Information School News

PhD student Gianmarco Ghiandoni recently attended well known chemoinformatics conference GCC 2019 , in Mainz, Germany, as an official speaker. 'I presented some content from my PhD project which describes the use of Reaction Class Recommendation models in de novo Drug Design', says Gianmarco. 'These models have shown to have a role as deterministic search components which maximise the chance of generating meaningful synthetic patterns in de novo design and compound optimisation.' 'In addition to this, the application of these models has resulted to yield product libraries characterised by higher synthetic accessibility, whilst reducing drastically the algorithmic enumeration times.'

Over 40 of Peter Willett’s ex-PhD students and long-time collaborators gathered in Sheffield in mid-September to celebrate Peter’s long and very influential career and to thank him for the personal support that he has provided to very many throughout this time. It is a mark of the very high regard in which Peter is held that so many people attended. They had travelled from as far as Canada, North America, Germany and Taiwan, as well as from all over the UK. Many of the attendees are now in very influential positions of their own including in academia, software companies and industry. Their connections to Peter spanned the full range of Peter’s career with one of his early PhD students having obtained her PhD over 30 years ago. A number of presentations were given that included reflections on Peter’s contribution to the fields of Chemoinformatics, Information Retrieval and Bibliometrics, a “Peter Willett: This is your Life” tribute, as well as many personal messages of thank...

The triennial conference on Chemoinformatics was held at the University of Sheffield Edge building earlier this month, organised by our own Professors Val Gillet and Peter Willett and Dr Antonio de la Vega de Leon. A new prize has been established at the conference: The Peter Willett Award for Outstanding Poster Presentation, established by the Royal Society of Chemistry Chemical Information and Computer Applications Group. The establishment of the prize is in recognition of Peter's outstanding contributions to the field, for which he was warmly congratulated. The Chemoinformatics research group at the conference The first winner of the prize is PhD student James Webster for his poster entitled 'Reaction Vector Based Monte Carlo Tree Search for De Novo Design'. James Webster with his poster and award In addition, PhD students Christina Founti, Giammy Ghiandoni and Jess Stacey were all given honourable mentions for their posters. The posters were judged by...

Gianmarco Ghiandoni, PhD student in our Chemoinformatics research group, recently attended and presented at the UK-QSAR conference in Cambridge. Gianmarco attended the conference and presented a part of his PhD project, which involves the development of "Reaction Class Recommender Systems in de novo Drug Design". 'These algorithms are machine learning models that have recently acquired great importance due to their effectiveness in product recommendation', Gianmarco said. 'In particular, companies such as Amazon, Netflix, Spotify, etc., have built their reputations and businesses on the top of these models. At Sheffield, we have decided to apply these methods in order to produce suggestions for decision making in automated molecular design. The results from their application indicate that recommender systems can improve the synthetic accessibility of the designed molecules whilst reducing the computational requirements.'

Congratulations to Gianmarco Ghiandoni, PhD student in the Chemoinformatics Research Group , who recently won the Best Student Poster prize at the UK QSAR (Quantitative Structure-Activity Relationship) Autumn 2018 Meeting, which took place at Lady Margaret Conference Centre, Oxford University, on September 26th. Gianmarco's poster was entitled 'Fingerprint-based recommendation Models in Reaction-driven Drug Design'. The prize gives Gianmarco the opportunity to convert his poster to a 30 minute talk which he will give at the next UK QSAR meeting on 4th April 2019 in Cambridge. Gianmarco's PhD research is on the topic of reaction-based molecular design, supervised by Professor Val Gillet of the Information School and Professor Beining Chen from the Department of Chemistry. You can find out more about his research here .

