[ccp4bb] Research Scientist at Hauptman-Woodward Institute

[Andrew Gulick]

Please see the posting below for an independent investigator at the 
Hauptman-Woodard Institute. Please direct any questions or applications to the 
opportun...@hwi.buffalo.edu email address.
Best wishes,
Andrew

--
Andrew M. Gulick, Ph.D.
-
Hauptman-Woodward Institute and
Dept. of Structural Biology, SUNY at Buffalo
700 Ellicott St Buffalo, NY 14203
--

The Hauptman-Woodward Medical Research Institute (HWI) invites applications for 
a full time Research Scientist in the areas of structural, computational, or 
molecular biology.  The Institute seeks exceptional faculty candidates who will 
direct an independently funded research program in important areas of human 
biology, health or disease.

A startup package will be provided to each individual hired.  Candidates are 
expected to have a Ph.D. or equivalent in a relevant field and a strong record 
of scientific productivity.  The position is open to candidates at the junior 
faculty level but senior level candidates will also be considered.

HWI is celebrating its 60th year as an independent research institute and 
expects to make several new hires over the next few years. Located in Buffalo, 
New York, HWI is at the heart of the growing Buffalo-Niagara Medical Campus and 
partners with the University at Buffalo, Roswell Park Cancer Institute, and the 
Kaleida Health System. It also has links to industry, houses a gene to 
structure company, HarkerBIO, and operates the IMCA-CAT beamline at the 
Advanced Photon Source.

Candidates are encouraged to develop academic and potentially industrial 
collaborations.  Interested candidates should send, as a single PDF file, a 
complete curriculum vitae, a statement of research accomplishments, an outline 
of future research plans, and arrange for three letters of recommendation to be 
sent separately to: Search Committee, Hauptman-Woodward Institute, 700 Ellicott 
Street, Buffalo, NY 14203, or by Email to opportun...@hwi.buffalo.edu.

HWI is an equal opportunity employer.

[ccp4bb] Research Scientist at Hauptman-Woodward Institute, Buffalo, USA

[Andrew Gulick]

Please see the posting below for an independent investigator at the 
Hauptman-Woodard Institute. Please direct any questions or applications to the 
opportun...@hwi.buffalo.edu email address.
Best wishes,
Andrew

--
Andrew M. Gulick, Ph.D.
-
Hauptman-Woodward Institute and
Dept. of Structural Biology, SUNY at Buffalo
700 Ellicott St Buffalo, NY 14203

[ccp4bb] Assistant Professor Opportunity at FSU

[Scott Stagg]

Dear colleagues, 

I am writing to draw your attention to a new Assistant Professor faculty 
position at FSU. The Department of Chemistry and Biochemistry at Florida State 
University seeks to fill a tenure-track faculty position at the Assistant 
Professor level in the area of biochemistry, broadly defined. We are especially 
interested in candidates specializing in cryogenic electron microscopy 
(cryo-EM) such as cryo-correlative light and electron microscopy or cryo-EM of 
membrane proteins. With well-established expertise in cryo-electron tomography 
and high-resolution single particle EM, FSU is a vibrant community for 
structural biologists. We are equipped with three cryo-capable microscopes 
including an FEI Titan Krios equipped with a DE64 direct detector. Appointees 
will be expected to develop a vigorous, externally supported research program 
and to teach both undergraduate and graduate courses. Applicants should upload 
application materials, including a cover letter, CV, brief statement of 
proposed research, and statement of teaching philosophy at 
www.chem.fsu.edu/biochem/recruit for consideration. Candidates should arrange 
for three letters of recommendation to be sent by email to 
biochemsea...@chem.fsu.edu for completion of their file. Review of applications 
will begin on November 1, 2017, and continue until the position is filled. FSU 
is An Equal Opportunity/Access/Affirmative Action/Pro Disabled & Veteran 
Employer; minority candidates and women are encouraged to apply. FSU’s Equal 
Opportunity Statement can be viewed at: 
http://www.hr.fsu.edu/PDF/Publications/diversity/EEO_Statement.pdf

