PhD proposal (Oct 2015): General purpose detection, characterization and comparison of molecular interactions.

Background:

Discovery of novel bioactive molecules (biologics and small chemical entities) is a complex endeavour and generally involves several years of research and development. During this discovery process several properties of such molecular candidates have to be optimized towards various endpoints, such as activity vs a therapeutic target, ADMET properties, pharmacokinetics without speaking about putative patentability issues. One of the most important hallmarks of a novel bioactive entity is its pattern of intermolecular interactions.
Since the seeding paper on SIFTs (Structural Interaction Fingerprints (Deng, Chuaqui, & Singh, 2004)), several studies have been proposed for the detection and comparison of molecular interactions. (Da & Kireev, 2014; Desaphy, Raimbaud, Ducrot, & Rognan, 2013). CREDO is an example of first attempts to make such information publicly available(A. Schreyer & Blundell, 2009; A. M. Schreyer & Blundell, 2013).
Most of these, as well as similar studies, reduce the representation of a molecular interaction to an easily comparable fingerprint. Unfortunately these representations have inherent drawbacks on querying large databases of molecular interactions and furthermore, none of the methods are easily available for privately held companies as well as for academics interested by high-throughput approaches.

Project:

This PhD project aims at providing methodological basics for a large-scale description and analysis of molecular interactions. The underlying methods should be able to describe molecular interactions allowing later comparison of subsets of such descriptions instantaneously when querying a large database. Furthermore, the underlying methods should be able to correctly treat non-curated data, such as available in the Protein Data Bank. Seeding work has been already performed in the scope of binding site comparison (Doppelt-Azeroual, Delfaud, Moriaud, & De Brevern, 2010; Schmidtke, n.d.).
The project is part of a larger development project within Discngine and carried out in collaboration with a major pharmaceutical company.

Profile:

We are seeking for a highly motivated and autonomous PhD candidate for a period of three years. This PhD project will be supervised by Vincent Le Guilloux, Ph.D. & Peter Schmidtke, Ph.D. Discngine (Paris based privately held company, http://www.discngine.com, publications at https://scholar.google.fr/citations?user=UtOSocMAAAAJ&hl=en) and Alexandre G. de Brevern, Ph.D., D.Sc. from the DSIMB lab (INSERM, Univ Paris Diderot, Sorbonne Paris Cité, INTS, GR-Ex, see publications athttps://scholar.google.fr/citations?user=NB4OJhoAAAAJ&hl=fr). The PhD will be conducted under CIFRE conventions (http://www.anrt.asso.fr/fr/pdf/plaquette_cifre_complete_avril2009_GB.pdf).
The ideal PhD candidate should hold a Master’s degree in bioinformatics, biophysics or informatics with a strong interest on structural biology and perception of intermolecular interactions. Notions of database design / querying, graph-based technologies, graph-theory and molecular perception are required for this positions. Strong programming expertise as well as analytical skills are a must. Previous experience in the area of peptide & small molecular design would facilitate the initial phase of the project.
Strong communicational skills in English are required (frequent oral & written communications in English). Experience in the development of web-based GUIs is a plus (HTML5, CSS3/CSS frameworks, WebGL, JavaScript/libraries).
Please send your curriculum and letter of intent to jobs@discngine.com and alexandre.debrevern@univ-paris-diderot.fr

Expected starting date: Octobre 2015
Duration: 3 years
Location: Paris (France)
Income: 23.5k€/annum

References:

Da, C., & Kireev, D. B. (2014). Structural Protein-Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study. Journal of Chemical Information and Modeling, 140813100524004. doi:10.1021/ci500319f

Deng, Z., Chuaqui, C., & Singh, J. (2004). Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein-Ligand Binding Interactions. Journal of Medicinal Chemistry, 47(2), 337–344. doi:10.1021/jm030331x

Desaphy, J., Raimbaud, E., Ducrot, P., & Rognan, D. (2013). Encoding protein-ligand interaction patterns in fingerprints and graphs. Journal of Chemical Information and Modeling, 53(3), 623–637. doi:10.1021/ci300566n

