[ccp4bb] UnityMol urgently looking for PhD candidates

[Marc Baaden]

Dear Colleagues,
We urgently are looking for a PhD candidate for the attached proposal. 
It involves UnityMol and the idea of crowdsourcing for drug design.
Please do send potential candidates our way :)
Thank you very much,
  Marc


Depiction of molecular fragments, their properties and chemical space 
for citizen science drug discovery

Project description out with the design of the UnityMol platform Citizen 
science has become more abundant (unitymol.sourceforge.net) and the proof-of- 
during the past decade. A striking example is concept serious game DocMolecules 
thescientificdiscoveryg ame Foldit,anonline(https://youtu.be/5x2nazXoiKw), 
providing a 3D jigsaw puzzle where players are invited to solid foundation for 
this project.shake and wiggle the 3D structure of proteins in order to find the 
most stable conformations. The project has brought biological results and lead 
to collaborative development of new algorithms. The type of problem Foldit is 
tackling shares similarities, in terms of complexity, with drug design, 
justifying to undertake a citizen science approach to rational drug design.


The goal of the project is to develop a serious game that will allow the player 
to participate in human-centered rational drug design.  The problem of 
optimization of drugs is complicated to undertake automatically because the 
chemical landscape that needs to be explored is multidimensional and the 
modifications do not sum up in a linear way. Challenges resemble those in 
protein folding, where foldit has shown that human analysis and intuition 
surpass computer algorithms. The scientific field to be explored comprises 
molecular structure, nonbonded interactions (between drug and target) and 
rational drug design.

A crucial step is to tackle the representation of chemical properties and space 
to guide players.  The project involves the following:- Representation of 
chemical properties and fragments. This feature will allow the player to 
intuitively apprehend 3D and 2D properties.- Definition of druggable fragments 
space. Definition of suitable fragments for each type of drug-target 
interaction.- Representation of the chemical space as a 2D map to be included 
in the game. This feature will allow the players to expand chemical space in 
the direction of unexplored possibilities and should facilitate collective 
intelligence.

Closing date:   25 March 2017




AnnoncePhd.pdf
Description: AnnoncePhd.pdf
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baa...@smplinux.de  -  http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

Re: [ccp4bb] Estimate NCS copies

[Eleanor Dodson]

No - not completely.
Better to at least start from matthews_coeff and get a guestimate of the
expected number of copies. Presumably you know the sequence of your crystal.

A native patterson can show a non-crystallographic translation.
A self-rotaton may suggest something, but best to start from the simplest
point - viz matthews.
Eleanor

On 15 March 2017 at 15:02, Mohamed Noor 
wrote:

> Dear all
>
> Is it possible to estimate the number of NCS copies by looking at
> reflections in the reciprocal space? If so, where can I find the details?
>
> Thanks.
> Mohamed
>

[ccp4bb] Estimate NCS copies

[Mohamed Noor]

Dear all

Is it possible to estimate the number of NCS copies by looking at reflections 
in the reciprocal space? If so, where can I find the details?

Thanks.
Mohamed

[ccp4bb] Updated Validation Reports for Archived PDB Structures Now Available

[Jasmine Young]

The wwPDB partners are pleased to announce that updated validation 
reports for all X-ray, NMR, and 3DEM structures deposited in the PDB 
archive are now available on March 15, 2017.


The updates include new percentile statistics reflecting the state of 
the PDB archive on December 31th 2016 and updated versions of the Mogul 
software (2017) and CSD archive (as538be).


The updated reports are accessible from the following FTP sites:

 * ftp://ftp.wwpdb.org/pub/pdb/validation_reports/ (wwPDB)
 * ftp://ftp.rcsb.org/pub/pdb/validation_reports/ (RCSB PDB)
 * ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe)
 * ftp://ftp.pdbj.org/pub/pdb/validation_reports/ (PDBj)

A copy of the previous version is archived at RCSB PDB 
 and PDBj 
.


These updated wwPDB validation reports provide an assessment of 
structure quality using widely accepted standards and criteria, 
recommended by community experts serving in the Validation Task Force 
. The wwPDB partners 
strongly encourage journal editors and referees to request them from 
authors as part of the manuscript submission and review process. The 
reports are date-stamped and display the wwPDB logo, and contain the 
same information, regardless of which wwPDB site processed the entry. 
Provision of wwPDB validation reports is already required by /Nature/, 
/eLife/, /The Journal of Biological Chemistry/, /the International Union 
of Crystallography (IUCr) journals/, /FEBS journals/, /Journal of 
Immunology/ and /Angew Chem Int Ed Engl/ as part of their 
manuscript-submission process.


Validation reports are also provided to depositors through OneDep - the 
wwPDB portal for validation, deposition and biocuration of structure 
data. The wwPDB partners encourage the use of the stand-alone validation 
server  and the webservice API 
 
at any time prior to data deposition. Depositors are required to review 
and accept the reports as part of the data submission process. 
Validation reports will continue to be developed and improved as we 
receive recommendations from the expert Validation Task Forces (VTF) for 
X-ray , NMR 
, EM , 
and on ligand validation, and as we collect feedback from depositors and 
users.


Further information and sample validation reports are available 
.


Your feedback, comments, and questions are welcome at 
validat...@mail.wwpdb.org .



--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

[ccp4bb] Structural biologist in metabolic diseases, SGC University of Oxford

[Wyatt W. Yue]

Dear all

We are recruiting a structural biologist at senior/postdoctoral level, to
join the metabolic research team at the SGC University of Oxford, led by
Assoc Prof Wyatt Yue.

You will be part of a dynamic and focused team, elucidating the molecular
mechanism and small molecule therapy for the causative gene products of
common (e.g. diabetes, obesity, endocrinology) and rare (e.g. inborn errors
of metabolism) disorders.


   - You have a PhD in structural biology/biochemistry
   - You have experience in structure-based drug discovery
   - You have interest in the field of metabolic diseases
   - You are a self-starter, team player and completer/finisher who enjoys
   a challenge

Interested applicants please refer to job description and apply online via
the page (Vacancy ID: 127848):

https://www.ndm.ox.ac.uk/current-job-vacancies/vacancy/127848-Structural-Biologist-in-Metabolic-and-Rare-Diseases



Closing date: *12.00 midday (UK) on Thursday 13 April 2017*


Informal enquiries to wyatt@sgc.ox.ac.uk

Visit Wyatt Yue’s SGC home page: http://www.thesgc.org/wyatt