BIGCHEM newsletter 8

October, 2019 Newsletter 8

Content of this newsletter

Last BIGCHEM School in Munich (Germany)
ICANN19 BIGCHEM special session
Complementary activities of the last School for BIGCHEM ESR fellows
New publications
Two first BIGCHEM ESRs fellows defended their PhDs.
Meet BIGCHEM partners at

Last BIGCHEM School in Munich (Germany)

The final BIGCHEM closing conference took place in Munich from the 16 ^th to 20 ^th of September 2019. It consisted of scientific sessions as well as complementary activities for BIGCHEM fellows.

The BIGCHEM scientific sessions (see ICANN19 BIGCHEM special session) were held on Thursday 19 ^th as part of the ICANN2019 - the 28th International Conference on Artificial Neural Networks – (17-19 September 2019, Klinikum rechts der Isar, Munich), which was co-organized by the BIGCHEM project. The full ICANN2019 program including the BIGCHEM Special session is presented here .

On the 16th and 20th September the BIGCHEM fellows attended several trips and complementary activities organized at the Helmholtz Zentrum Muenchen, the Bavaria biotechnology network BioM cluster and at the Technical University of Munich (TUM) (see complementary activities of the last School for BIGCHEM ESR fellows).

Participants of the final BIGCHEM school at ICANN2019

ICANN2019 BIGCHEM special session

The BIGCHEM special session at ICANN2019 conference comprised two sessions with a total of eleven talks given by BIGCHEM fellows and external speakers. The BIGCHEM fellows Amol Thakkar, Josep Arús-Pous, Dipan Ghosh, Michael Withnall and Laurianne David gave an overview of their PhD projects.

Several external speakers contributed to BIGCHEM sessions with excellent talks. Amid others those include Artem Cherkasov (University of British Columbia), who talked about "Progressive Docking - a Deep Learning Based Approach for Accelerated Virtual Screening, Alain Tchagang (National Research Council of Canada) with the talk "Prediction of the Atomization Energy of Molecules Using Coulomb Matrix and Atomic Composition in a Bayesian Regularized Neural Network, Lukasz Maziarka (Jagiellonian University), who give a talk entitled "Mol-CycleGAN-a generative model for molecular optimization" and "Application of materials informatics tools to the analysis of combinatorial libraries of all metal-oxides photovoltaic cells" by Hanoch Senderowitz (Bar-Ilan University).

Michael Withnall (left) and Amol Thakkar (right) talks at BIGCHEM Special Session at ICANN2019

Complementary activities of the last School for BIGCHEM ESR fellows

The activities of the last BIGCHEM School on the 16th and 20th September also included guided visits to the Munich Biotech Cluster incubator and to the NMR spectrometer at TUM (Garching) as well as a workshop on "How to prepare a job application" organized at the Personal Development department at the Helmholtz Zentrum Muenchen.

BIGCHEM ESR fellows' impressions

Laurianne David: " I really enjoyed our activities during this school as it gave us an overview of situations that we may face after our PhDs. We visited the NMR center in Garching and were given in-depth knowledge on how the NMR instruments function as well as on the manufacturing processes that lie behind them. Interestingly, we also learned about how the geopolitical situation can impact the NMR center. Finally, we had the opportunity to meet with Prof. Dr. Domdey, CEO of the BioM Biotech Cluster, who gave us a seminar on the financial system of the biotech companies in Germany and on the grant application process. It was very instructive!"

Michel Withnall: " The trip to the BioM cluster in Munich was very insightful. I got the opportunity to learn about all the available funding opportunities for progressing scientific research in the biotechnology sector around Munich. We got an overview of how this sector has grown to be a leading location in Germany, and how I could further my future career by considering these opportunities. The site itself was in a lovely location and I found the experience to be very enjoyable, getting a first-hand account of some success stories of the area and the history of their development"

