stand alone version is free for academia.
Christian
___
Dr. Christian Rausch
Lehrstuhl für Biologische Chemie
Technische Universität München, Germany
On Thu, Aug 26, 2010 at 12:03 AM, Paul Kraft wrote:
>
> Hello,
>
Hello,
I've been using an the on-line homology modeling program Jigsaw-3D, and would
like to run it on my own Linux box, but it requires CHARM, which I am
unvailable to get because I am currently looking for a faculty position... does
anyone know of an open source energy minimization program th
A metaserver such as bioinfobank is helpful if your sequence is not
super-secret, especially if one is not an experienced modeller.
http://meta.bioinfo.pl/submit_wizard.pl
It submits your sequence to a range of sequence-based and threading-
based servers. Models (c-alpha, built with modell
On 12:08 Tue 05 May , Anastassis Perrakis wrote:
> Modeller is indeed an excellent program (so are some others) but,
> without being an expert, I was told some time ago and I am still under
> the impression, that homology modeling with 20% identity (and many
> insertions and deletions as
Hi,
With 20% identity the main problem is the sequence alignment. Usually
programs that based only sequence data are not enough in such cases
and you need to add additional terms to get the "correct" structure
(e.g. threading). You can see list of such programs in our site
http://bip.weiz
Try Phyre (http://www.sbg.bio.ic.ac.uk/phyre/), it worked rather well for
some of my projects with very low sequence similarity.
Peter
On Tue, 5 May 2009 12:08:04 +0300, Anastassis Perrakis
wrote:
> Modeller is indeed an excellent program (so are some others) but,
> without being an expert, I
Modeller is indeed an excellent program (so are some others) but,
without being an expert, I was told some time ago and I am still under
the impression, that homology modeling with 20% identity (and many
insertions and deletions as you point out) is a dark art. Being able
to suggest the ide
Hi Rui
Very easy to use is EsyPred3D :
http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/
Also good performance server is 3d-JIGSAW :
http://bmm.cancerresearchuk.org/~3djigsaw/
Hope it helps
Cheers
Francisco
> Hi, All
> Suppose I have two proteins A and B, they are structurally
I would recommend Modeller
http://www.salilab.org/modeller/
Wai
Suppose I have two proteins A and B, they are structurally homologous,
however the sequence identity is only about 20%. A has crystal
structure available, so if I want to model protein B, what's the best
way to do it? I don't thin
Hi, All
Suppose I have two proteins A and B, they are structurally homologous,
however the sequence identity is only about 20%. A has crystal structure
available, so if I want to model protein B, what's the best way to do it? I
don't think I can just thread the sequence of B to A structure because
Dear Anagha,
just a guess...
I'm not sure I understood you properly, but you are only trying to
make a model of a solved protein which will lack 3-4 amino acids in a
loop... therefore, why not using a modeling soft, such as Coot,
remove the amino acids, and do one run of "Regularize Zone"?
Have you tried Modeller ?
-Sid.
On 2/28/07, anagha gupta <[EMAIL PROTECTED]> wrote:
Hi CCP4 community!
I have constructed a homology model of a deletion variant of a protein whose
structure has already been solved. These deletions are 3-4 amino acid in
length and are in a loop that connects tw
Hi CCP4 community!
I have constructed a homology model of a deletion variant of a protein whose
structure has already been solved. These deletions are 3-4 amino acid in
length and are in a loop that connects two helices. The model structures
look good with respect to bond lengths in the aforeme
18 matches
Mail list logo
