Re: [ccp4bb] Searching Sequence Motif

[Joana Pereira]

Hi,

You can also use PatternSearch in the MPI toolkit 
(https://toolkit.tuebingen.mpg.de/tools/patsearch 
<https://toolkit.tuebingen.mpg.de/tools/patsearch>). You can build the motif 
using the Prosite grammar or as a regular expression, and select the E coli 
proteome or the PDB as the search database.
I hope that helps :)

Best,
Joana

Dr. Joana Pereira | Postdoctoral fellow | Schwede group, Computational 
Structural Biology | Biozentrum, University of Basel
Klingelbergstr. 61, CH-4056 Basel |  Email: joana.pere...@unibas.ch 
<mailto:joana.pere...@unibas.ch> | www.biozentrum.unibas.ch 
<http://www.biozentrum.unibas.ch/>


> On 5. Sep 2021, at 17:23, Cryo EM  wrote:
> 
> Hi all,
> 
> I want to search NCBI/PDB for all E.coli proteins with a specific sequence 
> motif.
> Is there any server/software in which I can search and display all the 
> proteins in E.coli with this specific sequence motif?
> Suggestions are highly appreciated.
> 
> Thanks!
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
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Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

[Joana Pereira]

Hi everybody,


As one of the persons playing with the CASP14 data before all news came 
out, I can answer some of the questions raised in this thread.



- "Does anyone know how AlphaFold performs on sequences with little 
conservation?"


One of the things we looked at was how the accuracy of the models was 
dependent on the Neff (number of effective sequences, relates to how 
deep alignments are for that sequence and, thus, to the number of 
homologs and the conservation of the sequence). What we could see is 
that, basically, in CASP14 it does not anymore and that (near-)singleton 
sequences could be modeled with a pretty good accuracy.



- "It would be interesting to know how it performs with structures of 
new or uncertain fold."


It does pretty well! Similarly to the Neff relationship, we also see a 
basically flat line at a GDT of 70-80 at any level of target difficulty. 
Of course the accuracy is slightly higher for easy targets (those for 
which there are templates in the PDB), but to have a GDT of around 70 in 
Free-Modelling, hard targets, is quite impressive.



- "I don't think they have all the side chain placement so perfect as to 
be able to predict the fold _and_ how a compound or another protein binds"


Yap, sidechains remain the poorest modeled parts. Still, those modeled 
by AlphaFold were the closest to the "reality" of the target...



- "I'm curious how well AlphaFold would do on an*Intrinsically 
Disordered Protein (IDP)*"


Oh yes, that is a super good point and I have been thinking about it 
too. Maybe one should start throwing some IDPs into CASP too :) There's 
the CAID experiment but, on its current state, AlphaFold would not be 
possible to test.



Best wishes

Joana


---

Dr. Joana Pereira
Postdoctoral Researcher
Department of Protein Evolution

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



On 03.12.20 23:46, Reza Khayat wrote:


​Does anyone know how AlphaFold performs on sequences with little 
conservation? Virus and phage proteins are like this. Their structures 
are homologous, but sequence identity can be less than 10%.



Reza


Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031

*From:* CCP4 bulletin board  on behalf of 
Anastassis Perrakis 

*Sent:* Thursday, December 3, 2020 5:31 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [EXTERNAL] Re: [ccp4bb] AlphaFold: more thinking and less 
pipetting (?)
AlphaFold - or similar ideas that will surface up sooner or later - 
will beyond doubt have major impact. The accuracy it demonstrated 
compared to others is excellent.


“Our” target (T1068) that was not solvable by MR with the homologous 
search structure or a homology model (it was phased with Archimboldo, 
rather easily), is easily solvable with the AlphaFold model as a 
search model. In PHASER I get Rotation Z-score 17.9, translation 
Z-score 26.0, using defaults.



imho what remains to be seen is:

a. how and when will a prediction server be available?
b. even if training needs computing that will surely unaccessible to 
most, will there be code that can be installed in a “reasonable” 
number of GPUs and how fast will it be?
c. how do model quality metrics (that do not compared with the known 
answer) correlate with the expected RMSD? AlphaFold, no matter how 
impressive, still gets things wrong.
c. will the AI efforts now gear to ligand (fragment?) prediction with 
similarly impressive performance?


