Re: [ccp4bb] does 12 A diffraction worth optimization

[Debanu Das]

Hi Natalia,

One rule of thumb in crystallography: anything is possible!

We have seen many cases of individual proteins (or their complexes with small 
molecules, proteins or nucleic acids) where we ended up with structures 
starting from low resolution initial crystals. So before taking a decision, I 
would suggest considering the following:

a) How many of these crystals did you screen? If only a very few, you should 
try more.
b) How big are the crystals?
c) Are these diffraction results from home source or synchrotron?
d) Long long were crystals allowed to grow before you harvested?
e) Did you try a few different cryos to verify they don't show any difference 
despite no visible deterioration?
f) How long does it take to harvest and place in cryo? How long are you soaking 
in cryo before freezing?
g) Are there issues in crystals being stuck in the well or cover slide and you 
have to apply force to dislodge?
h) Are you doing single step cryo or multi-step in increasing amounts of cryo?
i) Did you try growing crystals at different temp (4C and 20C?) or growing with 
cryo?
j) Do you know what the construct of this apo protein can diffract to?

If you have tried all the above, you can then consider trying different DNA 
lengths and blunt-end vs overhangs or different protein constructs.

Happy to discuss more about the specific case.

Best,
Debanu 
Accelero Biostructures 


> On Fri, Mar 2, 2018 at 5:34 PM, Natalia O  wrote:
> Hello,
> 
> 
> 
> I got crystals of protein-nucleic acid complex, rod-shape, reproducible,
> don’t visibly get damaged upon freezing; however they gave diffraction only
> to about 12 A. I tried several crystals. My question is whether such
> crystals worth optimization. Clearly a 4A diffracting crystal could
> potentially be optimized to 3 – 2.5A, but if the diffraction that I am
> getting now is 12A it could suggest that the system is so flexible that
> getting to 3A with this crystal form is not possible at all. I just wonder
> if there is any statistics or a rule of thumb about what initial diffraction
> worth optimization?
> 
> 
> Thank you!
> 
> -Natalia
> 
> 

[ccp4bb] does 12 A diffraction worth optimization

[Natalia O]

Hello,



I got crystals of protein-nucleic acid complex, rod-shape, reproducible,
don’t visibly get damaged upon freezing; however they gave diffraction only
to about 12 A. I tried several crystals. My question is whether such
crystals worth optimization. Clearly a 4A diffracting crystal could
potentially be optimized to 3 – 2.5A, but if the diffraction that I am
getting now is 12A it could suggest that the system is so flexible that
getting to 3A with this crystal form is not possible at all. I just wonder
if there is any statistics or a rule of thumb about what initial
diffraction worth optimization?


Thank you!

-Natalia

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

[nathanielclar5 .]

I misstated something earlier, and I would like to correct the record:

Magic Eye books instruct you on using wall-eyed stereo (with excellent
instructions, highly recommended!).  Currently (with computer monitors) I
find cross-eyed much easier (and I think more people should try it).
Thanks,
Nat



On Fri, Mar 2, 2018 at 1:41 PM, nathanielclar5 . 
wrote:

> To learn how to cross eyes, just hold you index fingers strait up, ~12-18
> inches from your eyes, and cross your eyes until the two fingers overlap to
> form a third finger in the middle.  Then practice holding your eyes there.
> You can also practice with ceiling tiles, floor tiles, anything that
> repeats,  Just cross your eyes until adjacent things overlap, and that's
> it.
>
> It's best to start with a small image, like a small (4"x6") Coot window
> with a simple object like a sulfate ion displayed.  Once you get the hang
> if it, you can use larger windows.  It's totally worth learning to see in
> cross-eye stereo if you look at structures.
>
> I learned to see cross-eye as a kid from the 'Magic Eye' books.  I'm sure
> there are great tutorials and examples on the web.
> Nat
>
> On Fri, Mar 2, 2018 at 11:39 AM, Xiao Lei  wrote:
>
>> I never learn how to "cross eye", I may need to check if some video
>> instruction online...
>>
>>
> On Fri, Mar 2, 2018 at 11:28 AM, nathanielclar5 . <
> nathanielcl...@gmail.com> wrote:
>
>> You already have stereo built in, just turn on 'cross eyed stereo' and
>> learn to cross your eyes!  It's brighter than any 3d monitor, requires no
>> hardware, and no, it won't hurt your eyes (even for hours at a time)
>>
>> Nat
>>
>> On Fri, Mar 2, 2018 at 11:01 AM, Jim Fairman 
>> wrote:
>>
>>> Daniel,
>>>
>>> To best of my knowledge, options for 3d stereo on Mac are limited to
>>> Zalman:  https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php
>>> /Zalman_Stereo
>>>
>>> If you're willing to go to Linux or Windows, you can do an Nvidia Quadro
>>> Card with a 120 or 144Hz monitor with a 3D Vision glasses kit.
>>>
>>> Cheers, Jim
>>>
>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>>> Jim Fairman
>>> Principal Scientist II
>>> Roche Sequencing Solutions
>>> 2841 Scott Blvd
>>> 
>>> Santa Clara, CA 95050
>>> 
>>> fairman@gmail.com jim.fair...@roche.com
>>>
>>>
>>>
>>>
>>> 
>>> --
>>> Jim Fairman
>>> C: 1-240-479-6575 <(240)%20479-6575>
>>>
>>> On Fri, Mar 2, 2018 at 8:24 AM, Daniel M. Himmel, Ph. D. <
>>> danielmhim...@gmail.com> wrote:
>>>
 I'm looking for some computer hardware advice.
 I have a MacBook Pro with a "Retina" screen and
 an Intel HD Graphics 4000 1536 MB graphics card,
 running OS X 10.11.16 ("El Capitan"), and I would
 like to view structures in 3-D in Coot.