Best regards,
Scott


Scott Stagg
Associate Professor 
Institute of Molecular Biophysics
Department of Chemistry and Biochemistry
Florida State University
Tallahassee, FL 32306-4380
w: 850-645-7872
f: 850-644-7244
sst...@fsu.edu
http://www.sb.fsu.edu/~sstagg/

Re: [ccp4bb] NMR or Homology Model as a MR model

[Oganesyan, Vaheh]

Percent of identity/similarity is a number that might be often misleading when 
used as a judgement rule for molecular replacement. Very high or very low 
numbers are almost always indicative of corresponding outcome. The numbers in 
twilight zone of 20 to 35%, however, are not. When aligning sequences of target 
protein with potential MR models pay attention to residues like Cys, Trp, Phe, 
Tyr. Last three could be used in place of each other. Aligned Cys, for example, 
are very good indication of fold similarity. Ding between aligned Cys is 
indicative of difference in loop lengths, etc. When possible use more sequences 
to align, not just two. Also, there might be some info about your protein’s 
either binding partner or an active site, if it is an enzyme. In that case 
check out alignment of residues associated with the function.

Regards,

Vaheh Oganesyan
www.medimmune.com

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nishant 
Varshney
Sent: Tuesday, August 29, 2017 6:51 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] NMR or Homology Model as a MR model

Dear Crystallographers,

I am working to solve an human protein structure which has a domain sequence 
identity of 24% with domain of another protein.  As Phaser as well as Molrep 
failed to give any definite solution (TFZ=3.7 from MR), I want to ask, if 
solution structure of another protein having domain sequence similarity of 25% 
or a homology model can be used as a template for MR?
Many thanks and Regards
Nishant

--
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477
Mob: 8390564690
To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary. This communication is expected to 
be read and/or used only by the individual(s) for whom it is intended. If you 
have received this electronic communication in error, please reply to the 
sender advising of the error in transmission and delete the original message 
and any accompanying documents from your system immediately, without copying, 
reviewing or otherwise using them for any purpose. Thank you for your 
cooperation.

Re: [ccp4bb] CC(1/2) reference

[Fislage, Marcus]

Hi Nicola,


maybe you want to have a look at an older thread I started years ago:


https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg28031.html

[ccp4bb] CC1/2, XDS and resolution cut off - The Mail 
Archive
www.mail-archive.com
Dear all, We have in our lab a data set collected and are discussing where to 
cut the resolution for refinement. According to the work of Kai Diederichs and 
Andy ...




And especially the response from Kay Diederich


https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg28042.html


Cheers

Marcus

Re: [ccp4bb] CC1/2, XDS and resolution cut 
off
www.mail-archive.com
Dear Marcus, I have a few comments: - we do not suggest any fixed value (like 
0.125) for a CC1/2 cutoff. One reason why a fixed value should not be carved in 
stone is ...




Marcus Fislage, PhD

Howard Hughes Medical Institute (HHMI)
Columbia University
Department of Biochemistry and Biophysics
Lab of Joachim Frank
New York, NY

email address: mf2...@cumc.columbia.edu
Phone: 212.305.9524
Fax: 212.305.9500


From: CCP4 bulletin board  on behalf of Parthasarathy 
Sampathkumar 
Sent: Tuesday, August 29, 2017 10:16:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CC(1/2) reference

Hi Nicola,

Here are references for CC1/2;

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/

Best Wishes
Partha
On Tue, Aug 29, 2017 at 10:06 AM Nicola Evans 
mailto:nicola.1.ev...@kcl.ac.uk>> wrote:
Hello all, I have heard at several CCP4 meetings and also at Diamond training 
that a good "cut off" for CC(1/2) is around 0.3 and I/sig(I) is 0.2, but I am 
struggling to find any journal references to say this (other than demonstrating 
the merits of CC(1/2) over Rmeas).