Exciting times.

A.




On 3 Dec 2020, at 21:55, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk 
<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>> wrote:


Hello. A quick look suggests that a lot of the test structures were 
solved by phaser or molrep, suggesting it is a very welcome 
improvement on homology modelling. It would be interesting to know 
how it performs with structures of new or uncertain fold, if there 
are any left these days. Without resorting to jokes about artificial 
intelligence, I couldn't make that out from the CASP14 website or the 
many excellent articles that have appeared. Best wishes, Jon Cooper.



Sent from ProtonMail mobile



 Original Message 
On 3 Dec 2020, 11:17, Isabel Garcia-Saez < isabel.gar...@ibs.fr 
<mailto:isabel.gar...@ibs.fr>> wrote:



Dear all,

Just commenting that after the stunning performance of AlphaFold
that uses AI from Google maybe some of us we could dedicate
ourselves to the noble art of gardening, baking, doing Chinese
Calligraphy, enjoying the clouds pass or everything together
(just in case I have already prepared my subscription to Netflix).

https://www.nature.com/articles/d41586-020-03348-4

<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_article

Re: [ccp4bb] Omega angles with molprobity

[Joana Pereira]

Dear all,

Many thanks for such a great and quick feedback! Indeed, I forgot to run 
molprobity.omegalyze without input, and I am bit ashamed of that *insert 
blushed emoji here*. But now I can do what I was looking for and I am very 
grateful for your input :)

Best wishes,
Joana


> On 4. Sep 2020, at 19:35, Nigel Moriarty  wrote:
> 
> Joana 
> 
> The developers of molprobity.omegalyze have tried to make their tool easy to 
> use and understand by providing lots of help if you type the command without 
> inputs. This is a common technique that command line tools employ to provide 
> documentation.
> 
> > molprobity.omegalyze
> usage: molprobity.omegalyze [-h] [--show-defaults [{0,1,2,3}]]
> [--attributes-level [{0,1,2,3}]] [--write-data]
> [--write-modified] [--write-all] [--overwrite]
> [--citations [{default,cell,iucr}]]
> [files [files ...]] [phil [phil ...]]
> 
> ---
> molprobity.omegalyze file.pdb [params.eff] [options ...]
> 
> Options:
> 
>   model=input_file  input PDB or mmCIF file
>   nontrans_only=Trueonly print nontrans residues (does not affect 
> kinemage)
>   text=True  verbose colon-delimited text output (default)
>   kinemage=FalseCreate kinemage markup (overrides text output)
>   help = False  Prints this help message if true
> 
>   text output is colon-delimited and follows the format:
> residue:type:omega:conformation
>   'residue' is a unique residue identifier
>   'type' is either proline or general case
>   'omega' is the calculated omega dihedral for the peptide between this
> residue and the preceeding residue
>   'conformation' is: cis for omega within 30 degrees of planar cis
>  trans for omega within 30 degrees of planar trans
>  twisted for omega not within 30 degrees of planar
> 
>   SUMMARY statistics provide:
> counts of cis prolines and twisted prolines relative to total prolines 
> with
>   measurable omega dihedrals across all chains
> counts of non-proline cis and twisted peptides relative to total 
> non-proline
>   peptides with measurable omega dihedrals across all chains
> 
>   Cis Prolines occur in ~5% of prolines (1 in 20) at high resolution
>   Non-Proline Cis residues occur in ~0.05% of residues (1 in 2000) and require
> clear support from experimental data or homology.
>   Twisted peptides are even less frequent and are highly suspect without
> high-resolution data.
> 
> Example:
> 
>   molprobity.omegalyze model=1ubq.pdb kinemage=True
> ---
> 
> positional arguments:
>   files Input file(s) (e.g. model.cif)
>   phil  Parameter(s) (e.g. d_min=2.0)
> 
> optional arguments:
>   -h, --helpshow this help message and exit
>   --show-defaults [{0,1,2,3}], --show_defaults [{0,1,2,3}]
> show default parameters with expert level (default=0)
>   --attributes-level [{0,1,2,3}], --attributes_level [{0,1,2,3}]
> show parameters with attributes (default=0)
>   --write-data, --write_data
> write DataManager PHIL parameters to file
> (omegalyze_data.eff)
>   --write-modified, --write_modified
> write modifed PHIL parameters to file
> (omegalyze_modified.eff)
>   --write-all, --write_all
> write all (modified + default + data) PHIL parameters
> to file (omegalyze_all.eff)
>   --overwrite   overwrite files, this overrides the output.overwrite
> PHIL parameter
>   --citations [{default,cell,iucr}]
> show citation(s) for program in different formats
> 
> ---
> For additional help, you can contact the developers at 
> cctb...@phenix-online.org <mailto:cctb...@phenix-online.org>
> or https://github.com/cctbx/cctbx_project 
> <https://github.com/cctbx/cctbx_project>
> Cheers
> 
> Nigel
> 
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
> Fax   : 510-486-5909   Web  : CCI.LBL.gov <http://cci.lbl.gov/>
> 
> On Fri, Sep 4, 2020 at 5:35 AM Tim Gruene  &l