Doppelt-Azeroual, O., Delfaud, F., Moriaud, F., & De Brevern, A. G. (2010). Fast and automated functional classification with MED-SuMo: An application on purine-binding proteins. Protein Science, 19(4), 847–867. doi:10.1002/pro.364

Schmidtke, P. (n.d.). Protein-ligand binding sites. Identification, characterization and interrelations. Universitat de Barcelona. Retrieved from http://tdx.cat/handle/10803/51340

Schreyer, A., & Blundell, T. (2009). CREDO: A protein-ligand interaction database for drug discovery. Chemical Biology and Drug Design, 73, 157–167. doi:10.1111/j.1747-0285.2008.00762.x

Schreyer, A. M., & Blundell, T. L. (2013). CREDO: A structural interactomics database for drug discovery. Database, 2013. doi:10.1093/database/bat049

Weill, N., & Rognan, D. (2009). Development and validation of a novel protein-ligand fingerprint to mine chemogenomic space: Application to G protein-coupled receptors and their ligands. Journal of Chemical Information and Modeling, 49(4), 1049–1062. doi:10.1021/ci800447g

JOBIM 2013


J O B I M 2 0 1 3
French Conference on Biology, Computer Science and Mathematics

Toulouse, 1 – 4 July 2013


This is the first call for papers for JOBIM 2013.

The annual meeting of the French bioinformatics population, organized
via the SFBI, will hold its 14th edition in Toulouse (1st to 4th July
2013). This year this conference will also be the opportunity to invite
in a privileged manner colleagues from the Catalan region around
Barcelona.

The necessary information for submissions and inscriptions can be found
on the conference website:

https://colloque.inra.fr/jobim2013

CALL FOR PAPERS
——————

The last date for propositions to be submitted is the 18th March 2013.

Three categories of submissions are possible:
* original articles (8 to 10 pages), restricted to unpublished results
* extended abstracts(2 to 8 pages), corresponding to recent work under
submission or accepted elsewhere
* short summary (1 to 2 pages), corresponding to recent work or in
progress, already published or not.

The original articles and extended summaries will be selected based on
critical review by at least two members of the program committee and
will be published in the conference proceedings. They will be proposed
for oral presentation (and, if desired by the authors as poster
presentation). The short summaries are destined to be presented only as
posters.
As in previous editions, JOBIM will be structured around plenary
sessions as well as thematic parallel sessions so as to increase the
number of possibilities of participants to present their work orally and
to create an informal forum to encourage scientific discussion. The
choice of themes will be decided later on the basis of the selected
contributions. The existence of a parallel session will therefore be
conditioned by the number of quality submissions. If you want particular
themes to be the object of a session please send as many good
propositions as possible and don’t hesitate to encourage colleagues to
do likewise.

We particularly encourage PhD students and post-docs to use this
opportunity to present their work at JOBIM. Awards will be given to the
young scientists giving the best poster and oral presentations.

The themes covered by JOBIM include all the major aspects of
bioinformatics and will include fundamental methodology (mathematical
modeling, computing, statistical analysis and physical methodology), the
software tools and contributions describing specific applications and
ground-breaking research leading to new biological concepts. A
non-exhaustive listing of potential themes is as follows:

* genomics, comparative analysis, metagenomics
* evolution and phylogeny
* biodiversity, genetics and population genomics
* sequence analysis
* cartography and genome annotation
* systems biology and biological networks
* macromolecule structures
* proteomics
* gene expression and functional genomics
* NGS data analysis
* non-coding RNA
* epigenetics and epigenomics
* ontology databases
* data integration
* algorithmics and statistics for bioinformatics

IMPORTANT DATES
—————-
February 1st: Call open for oral communications and poster submissions
March 18th: Closing date for submission of oral and poster
communications
April 29th: Author notification of the decision of the Scientific Committee
May 13th: Final Program announcement
July 1st: Beginning of the JOBIM 2013 conference

New student

Claudine Guyon is now in the lab for two months. She will be
supervised by Pierre Poulain on a project dealing with the
polymorphisms of the integrins alphaIIb/beta3.

New Post-Doc

Welcome to Dr Giulia Rossi who join our team as a Marie Curie post-doctoral fellow.
She will work with Luca Monticelli on the interaction of nanomaterials.