Can anyone point me in the right direction? Thanks all!

Nicola

Re: [ccp4bb] CC(1/2) reference

[Savvas Savvides]

Dear Nicola
the most thorough discussion I have seen regarding recommendations on cutoffs 
(or at least ways to think about them) for such crystallographic data 
indicators can be found in:

Assessing and maximizing data quality in macromolecular crystallography
P Andrew Karplus and Kay Diederichs
Current Opinion in Structural Biology 2015, 34:60–68
http://dx.doi.org/10.1016/j.sbi.2015.07.003 

best wishes
Savvas



Savvas Savvides
VIB-UGent Center for Inflammation Research
Dept. Biochemistry & Microbiology, Ghent University
Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium
+32 (0)472 928 519 (mobile) ; +32 9 331 36 60 (office) ; Skype: 
savvas.savvides_skype
http://www.vib.be/en/research/scientists/Pages/Savvas-Savvides-Lab.aspx 




> On 29 Aug 2017, at 16:05, Nicola Evans  wrote:
> 
> Hello all, I have heard at several CCP4 meetings and also at Diamond training 
> that a good "cut off" for CC(1/2) is around 0.3 and I/sig(I) is 0.2, but I am 
> struggling to find any journal references to say this (other than 
> demonstrating the merits of CC(1/2) over Rmeas). 
> 
> Can anyone point me in the right direction? Thanks all!
> 
> Nicola

Re: [ccp4bb] CC(1/2) reference

[Parthasarathy Sampathkumar]

Hi Nicola,

Here are references for CC1/2;

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/

Best Wishes
Partha
On Tue, Aug 29, 2017 at 10:06 AM Nicola Evans 
wrote:

> Hello all, I have heard at several CCP4 meetings and also at Diamond
> training that a good "cut off" for CC(1/2) is around 0.3 and I/sig(I) is
> 0.2, but I am struggling to find any journal references to say this (other
> than demonstrating the merits of CC(1/2) over Rmeas).
>
> Can anyone point me in the right direction? Thanks all!
>
> Nicola
>

[ccp4bb] CC(1/2) reference

[Nicola Evans]

Hello all, I have heard at several CCP4 meetings and also at Diamond training 
that a good "cut off" for CC(1/2) is around 0.3 and I/sig(I) is 0.2, but I am 
struggling to find any journal references to say this (other than demonstrating 
the merits of CC(1/2) over Rmeas). 

Can anyone point me in the right direction? Thanks all!

Nicola

Re: [ccp4bb] NMR or Homology Model as a MR model

[Daniel Rigden]

Hi Nishant

AMPLE can work with ensembles from NMR structures 
(http://ample.readthedocs.io/en/latest/examples/rst/nmr_ensemble.html#example-nmr-ensemble; 
see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817692/) or sets of 
distant homologues 
(http://ample.readthedocs.io/en/latest/examples/rst/homologs.html#example-dist-homologs), 
trialling a large number of edited variant ensembles (from mildly 
truncated to brutally) in an automated fashion. With AMPLE you select 
Phaser and/or Molrep for the actual MR step and, resolution permitting, 
can use Shelxe's statistics to give you a particularly clear indication 
of success/failure.


Good luck

Dan

On 29/08/17 13:31, Randy Read wrote:

Hi,

Molecular replacement gets progressively more difficult as the 
sequence identity drops, though the correlation between sequence 
identity and model quality is not perfect.  With the best models 
having sequence identities around 24%, success is by no means 
guaranteed, so you might have to try lots of strategies or resort to 
experimental phasing.  NMR models do tend to be worse for molecular 
replacement, so that will probably lower the chances of success further.