 Which computer monitors and which 3-D glasses brands
 would allow me to view 3-D graphics in Coot?  Should I
 be going for dynamic 3-D glasses?

 -Daniel


>>>
>>
>

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

[wtempel]

Hi Nat,
could you be referring to side-by-side stereo in this (computer monitor)
use case?
http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node97.html
W.


On Fri, Mar 2, 2018 at 2:41 PM, nathanielclar5 . 
wrote:

> To learn how to cross eyes, just hold you index fingers strait up, ~12-18
> inches from your eyes, and cross your eyes until the two fingers overlap to
> form a third finger in the middle.  Then practice holding your eyes there.
> You can also practice with ceiling tiles, floor tiles, anything that
> repeats,  Just cross your eyes until adjacent things overlap, and that's
> it.
>
> It's best to start with a small image, like a small (4"x6") Coot window
> with a simple object like a sulfate ion displayed.  Once you get the hang
> if it, you can use larger windows.  It's totally worth learning to see in
> cross-eye stereo if you look at structures.
>
> I learned to see cross-eye as a kid from the 'Magic Eye' books.  I'm sure
> there are great tutorials and examples on the web.
> Nat
>
> On Fri, Mar 2, 2018 at 11:39 AM, Xiao Lei  wrote:
>
>> I never learn how to "cross eye", I may need to check if some video
>> instruction online...
>>
>>
> On Fri, Mar 2, 2018 at 11:28 AM, nathanielclar5 . <
> nathanielcl...@gmail.com> wrote:
>
>> You already have stereo built in, just turn on 'cross eyed stereo' and
>> learn to cross your eyes!  It's brighter than any 3d monitor, requires no
>> hardware, and no, it won't hurt your eyes (even for hours at a time)
>>
>> Nat
>>
>> On Fri, Mar 2, 2018 at 11:01 AM, Jim Fairman 
>> wrote:
>>
>>> Daniel,
>>>
>>> To best of my knowledge, options for 3d stereo on Mac are limited to
>>> Zalman:  https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php
>>> /Zalman_Stereo
>>>
>>> If you're willing to go to Linux or Windows, you can do an Nvidia Quadro
>>> Card with a 120 or 144Hz monitor with a 3D Vision glasses kit.
>>>
>>> Cheers, Jim
>>>
>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>>> Jim Fairman
>>> Principal Scientist II
>>> Roche Sequencing Solutions
>>> 2841 Scott Blvd
>>> 
>>> Santa Clara, CA 95050
>>> 
>>> fairman@gmail.com jim.fair...@roche.com
>>>
>>>
>>>
>>>
>>> 
>>> --
>>> Jim Fairman
>>> C: 1-240-479-6575 <(240)%20479-6575>
>>>
>>> On Fri, Mar 2, 2018 at 8:24 AM, Daniel M. Himmel, Ph. D. <
>>> danielmhim...@gmail.com> wrote:
>>>
 I'm looking for some computer hardware advice.
 I have a MacBook Pro with a "Retina" screen and
 an Intel HD Graphics 4000 1536 MB graphics card,
 running OS X 10.11.16 ("El Capitan"), and I would
 like to view structures in 3-D in Coot.