Re: [ccp4bb] Omega angles with molprobity

[Joana Pereira]

Hi Robbie,

Thanks for the quick response :) That was my first try but it does not 
list me the angles.. see the output below:


Starting molprobity.omegalyze
on Fri Sep  4 12:00:35 2020 by jpereira
===

Processing files:
---

  Found model, .pdb

Processing PHIL parameters:
---

  No PHIL parameters found

Final processed PHIL parameters:
---
  data_manager {
    model {
  file = ".pdb"
    }
    default_model = ".pdb"
  }


Starting job
===
residues:type:omega:conformation:mc_bmax
SUMMARY: 0 cis prolines out of 5 PRO
SUMMARY: 0 twisted prolines out of 5 PRO
SUMMARY: 0 other cis residues out of 140 nonPRO
SUMMARY: 0 other twisted residues out of 140 nonPRO

===

What I would like to have is a per residue assignment of omega angles, 
as molprobity.ramanalyse does. Of course i could code it, but I was 
trying to avoid that ;)


Cheers,

Joana


On 04.09.20 11:45, Robbie Joosten wrote:

Hi Joana,

molprobity.omegalyze seems to do what you want. Just run it on the command 
prompt.

Cheers,
Robbie


-Original Message-
From: CCP4 bulletin board  On Behalf Of Joana
Pereira
Sent: Friday, September 4, 2020 11:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Omega angles with molprobity

Dear all,

Does anyone know which molprobity tool in ccp4/bin lists the omega angles
for each residue? I see Phenix provides a comprehensive validation based on
Molprobity and, from what I understand, lists the omega angles for each
residue. However, I am having troubles to find which molprobity tool
provides that info. Any idea?

Many thanks!

Best wishes

Joana Pereira

--
Postdoctoral Researcher
Department of Protein Evolution

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

###
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--
Postdoctoral Researcher
Department of Protein Evolution

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




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[ccp4bb] Omega angles with molprobity

[Joana Pereira]

Dear all,

Does anyone know which molprobity tool in ccp4/bin lists the omega 
angles for each residue? I see Phenix provides a comprehensive 
validation based on Molprobity and, from what I understand, lists the 
omega angles for each residue. However, I am having troubles to find 
which molprobity tool provides that info. Any idea?


Many thanks!