In addition to what others have said already, it's worth mentioning 
that, in a number of very difficult structure determinations (best 
models around 20% sequence identity), the key thing that made the 
difference between failure and success was pruning off the parts of 
the ensemble that do not agree among the members of the ensemble, 
leaving just the conserved core.  This can be done, for instance, in 
the Ensembler program with the "trim=True" flag.  For this to work 
best, it's helpful if you happen to have a number of potential models 
that are also relatively distantly related to each other, to really 
highlight what is conserved in the fold.


Best wishes,

Randy Read

On 29 Aug 2017, at 12:42, Andreas Forster > wrote:


Dear Nishant,

Rosetta is a good suggestion.  You can also use an ensemble of 
several related (superposed) structures as your search model.  This 
will improve your chances of success.


All best.


Andreas



On Tue, Aug 29, 2017 at 12:50 PM, Nishant Varshney > wrote:


Dear Crystallographers,

I am working to solve an human protein structure which has a
domain sequence identity of 24% with domain of another protein.
As Phaser as well as Molrep failed to give any definite solution
(TFZ=3.7 from MR), I want to ask, if solution structure of
another protein having domain sequence similarity of 25% or a
homology model can be used as a template for MR?
Many thanks and Regards
Nishant

-- 
Dr. Nishant Kumar Varshney,

Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477 
Mob: 8390564690




--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills Road  E-mail: rj...@cam.ac.uk 
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk 





--
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.

Re: [ccp4bb] NMR or Homology Model as a MR model

[Randy Read]

Hi,

Molecular replacement gets progressively more difficult as the sequence 
identity drops, though the correlation between sequence identity and model 
quality is not perfect.  With the best models having sequence identities around 
24%, success is by no means guaranteed, so you might have to try lots of 
strategies or resort to experimental phasing.  NMR models do tend to be worse 
for molecular replacement, so that will probably lower the chances of success 
further.

In addition to what others have said already, it's worth mentioning that, in a 
number of very difficult structure determinations (best models around 20% 
sequence identity), the key thing that made the difference between failure and 
success was pruning off the parts of the ensemble that do not agree among the 
members of the ensemble, leaving just the conserved core.  This can be done, 
for instance, in the Ensembler program with the "trim=True" flag.  For this to 
work best, it's helpful if you happen to have a number of potential models that 
are also relatively distantly related to each other, to really highlight what 
is conserved in the fold.

Best wishes,

Randy Read

> On 29 Aug 2017, at 12:42, Andreas Forster  wrote:
> 
> Dear Nishant,
> 
> Rosetta is a good suggestion.  You can also use an ensemble of several 
> related (superposed) structures as your search model.  This will improve your 
> chances of success.
> 
> All best.
> 
> 
> Andreas
> 
> 
> 
> On Tue, Aug 29, 2017 at 12:50 PM, Nishant Varshney  > wrote:
> Dear Crystallographers,
> 
> I am working to solve an human protein structure which has a domain sequence 
> identity of 24% with domain of another protein.  As Phaser as well as Molrep 
> failed to give any definite solution (TFZ=3.7 from MR), I want to ask, if 
> solution structure of another protein having domain sequence similarity of 
> 25% or a homology model can be used as a template for MR?
> Many thanks and Regards
> Nishant
> 
> -- 
> Dr. Nishant Kumar Varshney,
> Research Associate,
> C/O Dr. Sameena Khan,
> Drug Discovery Research Center,
> Translational Health Science and Technology Institute (THSTI)
> NCR Biotech Science Cluster,
> 3rd Milestone, Faridabad – Gurgaon Expressway,
> Faridabad – 121001 (HARYANA), India
> Ph: +91- 0129-2876477 
> Mob: 8390564690
> 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] NMR or Homology Model as a MR model

[Isupov, Michail]

Dear Nishant,

For successful MR a choice of domain boundaries and loop trimming is
crucial.
Last couple of years I do not even try to run molrep/phaser before
running MrBump and Morda, which do a good job with model preparation.
Only when these pipelines give leads, but not quite the results I use
molrep/phaser/amore.