Professor Val Gillet and six other members of the Chemoinformatics Research Group are attending the 11th International Conference on Chemical Structures in Noordwijkerhout, The Netherlands, May 27-31st 2018. This is the major international conference in the field, with over 200 delegates from more than 20 countries. As usual, the Sheffield Chemoinformatics Group is making a strong contribution to the meeting with one oral presentation (Matt Seddon) and three posters (Antonio de le Vega de Leon, Christina Founti and Gian Marco Ghiandoni). Professor Gillet is on the Scientific Advisory Board and is a member of the Poster Jury. The final session of the meeting on Chemoinformatics is dedicated to Prof. Peter Willett to celebrate his outstanding contribution to the field over 40 years. Val will chair this session and will open it by presenting some highlights of Peter’s career.

Matt Seddon, PhD student in the Chemoinformatics research group, has won the CINF Scholarship for Scientific Excellence at the American Chemical Society meeting in San Francisco, April 2-6. The scholarship program of the Division of Chemical Information (CINF) is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence. The award was made for his PhD work which he presented as a long abstract and in poster format: Global spectral and diffusion geometry descriptors of 3D molecular shape for virtual screening Authors: Matthew Seddon, David Cosgrove, Martin Packer and Val Gillet Matt also gave an oral presentation. Matt Seddon (second from right) and colleagues Matt's PhD is being funded by a BBSRC Industrial CASE Partnership Studentship in collaboration with AstraZeneca. He is supervised by Professor Val Gillet.

In association with the Chemical Structure Association Trust and the Molecular Graphics and Modelling Society, the School hosted the Seventh Joint Sheffield Conference on Chemoinformatics from the 4 to the 6 July 2016.   This triennial conference is now firmly established in the chemoinformatics calendar, and attracted 116 delegates from around the world.   The ten sessions included 37 poster and 28 oral presentations, with the conference dinner being held in the splendid surroundings of Sheffield Cathedral.

On Thursday 29 January, PhD student Lucyantie Mazalan will present a research seminar on The Effect of Dimensionality on the Effectiveness of Nearest Neighbour Searching Methods in Chemoinformatics Applications. Nearest neighbour search in chemoinformatics application aims to identify the closest molecule to the query molecule. This involves measurements using different molecular similarity coefficients to the highly dimensional molecular descriptors. However, the performance of nearest neighbour search has been found to decrease as the dimensionality increases. One reason is because, as the dimensionality increases, the ratio of the distance from the query point to the nearest and farthest neighbour approaches unity. This study will investigate a range of different similarity coefficients on different molecular dimensionality. The results of this analysis will be used to assess the effect of the dimensionality on the effectiveness of nearest neighbour searching methods in chemoinf...

Professor Val Gillet, Head of School at the Information School, will be in Bari from 8 to 10 December 2014 at the kick off meeting for an EU-IAPP (Industry Academia Partnerships and Pathways) project which will explore a "Diagnostic and Drug Discovery Initiative for Alzheimer’s Disease". The University of Sheffield is represented in this project by Professor Gillet and by Professor Beining Chen, Professor of Medicinal Chemistry in the University's Department of Chemistry.  Professor Chen is the project lead and the orher project partners are are Eli Lilly of Bari SME Biofordrug, Lisbon Univeristy and Canadian company Amorfit. The scheme is part of the Marie Curie FP7 scheme.  It includes a considerable amount of exchange of existing researchers (both PhD and more established).  It will also fund 5 post-doctoral researchers, two of which will come to the University of Sheffield.  One will be based in the Information School and one in the Department of Chemistr...

Information School PhD student Matthew Seddon will present a seminar on Tuesday 14 October on the development of novel techniques for assessing bioisosteric similarity of chemical fragments. Bioisosterism, which is related to the similarity of biological function between two molecules, is an important concept in drug development.  Matthew’s presentation will introduce his current research project, which is concerned with developing new techniques for bioisosteric similarity of chemical fragments. The presentation will start with a general overview of chemoinformatics techniques and will highlight relevant themes for the project such as molecular similarity, 3D molecular shape, and the similarity property principle. The presentation will then cover experimental work that has been carried out to produce a test set of bioisosteric pairs that can be used to evaluate bioisosteric similarity methods before concluding with an overview of future work.  In parti...

