Subject: Pharma-IT Platform @ Leiden University - Fall 2008 Newsletter Dear Recipients of the Pharma-IT Newletter, We would like to update you on exciting recent developments in the Pharma-IT Platform - our next Interaction Meeting is coming up, 5 peer-reviewed publications are about to appear, we had two new collaborators joining us, and we will visit two conferences in the coming months. For up-to-the-minute information visit http://www.PHARMA-IT.net. ** Save the date ** The 3rd 'Pharma IT Interaction Meeting' is coming! Day and time: Tuesday, October 21st, 12pm Program: Miquel Rojas Cherto will talk on "Strategies in Metabolite Identification using Multi-stage Mass Spectrometry Techniques", followed by coffee and socializing Location: Gorlaeus Laboratoria, Room L144, Leiden University Map http://tinyurl.com/4xuow6 More information in the Events section of this mail. Contents 1. Publications 2. New Collaborators 3. Conferences 4. Events 1. Publications Five publications from the Pharma-IT Platform are about to appear in the coming months, which have been submitted at the current state to either legal approval from TI Pharma or already to the respective publishers. They are as follows: a) "Chemogenomics: Looking at Chemistry through the Lens of Biology", by Munikumar R. Doddareddy, Gerard J. P. van Westen, Eelke van der Horst, Julio E. Peironcely, Frans Corthals, Adriaan P. IJzerman, Michael Emmerich, Jeremy L. Jenkins and Andreas Bender (submitted to publisher). This manuscript combines a review of current chemogenomics work with an extensive overview of the various research areas currently being pursued in the Pharma-IT Platform. b) "Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner", by Eelke van der Horst, Yasushi Okuno, Andreas Bender, and Adriaan P. IJzerman (submitted to TI Pharma Approval System). c) "Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs", by Jose L. Medina-Franco, Karina Martinez-Mayorga, Andreas Bender, Ray M. Marin, Marc A. Giulianotti, Clemencia Pinilla and Richard A. Houghten (submitted to TI Pharma Approval System). d) "How Similar are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space", by Andreas Bender, Jeremy L. Jenkins, Josef Scheiber, Sai Chetan K. Sukuru, Meir Glick and John W. Davies (submitted to publisher). e) "Computational Methods to Support High-Content Screening: From Compound Selection and Data Analysis to Postulating Target Hypotheses", by Anne Kümmel, Daniela Gabriel, Christian N. Parker and Andreas Bender (submitted to publisher). 2. New Collaborators / Student Updates a) Xiaofei Chao started her MSc project in the Pharma-IT Framework, entitled "Finding matching subgraphs in trees" which is closely related to subtree statistics for mass-spectroscopy in cooperation with the Metabolomics Center of Leiden University. b) Alexander Aleman started his MSc project in the Pharma-IT Framework, entitled "Diversity Maintenance in Molecular Drug Discovery using Niching", of relevance not only for the software "Molecule Evoluator", being developed in the group of Prof Ad IJzerman. c) Julio Peironcely successfully finished his MSc thesis on "Chemogenomics Analysis of GPCR Ligands by Molecular Subgraph Mining" on 5 September 2008 with the highest possible grade - Julio, congratulations! Julio now accepted a PhD position with the Metabolomics Center so he will remain at Leiden University doing research. d) Eric Faddiev is about to finish his MSc thesis in collaboration with Prof Herman Spaink from the Biology Department on "De-Novo Design of a selective Ligand for a 14-3-3 Isoform using Bilevel Multi-Objective Optimization". e) Anyi Zhang finished her Master Thesis on "Bayesian Mixed Integer Optimization using A-Priori Knowledge on Variable Dependences" - congratulations! f) Viktoria Li finished her Master Thesis on "Analysing Molecular Landscapes Using Random Walks and Information Theory" - congratulations! For a list of all current collaborators please visit http://www.pharma-it.net/members.html. 3. Conferences The Pharma-IT Platform will be present at two conferences in the coming months with poster and/or oral presentations: a) "Molecular Landscape Analysis using Random Walks and Information Theory", by B.V. Li, M.Emmerich, A.Bender, J. Kruisselbrink, E. Faddiev, A. Deutz, A. IJzerman, Th. Baeck. Extended Abstract for Presentation at the 4th German Conference on Cheminformatics, Goslar, November 2008: http://www.gdch.de/vas/tagungen/tg/5327__e.htm b) We will present the Pharma-IT Platform with a poster at the "FIGON Dutch Medicines Days 2008": http://www.figongmd.nl/ 4. Events a) On Tuesday, 21st of October, at 12pm, our 3rd Pharma IT Interaction Meeting will take place. Location will be room L144 of the Gorlaeus Laboratoria (Map http://tinyurl.com/4xuow6). Everyone is welcome and feel free to bring your lunch! Firstly, we will give a brief update on recent developments in the Pharma-IT framework where your input is more than welcome. Afterwards, Miguel Rojas Cherto from the Metabolomics Center will give a presentation on his current work on "Strategies in Metabolite Identification using Multi-stage Mass Spectrometry Techniques". This will be followed by coffee and socializing. You are very welcome to attend the event and to forward the information to a colleague. Hope to see you at the Interaction Meeting, October 21st! b) Michael Emmerich is teaching a course relevant to the topics of the Pharma-IT Platform starting this semester, on "Computer Simulations with Applications in the Life Sciences". The course takes place on Tuesdays, from 9am onwards, LIACS room 312. Students/scientists interested in the topic are very welcome to attend. c) We are currently planning a Workshop at the Lorentz Center with the working title "Optimizing Drug Design: Multi-criterion Decision Making and Optimization in Drug Discovery and Cheminformatics". More details with precise timings in the next newsletter! Best wishes and looking forward to seeing you next time! Andreas Bender and Michael Emmerich Academic Leadership Team of the Pharma-IT Platform http://www.PHARMA-IT.net ** The 'Pharma-IT Platform': An Initiative by Leiden University to Analyze Life Science Data Using Computer Science Methods. Find more information at http://www.PHARMA-IT.net. ** Do you know anyone else who would be interested to hear from the Pharma-IT Platform? Please forward this newsletter to him or her and ask him to subscribe to our update approximately every 3 months. ** In case you would like to change your subscription to this newsletter please just reply to this mail and let us know your requirements. Thank you!