 Which computer monitors and which 3-D glasses brands
 would allow me to view 3-D graphics in Coot?  Should I
 be going for dynamic 3-D glasses?

 -Daniel


>>>
>>
>

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

[nathanielclar5 .]

To learn how to cross eyes, just hold you index fingers strait up, ~12-18
inches from your eyes, and cross your eyes until the two fingers overlap to
form a third finger in the middle.  Then practice holding your eyes there.
You can also practice with ceiling tiles, floor tiles, anything that
repeats,  Just cross your eyes until adjacent things overlap, and that's
it.

It's best to start with a small image, like a small (4"x6") Coot window
with a simple object like a sulfate ion displayed.  Once you get the hang
if it, you can use larger windows.  It's totally worth learning to see in
cross-eye stereo if you look at structures.

I learned to see cross-eye as a kid from the 'Magic Eye' books.  I'm sure
there are great tutorials and examples on the web.
Nat

On Fri, Mar 2, 2018 at 11:39 AM, Xiao Lei  wrote:

> I never learn how to "cross eye", I may need to check if some video
> instruction online...
>
>
On Fri, Mar 2, 2018 at 11:28 AM, nathanielclar5 . 
wrote:

> You already have stereo built in, just turn on 'cross eyed stereo' and
> learn to cross your eyes!  It's brighter than any 3d monitor, requires no
> hardware, and no, it won't hurt your eyes (even for hours at a time)
>
> Nat
>
> On Fri, Mar 2, 2018 at 11:01 AM, Jim Fairman 
> wrote:
>
>> Daniel,
>>
>> To best of my knowledge, options for 3d stereo on Mac are limited to
>> Zalman:  https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php
>> /Zalman_Stereo
>>
>> If you're willing to go to Linux or Windows, you can do an Nvidia Quadro
>> Card with a 120 or 144Hz monitor with a 3D Vision glasses kit.
>>
>> Cheers, Jim
>>
>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>> Jim Fairman
>> Principal Scientist II
>> Roche Sequencing Solutions
>> 2841 Scott Blvd
>> 
>> Santa Clara, CA 95050
>> 
>> fairman@gmail.com jim.fair...@roche.com
>>
>>
>>
>>
>> 
>> --
>> Jim Fairman
>> C: 1-240-479-6575 <(240)%20479-6575>
>>
>> On Fri, Mar 2, 2018 at 8:24 AM, Daniel M. Himmel, Ph. D. <
>> danielmhim...@gmail.com> wrote:
>>
>>> I'm looking for some computer hardware advice.
>>> I have a MacBook Pro with a "Retina" screen and
>>> an Intel HD Graphics 4000 1536 MB graphics card,
>>> running OS X 10.11.16 ("El Capitan"), and I would
>>> like to view structures in 3-D in Coot.
>>>
>>> Which computer monitors and which 3-D glasses brands
>>> would allow me to view 3-D graphics in Coot?  Should I
>>> be going for dynamic 3-D glasses?
>>>
>>> -Daniel
>>>
>>>
>>
>

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

[nathanielclar5 .]

You already have stereo built in, just turn on 'cross eyed stereo' and
learn to cross your eyes!  It's brighter than any 3d monitor, requires no
hardware, and no, it won't hurt your eyes (even for hours at a time)

Nat

On Fri, Mar 2, 2018 at 11:01 AM, Jim Fairman  wrote:

> Daniel,
>
> To best of my knowledge, options for 3d stereo on Mac are limited to
> Zalman:  https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.
> php/Zalman_Stereo
>
> If you're willing to go to Linux or Windows, you can do an Nvidia Quadro
> Card with a 120 or 144Hz monitor with a 3D Vision glasses kit.
>
> Cheers, Jim
>
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> Jim Fairman
> Principal Scientist II
> Roche Sequencing Solutions
> 2841 Scott Blvd
> 
> Santa Clara, CA 95050
> 
> fairman@gmail.com jim.fair...@roche.com
>
>
>
>
> --
> Jim Fairman
> C: 1-240-479-6575 <(240)%20479-6575>
>
> On Fri, Mar 2, 2018 at 8:24 AM, Daniel M. Himmel, Ph. D. <
> danielmhim...@gmail.com> wrote:
>
>> I'm looking for some computer hardware advice.
>> I have a MacBook Pro with a "Retina" screen and
>> an Intel HD Graphics 4000 1536 MB graphics card,
>> running OS X 10.11.16 ("El Capitan"), and I would
>> like to view structures in 3-D in Coot.
>>
>> Which computer monitors and which 3-D glasses brands
>> would allow me to view 3-D graphics in Coot?  Should I
>> be going for dynamic 3-D glasses?
>>
>> -Daniel
>>
>>
>

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

[Jim Fairman]

Daniel,

To best of my knowledge, options for 3d stereo on Mac are limited to
Zalman:
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Zalman_Stereo

If you're willing to go to Linux or Windows, you can do an Nvidia Quadro
Card with a 120 or 144Hz monitor with a 3D Vision glasses kit.