Best wishes

Joana Pereira

--
Postdoctoral Researcher
Department of Protein Evolution

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



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Re: [ccp4bb] cavities volume calculations

[Joana Pereira]

Hi Nathalie,

I think Caver tools can do that: https://caver.cz/index.php?sid=133 


Best wishes
Joana

> On 6. Jul 2020, at 15:39, Nathalie Colloc'h  wrote:
> 
> Hi everybody,
> 
> I am aware of programs which compute the volume of cavities and pockets.
> 
> However, I am looking for a program which can compute the volume around a 
> given point (given by its coordinates), and return also the information about 
> if it is an open surface pocket or an internal cavity.
> 
> Thanks a lot
> 
> Nathalie
> 
> 
> -- 
> Dr. Nathalie Colloc'h
> équipe CERVOxy
> ISTCT UMR 6030 -  CNRS - Université Caen-Normandie - CEA
> Centre Cyceron
> bd Becquerel
> 14074 Caen cedex
> France
> 33.2.31.47.01.32
> coll...@cyceron.fr
> http://www.istct.cyceron.fr/
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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[ccp4bb] [Off-topic] Job offer for a Postdoc position in Macromolecular Modelling and Design (MPI Dev. Biology)

[Joana Pereira]

Dear CCP4 community,

In case any of you is interested in Computational Structural Biology, Protein 
Evolution and Protein Design, and is looking for a postdoc position, I share 
with you a job advertisement for a
Postdoctoral Position in Macromolecular Modelling and Design at our department 
of Protein Evolution at the MPI for Developmental Biology. You can find more 
details on the attached file :)

Best regards,
Dr. Joana Pereira

Postdoctoral Researcher
Department of Protein Evolution

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



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<>

[ccp4bb] Off-topic: protein 2d diagrams

[Joana Pereira]

Dear CCP4 community,

I have seen many papers with detailed protein 2d diagrams like this one:


However, I can never find a reference for any tool that can compute such 
diagrams from a 3D structure. Do you know of any?

Many thanks and enjoy the warm weather!

Joana


—
Dr. Joana Pereira
Postdoctoral Researcher 
Department of Protein Evolution 

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


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[ccp4bb] Senior Postdoctoral Position on Cryo-EM in the Dep. for Protein Evolution at the MPI for Dev. Biology

[Joana Pereira]

Dear CCP4 colleagues,Our department is looking for a senior postdoc with experience on Cryo-EM to provide
the department with cutting-edge competence in protein structure determination with this method. The position is suitable to start an independent group and independent publication and grant
acquisition are encouraged. Please find more information on the attached file :) The deadline for application is the 15th of September 2018.All the best,Dr. Joana PereiraPostdoctoral Researcher Department of Protein Evolution Max Planck Institute for Developmental Biology Max-Planck-Ring 572076 Tübingen GERMANY

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<>
Begin forwarded message:From: "Karin Lehmann" Subject: Job offer for a Postdoc positionDate: 25. July 2018 at 10:54:57 CESTTo: Dear all,Please find attached a job advertisement for a Senior Postdoctoral Position in Protein Structure Determination.Best,Karin*Karin LehmannAssistant to Prof. Dr. Andrei LupasMax Planck Institute for Developmental BiologyMax-Planck-Ring 572076 Tuebingen/GermanyTel. +49-(0)7071-601340 Fax  +49-(0)7071-601352 e-mail: karin.lehm...@tuebingen.mpg.de

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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] Finding Homologs with Specific Residues Conserved

[Joana Pereira]

I am also not sure of what your goal is, but you can build a sequence profile 
for your sequence and use that profile as input instead of your sequence. You 
can do this by aligning a set of sequences homologous to your target sequence, 
and use that alignment as input for, for example, HMMER or HHPred. You can also 
let HMMER or HHPred build these profiles for you by giving your sequence as 
input and play with the parameters.