Morda also prepares NMR-like models (assemblies) from homology models.

Regards,
Misha





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Andreas Forster 
[docandr...@gmail.com]
Sent: Tuesday, August 29, 2017 12:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] NMR or Homology Model as a MR model

Dear Nishant,

Rosetta is a good suggestion.  You can also use an ensemble of several related 
(superposed) structures as your search model.  This will improve your chances 
of success.

All best.


Andreas



On Tue, Aug 29, 2017 at 12:50 PM, Nishant Varshney 
mailto:nik...@gmail.com>> wrote:
Dear Crystallographers,

I am working to solve an human protein structure which has a domain sequence 
identity of 24% with domain of another protein.  As Phaser as well as Molrep 
failed to give any definite solution (TFZ=3.7 from MR), I want to ask, if 
solution structure of another protein having domain sequence similarity of 25% 
or a homology model can be used as a template for MR?
Many thanks and Regards
Nishant

--
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477
Mob: 8390564690

Re: [ccp4bb] NMR or Homology Model as a MR model

[Andreas Forster]

Dear Nishant,

Rosetta is a good suggestion.  You can also use an ensemble of several
related (superposed) structures as your search model.  This will improve
your chances of success.

All best.


Andreas



On Tue, Aug 29, 2017 at 12:50 PM, Nishant Varshney  wrote:

> Dear Crystallographers,
>
> I am working to solve an human protein structure which has a domain
> sequence identity of 24% with domain of another protein.  As Phaser as well
> as Molrep failed to give any definite solution (TFZ=3.7 from MR), I want to
> ask, if solution structure of another protein having domain sequence
> similarity of 25% or a homology model can be used as a template for MR?
> Many thanks and Regards
> Nishant
>
> --
> Dr. Nishant Kumar Varshney,
> Research Associate,
> C/O Dr. Sameena Khan,
> Drug Discovery Research Center,
> Translational Health Science and Technology Institute (THSTI)
> NCR Biotech Science Cluster,
> 3rd Milestone, Faridabad – Gurgaon Expressway,
> Faridabad – 121001 (HARYANA), India
> Ph: +91- 0129-2876477 <+91%20129%20287%206477>
> Mob: 8390564690
>

Re: [ccp4bb] NMR or Homology Model as a MR model

[Briggs, David C]

Dear Nishant,

You can use anything you want as a molecular replacement search model including 
NMR models/ensembles or homology models. Whether or not it will be successful 
is another matter!

For borderline cases, some have reported success using Phaser in combination 
with the Rosetta modelling suite.

E.g.
https://www.phenix-online.org/documentation/reference/mr_rosetta.html

HTH,

Dave

--
Dr David C Briggs
Hohenester Lab
Department of Life Sciences
Imperial College London
UK
http://about.me/david_briggs



From: Nishant Varshney
Sent: Tuesday, 29 August, 11:51
Subject: [ccp4bb] NMR or Homology Model as a MR model
To: ccp4bb@jiscmail.ac.uk


Dear Crystallographers,

I am working to solve an human protein structure which has a domain sequence 
identity of 24% with domain of another protein.  As Phaser as well as Molrep 
failed to give any definite solution (TFZ=3.7 from MR), I want to ask, if 
solution structure of another protein having domain sequence similarity of 25% 
or a homology model can be used as a template for MR?
Many thanks and Regards
Nishant

--
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477
Mob: 8390564690

[ccp4bb] NMR or Homology Model as a MR model

[Nishant Varshney]

Dear Crystallographers,

I am working to solve an human protein structure which has a domain
sequence identity of 24% with domain of another protein.  As Phaser as well
as Molrep failed to give any definite solution (TFZ=3.7 from MR), I want to
ask, if solution structure of another protein having domain sequence
similarity of 25% or a homology model can be used as a template for MR?
Many thanks and Regards
Nishant

-- 
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477 <+91%20129%20287%206477>
Mob: 8390564690