Cheers, Jim

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Jim Fairman
Principal Scientist II
Roche Sequencing Solutions
2841 Scott Blvd
Santa Clara, CA 95050
fairman@gmail.com jim.fair...@roche.com




--
Jim Fairman
C: 1-240-479-6575

On Fri, Mar 2, 2018 at 8:24 AM, Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:

> I'm looking for some computer hardware advice.
> I have a MacBook Pro with a "Retina" screen and
> an Intel HD Graphics 4000 1536 MB graphics card,
> running OS X 10.11.16 ("El Capitan"), and I would
> like to view structures in 3-D in Coot.
>
> Which computer monitors and which 3-D glasses brands
> would allow me to view 3-D graphics in Coot?  Should I
> be going for dynamic 3-D glasses?
>
> -Daniel
>
>

[ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

[Daniel M. Himmel, Ph. D.]

I'm looking for some computer hardware advice.
I have a MacBook Pro with a "Retina" screen and
an Intel HD Graphics 4000 1536 MB graphics card,
running OS X 10.11.16 ("El Capitan"), and I would
like to view structures in 3-D in Coot.

Which computer monitors and which 3-D glasses brands
would allow me to view 3-D graphics in Coot?  Should I
be going for dynamic 3-D glasses?

-Daniel

[ccp4bb] Positions in membrane protein structural biology

[Liz Carpenter]

Hi all,
We have two positions available at the Structural Genomics Consortium (SGC) in 
Oxford, a post-doc and a technician position, to work with Liz Carpenter's 
group on human integral membrane protein structural biology.

The post-doc position will involve running and optimizing our pipeline for 
membrane protein production, developing novel methods for making membrane 
proteins, as well as helping with structure determination and the study of 
protein function.
The technician position will support this post-doc and other members of the 
group in tissue culture, protein production and crystallisation.

The SGC in Oxford is well equipped for membrane protein structural biology and 
has solved more than 10 structures of human membrane proteins, many of which 
are involved in genetic disease.

If you are interested in either of these positions, please follow the links 
below:

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.display_form?p_company=10_internal_external=E_display_in_irish=N_process_type=_applicant_no=_form_profile_detail=_display_apply_ind=Y_refresh_search=Y_recruitment_id=133634

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.display_form?p_company=10_internal_external=E_display_in_irish=N_process_type=_applicant_no=_form_profile_detail=_display_apply_ind=Y_refresh_search=Y_recruitment_id=133540


Also please feel free to contact Liz Carpenter 
(liz.carpen...@sgc.ox.ac.uk) for informal 
discussion of the positions.

With best wishes,
Liz

Re: [ccp4bb] phenix refinement about cis-proline

[Philippe BENAS]

Dear Niegel,
May be Shijun had to cancel his registration to the PhenixBB as I had to do 
since 2015 due to "too many bounces" whatever the email address I used, 
professional, yahoo or gmail ?... Has this been fixed at some point ?

All the best,Philippe
 Philippe BENAS, Ph.D.

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Nigel Moriarty 
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Vendredi 2 mars 2018 8h25
 Objet : Re: [ccp4bb] phenix refinement about cis-proline
  


Shijun
You can ask all the questions you like about Phenix on PhenixBB. However, to 
answer your question, you can set all peptides to trans using
apply_all_trans=True
or more specific control using
apply_cis_trans_specification {    cis_trans_mod = cis *trans    
residue_selection = None  }
to any number of peptides.
Cheers
Nigel
---Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence 
Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : nwmoria...@lbl.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
On Thu, Mar 1, 2018 at 10:58 PM, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

Dear all    I am refining a structure which has cis-Pro and trans-Pro, the 
tans-Pro is gone when I set the "threshold degrees for cis-peptide " from 
default 45 to 65, but still has cis-Pro. While no significant change when I set 
it to 15. My question is how to set in phenix refinement to clear the Pro 
residues in cis- or trans- conformations.Best Regards shijun  



   

Re: [ccp4bb] Protein-Protein Interaction prediction

[Jared Sampson]

Hi Sayli - 

PrePPI may be helpful if you're interested in interactions among human proteins.

http://honig.c2b2.columbia.edu/preppi/

Cheers,
Jared

Re: [ccp4bb] validating a homlology model

[Joana Pereira]

Dear Careina,

Your message is a bit confusing... Which kind of validation are you 
referring to? Do you want to check the geometrical quality of the 
backbone and side-chain rotamers, or do you want to evaluate how likely 
it is that the fold proposed by homology actually represents the fold of 
your protein?