New publications

Thakkar A, Selmi N, Reymond JL, Engkvist O, Bjerrum EJ, Ring Breaker’: Assessing Synthetic Accessibility of the Ring System Chemical Space ChemRxiv
David L, Arús-Pous J, Karlsson J, Engkvist O, Bjerrum EJ, Kogej T, Kriegl J, Beck B, Chen H, Applications of deep-learning in exploiting large-scale and heterogeneous compound data in industrial pharmaceutical research Front. Pharmacol (in press)
David L, Walsh J, Sturm N, Feierberg I, Nissink JWM, Chen H, Bajorath J, Engkvist O, Identification of Compounds That Interfere with High-Throughput Screening Assay Technologies ChemMedChem 2019, Sep 3
Lin A, Beck B, Horvath D, Marcou G, Varnek A, Diversifying chemical libraries with generative topographic mapping. J Comput Aided Mol Des. 2019, Aug 12
Thakkar A, Bjerrum EJ, Engkvist O, Reymond JL, Neural Network Guided Tree-Search Policies for Synthesis Planning. In: Tetko I., Kůrková V., Karpov P., Theis F. (eds) Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions. ICANN 2019. Lecture Notes in Computer Science, vol 11731. Springer, Cham
Arús-Pous, J, Johansson, S, Prykhodko, O, Bjerrum, E J, Tyrchan, C, Reymond, JL, Chen, H, Engkvist, O, Improving Deep Generative Models with Randomized SMILES. In: Tetko I., Kůrková V., Karpov P., Theis F. (eds) Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions. ICANN 2019. Lecture Notes in Computer Science, vol 11731. Springer, Cham
Withnall M, Lindelöf E, Engkvist O, Chen H, Attention and Edge Memory Convolution for Bioactivity Prediction. In: Tetko I., Kůrková V., Karpov P., Theis F. (eds) Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions. ICANN 2019. Lecture Notes in Computer Science, vol 11731. Springer, Cham
Ghosh D, Tetko I, Klebl B, Nussbaumer P, Koch U, Analysis and Modelling of False Positives in GPCR Assays. In: Tetko I., Kůrková V., Karpov P., Theis F. (eds) Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions. ICANN 2019. Lecture Notes in Computer Science, vol 11731. Springer, Cham
Karpov P, Godin G, Tetko IV, A Transformer Model for Retrosynthesis. In: Tetko I., Kůrková V., Karpov P., Theis F. (eds) Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions. ICANN 2019. Lecture Notes in Computer Science, vol 11731. Springer, Cham
Tetko IV, Karpov P, Bruno E, Kimber TB, Godin G, Augmentation Is What You Need!. In: Tetko I., Kůrková V., Karpov P., Theis F. (eds) Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions. ICANN 2019. Lecture Notes in Computer Science, vol 11731. Springer, Cham
Lin A, Beck B, Horvath D, Varnek A, Diversify Libraries Using Generative Topographic Mapping. In: Tetko I., Kůrková V., Karpov P., Theis F. (eds) Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions. ICANN 2019. Lecture Notes in Computer Science, vol 11731. Springer, Cham9.
David L, Walsh J, Bajorath J, Engkvist O, Detection of Frequent-Hitters Across VariousHTS Technologies. In: Tetko I., Kůrková V., Karpov P., Theis F. (eds) Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions. ICANN 2019. Lecture Notes in Computer Science, vol 11731. Springer, Cham
Laufkötter O, Sturm N, Bajorath J, Chen H, Engkvist O, Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold hopping capability J Cheminformatics, 2019 4Aug 8;11(1):54
Thakkar A, Kogej T, Reymond JL, Engkvist O, Bjerrum EJ, Datasets and Their Influence on the Development of Computer Assisted Synthesis Planning Tools in the Pharmaceutical Domain ChemRxiv
Laufkötter O, Miyao T, Bajorath J, Large-Scale Comparison of Alternative Similarity Search Strategies with Varying Chemical Information Contents ACS Omega 2019, Sep 5;4(12):15304-15311

See full list of project publications at the BIGCHEM web site.

Two first BIGCHEM ESRs fellows defended their PhDs

The BIGCHEM ESRs fellows Xuejin Zhang and Arkadii Lin successfully defended their PhDs on September 2019. Xuejin Zhang carried out her PhD work jointly on ETH Zürich and Boehringer Ingelheim on the topic " Exploration of chemical space by reaction-driven de novo design ". Arkadii Lin (right photo) performed his doctoral work at the University of Strasbourg and Boehringer Ingelheim on the " Big data visualisation and modelling using Generative Topographic Mapping (GTM) approach " subject.

BIGCHEM network partners sincerely congratulate Xuejin and Arkadii and wish them all the best in their scientific carrier!

Meet BIGCHEM partners at:

AstraZenenca BioPharmaceuticals R&D Science Symposium (Poster Presentation) – 30-31^st October, 2019, Gothenburg, Sweden. Amol Thakkar
German Cheminformatics Conference (Oral Presentation) – 3^rd-5^th November 2019, Mainz, Germany. Amol Thakkar
AI Powered Drug Discovery and Manufacturing (Submitting Abstract, Conference booked) – 27^th-28^th February 2020, MIT, Cambridge, MA, USA. Amol Thakkar
IUPAC Conference 13^th-17^th July 2019, Paris, France (Poster Presentation). Laurianne David
9th Meeting of the SFCi (French Society of Chemoinformatics) (Oral Presentation) - November 21-22 2019, Paris. Laurianne David

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This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 676434.

Disclaimer: the newsletter reflects only the authors’ view and neither the European Commission nor the Research Executive Agency are responsible for any use that may be made of the information it contains.