Best,

Dr. Joana Pereira
--
Postdoctoral Researcher
Department of Protein Evolution

Max Planck Institute for Developmental Biology
Spemannstraße 35
72076 Tübingen
GERMANY

> On 20 Dec 2017, at 18:35, Keller, Jacob <kell...@janelia.hhmi.org> wrote:
> 
> Dear Crystallographer-Bioinformaticians,
>  
> Is anyone aware of a way to tweak BLAST or similar software to be able to 
> specify certain residues to be absolutely required, e.g., active site 
> residues? I guess one can winnow broad-scale resuts with scripts, but it 
> would seem to be a pretty common type of thing to do, and might change 
> results slightly a la psi-BLAST.
>  
> All the best,
>  
> Jacob Keller
>  
> +
> Jacob Pearson Keller
> Research Scientist / Looger Lab
> HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> (571)209-4000 x3159
> +
>  
> The content of this email is confidential and intended for the recipient 
> specified in message only. It is strictly forbidden to share any part of this 
> message with any third party, without a written consent of the sender. If you 
> received this message by mistake, please reply to this message and follow 
> with its deletion, so that we can ensure such a mistake does not occur in the 
> future.

Re: [ccp4bb] secondary structure prediction

[Joana Pereira]

Dear Zheng,

There are some things you can try, which depend on the computational resources 
you have available and the time you want to wait. The best would be to try 
Rosetta ab initio modelling. Preferably, you would run Rosetta using your local 
installation but if you don’t have Rosetta installed, this can be annoying to 
do. You can also use the Rosie web server (the Rosetta web server), but it 
takes long time to compute. Other faster solutions for "ab initio" modelling 
would be Quark (in case your protein is short), I-tasser or RaptorX Contact 
Prediction web servers. I am very happy with the latter, I use it frequently 
when I don’t want to wait for Rosetta. You can also try homology modelling, but 
this would be less reliable when the few motifs you find do not overlap and do 
not cover the entire protein. Anyway, for homology modelling you can try , for 
example, Modeller after HHPred (you can do this using the MPI Bioinformatics 
toolkit) or RaptorX Structure Prediction.

I hope this helps you.

Best regards and good luck!

Dr. Joana Pereira
--
Postdoctoral Researcher
Department of Protein Evolution

Max Planck Institute for Developmental Biology
Spemannstraße 35
72076 Tübingen
GERMANY


> On 06 Dec 2017, at 15:14, zheng zhou <zhengzho...@gmail.com> wrote:
> 
> Dear CCP4 community,
> 
> Sorry for the off-topic question. I am trying to design constructs for
> structure studies. It only has a homolog structure in PDB with
> sequence identity ~20%. When I blast against PDB sequence, there are
> quite a few motif hits (30~40aa, identity 40~50%). Any prediction
> tools utilize this information?
> 
> Thanks for your advice in advance.
> 
> Best,
> 
> Zheng

Re: [ccp4bb] books to go

[Joana Pereira]

Hey,

Are you giving them away or selling them? ;)

Cheers

Joana Pereira
--
PhD student
Lamzin Group

EMBL Hamburg ℅ DESY
Notkestrasse 85
DE-22603 HAMBURG
GERMANY
Tel:+49 40 89902-276

On 23 Apr 2014, at 21:33, Skrzypczak-Jankun, Ewa 
ewa.skrzypczak-jan...@utoledo.edu wrote:

 Hi,
 I have a collection of books that I would gladly give away to someone who may 
 cherish them. The list is enclosed.
 J Ewa SJ
  
  
 Ewa Skrzypczak-Jankun, PhD
   DH r.2250
 Prof. emerita 
  ph 419-383-5414 or 419-383-6471
 University of Toledo – HSC
  fax 419-383-3785
 College of Medicine, Urology Mail Stop#1091   
email: ewa.skrzypczak-jan...@utoledo.edu
 3000 Arlington Ave.
 Toledo OH 43614, USA
  
 Books to go.docx