Best,

Joana

--
Postdoctoral Researcher
Department of Protein Evolution

Max Planck Institute for Developmental Biology
Max-Planck-Ring 5
72076 Tübingen
GERMANY

On 02.03.2018 13:09, Tristan Croll wrote:

Hi Careina,

This is a little confusing. A homology model *is* a set of coordinates 
(usually provided as a PDB file by most servers/packages I know of). 
The MolProbity site at http://molprobity.biochem.duke.edu/ allows you 
to upload your own PDB file, and in my experience is quite forgiving 
regarding format.


Hope this helps,

Tristan

On 2018-03-02 11:44, Careina Edgooms wrote:

Dear all

What programs are best used for validate homology models? I know of
molprobity but if there are no coordinates I cannot use it. Is there a
way to use such programs with homology models?

Also I wish to use pdbepisa for to charaterise dimer interface but
again for homology model this cannot be done as there is no PDB model.
Does anybody know way to use PISA software on my own model that is not
deposited in PDB?

Thank you in advance
Careina

Re: [ccp4bb] validating a homlology model

[Tristan Croll]

Hi Careina,

This is a little confusing. A homology model *is* a set of coordinates 
(usually provided as a PDB file by most servers/packages I know of). The 
MolProbity site at http://molprobity.biochem.duke.edu/ allows you to 
upload your own PDB file, and in my experience is quite forgiving 
regarding format.


Hope this helps,

Tristan

On 2018-03-02 11:44, Careina Edgooms wrote:

Dear all

What programs are best used for validate homology models? I know of
molprobity but if there are no coordinates I cannot use it. Is there a
way to use such programs with homology models?

Also I wish to use pdbepisa for to charaterise dimer interface but
again for homology model this cannot be done as there is no PDB model.
Does anybody know way to use PISA software on my own model that is not
deposited in PDB?

Thank you in advance
Careina

Re: [ccp4bb] Protein-Protein Interaction prediction

[Dipak Patil]

Dear Sayli,

I have used cluspro in past:

https://cluspro.bu.edu/publications.php


Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda
S. The ClusPro web server for protein-protein docking. *Nature Protocols.*2017
Feb;12(2):255-278

Best,
Dipak



On Fri, Mar 2, 2018 at 3:28 AM, Daniel Rigden 
wrote:

> Dear Sayli
>
> Here are some options from Table 10.1 of this book chapter
>
> https://link.springer.com/chapter/10.1007/978-94-024-1069-3_10
> cons-PPISP
>
> Uses sequence profiles and solvent accessibility for residues and their
> neighbours
>
> http://pipe.scs.fsu.edu/ppisp.html
>
> Zhou and Shan (2001
> )
>
> meta-PPISP
>
> Metaserver using cons-PPISP, PINUP and Promate predictions
>
> http://pipe.scs.fsu.edu/meta-ppisp.html
>
> Qin and Zhou (2007
> )
>
> CPORT
>
> Consensus prediction from six different methods
>
> http://haddock.science.uu.nl/services/CPORT
>
> de Vries and Bonvin (2011
> )
>
> PRISE
>
> Atomic composition, residue type and solvent exposure of a central surface
> residue plus its neighbours
>
> http://prise.cs.iastate.edu/index.py
>
> Jordan et al. (2012
> )
>
> VORFFIP
>
> Considers a variety of structural, energetic, evolutionary and
> crystallographic parameters
>
> http://www.bioinsilico.org/VORFFIP
>
> Segura et al. (2011
> )
>
>
> i
>
>
> I don't know if they are all still functional: unhappily there tends to be
> quite a high turnover of such servers
>
> Best wishes
>
> Daniel
>
>
> On 02/03/18 07:47, Sayli Dalal wrote:
>
> Dear all,
>
> Can anyone help me with a web server  or method for prediction of
> interfaces for protein-protein interaction?
>
> Thanks and best regards,
>
> Sayli Dalal
> Post-Doctoral Fellow
> Dept. of Biophysics
> NIMHANS
>
>
>
>
> --
> Dr Daniel John Rigden Tel:(+44) 151 795 4467 
> <+44%20151%20795%204467>
> Institute of Integrative Biology  FAX:(+44) 151 795 4406 
> <+44%20151%20795%204406>
> Room 101, Biosciences Building
> University of Liverpool   http://pcwww.liverpool.ac.uk/~drigden/
> Crown St.,
> Liverpool L69 7ZB, U.K.
>
>