The Information School’s Chemoinformatics Research Group has released a paper which will help the European Medicines Agency to decide whether new orphan drugs should be granted licences.   Evaluation and supervision of medicines throughout the European Union is the responsibility of the European Medicines Agency.   One particular activity which the Agency is involved in is the licensing of orphan drugs – medicines which are designed to treat people with rare diseases.   This activity is currently carried out by a panel of human experts.   However the Chemoinformatics Research Group’s paper outlines computer techniques that could be used to help the panel in deciding whether or not a new orphan drug should be granted a licence.   The paper (Franco, P., Porta, N., Holliday, J. D. & Willett, P. “The use of 2D fingerprint methods to support the assessment of structural similarity in orphan drug legislation” Journal of Cheminformatics , 6:5, 2014) ca...

The Sheffield conference on Chemoinformatics ( cisrg.shef.ac.uk/shef2013 ) is being held at The Edge and is being run by Val Gillet, John Holliday and Peter Willett on behalf of the Molecular Graphics and Modelling Society and the Chemical Structure Association Trust.  The conference has brought together over 140 delegates from industry and academia from across the globe to discuss the latest techniques in computer-aided drug discovery.  With over 75 oral and poster presentations and an exhibition from leading software companies, it has been a very busy but enjoyable three days.

The Call for papers has recently appeared for the 6th Joint Sheffield Conference on Chemoinformatics .  This major international meeting, which is again being co-sponsored by the Molecular Graphics and Modelling Society and by  the Chemical Structure Association Trust, will be held at The Edge, University of Sheffield, 22nd-24th July 2013.

Peter Willett attended the Internet Librarian International 2012 conference in Olympia, where he received the Jason Farradane Award on behalf of the School's Chemoinformatics Research Group (Val Gillet, John Holliday and Peter Willett). Next week he will be visiting the USA to give talks on "Introduction to chemoinformatics" at Fordham University and "Fusing database rankings in similarity-based virtual screening" at Rutgers University.

The Information School's Chemoinformatics Research Group has been awarded the 2012 UKeiG Jason Farradane Award , in recognition of its outstanding 40 year contribution to the information field. The prize is awarded to the three current members of the group,  Professor Val Gillet , Dr John Holliday and Professor Peter Willett . The judges recognised the Group's status as one of the world's leading centres of chemoinformatics research, a major contributor to the field of information science, and an exemplar in raising the profile of the information profession. The School has a long association with the Farradane prize. Its second recipient was long time member of staff Professor Mike Lynch in 1980.

Val Gillet is presenting a paper on "Multiobjective design of drug-like molecules" at a workshop on multi-disciplinary integration and optimisation in science and engineering at University College London on April 2nd.

Val Gillet, Sonny Gan and Jorge Valencia, members of the Chemoinformatics Research Group, are all presenting at the Spring 2012 American Chemical Society Meeting in San Diego, March 25-29th. Val is presenting an oral paper on "De novo design of synthetically accessible molecules". Sonny and Jorge are presenting posters on "Identification of alternative druggable targets for prion diseases" and "A Lanczos-based approach to the spectral clustering of chemical data", respectively.

Eight current members of the School's Chemoinformatics Research Group are participating in the 9th International Conference on Chemical Structures in The Netherlands June 5-9th - the major conferences in the field in 2011. 9th International Conference on Chemical Structures Sheffield has a very strong presence at the meeting. The group is contributing two oral presentations: Richard Sherhod (Mining of emerging structural patterns for http://www.blogger.com/img/blank.gifidentification of toxicophores) and Ben Allen (De novo design of synthetically feasible compounds using reaction vectors and evolutionary multiobjective optimisation); three poster presentations: Hua Xiang, Sonny Gan and Jorge Valencia; and Val Gillet is a member of the Scientific Advisory Board. In addition, there are three oral presentations by our ex-PhD students (Sarah Aaron, Dave Wood and George Papadatos) and three posters (Richard Martin, Maciej Haranczyk, Nathan Brown).