-- 

Dr. Dipak N. Patil

Department of Neuroscience

The Scripps Research Institute

130 Scripps Way, 3C2

Jupiter, Florida 33458

[ccp4bb] AW: [ccp4bb] validating a homlology model

[Herman . Schreuder]

Dear Careina,

If you do not have coordinates, what do you have then? A sequence alignment? In 
that case you can look at the %identity and %homology to see how well the known 
structure fits the unknown structure.

If you do have coordinates in some other format generated by some modeling 
software, you have to convert these coordinates into pdb format. Most modeling 
program do have a “save as” or “export” option to generate a file in pdb 
format. If that fails, there are also all kind of format converting programs, 
but then you need to tell us the format you have right now.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Careina 
Edgooms
Gesendet: Freitag, 2. März 2018 12:44
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] validating a homlology model

Dear all

What programs are best used for validate homology models? I know of molprobity 
but if there are no coordinates I cannot use it. Is there a way to use such 
programs with homology models?

Also I wish to use pdbepisa for to charaterise dimer interface but again for 
homology model this cannot be done as there is no PDB model. Does anybody know 
way to use PISA software on my own model that is not deposited in PDB?

Thank you in advance
Careina

Re: [ccp4bb] validating a homlology model

[Paul Emsley]

On 02/03/2018 11:44, Careina Edgooms wrote:



What programs are best used for validate homology models? I know of molprobity but if there are no 
coordinates I cannot use it. Is there a way to use such programs with homology models?


Also I wish to use pdbepisa for to charaterise dimer interface but again for homology model this cannot be 
done as there is no PDB model. Does anybody know way to use PISA software on my own model that is not 
deposited in PDB?
Answers to your questions depend on your answer to this one: What is a homology model? Along with that, we 
might also ask: which software (if any) might you use to create a homology model?

[ccp4bb] validating a homlology model

[Careina Edgooms]

Dear all
What programs are best used for validate homology models? I know of molprobity 
but if there are no coordinates I cannot use it. Is there a way to use such 
programs with homology models?
Also I wish to use pdbepisa for to charaterise dimer interface but again for 
homology model this cannot be done as there is no PDB model. Does anybody know 
way to use PISA software on my own model that is not deposited in PDB?
Thank you in advanceCareina

Re: [ccp4bb] Protein-Protein Interaction prediction

[Daniel Rigden]

Dear Sayli

Here are some options from Table 10.1 of this book chapter

https://link.springer.com/chapter/10.1007/978-94-024-1069-3_10

cons-PPISP


Uses sequence profiles and solvent accessibility for residues and their 
neighbours




http://pipe.scs.fsu.edu/ppisp.html



Zhou and Shan (2001 
)


meta-PPISP



Metaserver using cons-PPISP, PINUP and Promate predictions



http://pipe.scs.fsu.edu/meta-ppisp.html



Qin and Zhou (2007 
)


CPORT



Consensus prediction from six different methods



http://haddock.science.uu.nl/services/CPORT



de Vries and Bonvin (2011 
)


PRISE



Atomic composition, residue type and solvent exposure of a central 
surface residue plus its neighbours




http://prise.cs.iastate.edu/index.py



Jordan et al. (2012 
)


VORFFIP



Considers a variety of structural, energetic, evolutionary and 
crystallographic parameters




http://www.bioinsilico.org/VORFFIP



Segura et al. (2011 
)





i



I don't know if they are all still functional: unhappily there tends to 
be quite a high turnover of such servers


Best wishes

Daniel

On 02/03/18 07:47, Sayli Dalal wrote:

Dear all,

Can anyone help me with a web server  or method for prediction of 
interfaces for protein-protein interaction?


Thanks and best regards,

Sayli Dalal
Post-Doctoral Fellow
Dept. of Biophysics
NIMHANS





--
Dr Daniel John Rigden Tel:(+44) 151 795 4467
Institute of Integrative Biology  FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool   http://pcwww.liverpool.ac.uk/~drigden/
Crown St.,
Liverpool L69 7ZB, U.K.