Subject: Pharma-IT Platform - What's New in Spring 2008? Dear Recipient of the Pharma-IT Newletter, We would like to update you on recent developments in the Pharma-IT Platform - our next Interaction Meeting is coming, four publications appeared, we have three new collaborators joining us, and we will visit several conferences in the coming months. For up-to-the-minute information please visit http://www.pharma-it.net. ** Save the date ** The 2nd 'Pharma IT Interaction Meeting' is coming! Day and time: Tuesday, 13th May, 2pm Program: Hendrik Blockeel will talk on "Inductive Logic Programming and its applications in drug discovery", followed by coffee and socializing Location: Gorlaeus Laboratoria, Room C06, 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. Personal News 5. Events 1. Publications a) How do you predict which compounds to screen for bioactivity against a target? A publication on "“Virtual Fragment Linking”: An Approach To Identify Potent Binders from Low Affinity Fragment Hits" by members of the Pharma-IT Platform appeared in the Journal of Medicinal Chemistry (DOI: http://dx.doi.org/10.1021/jm701314u) b) Distributed Chemical Computing is on the rise - read about a JavaRMI implementation and chemical applications in "Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem", published in the Journal of Chemical Information and Modeling: http://dx.doi.org/10.1021/ci700334f c) Multidimensional optimization of molecules is the topic of an extended abstract on the "Molecule Evoluator" that will appear in the proceedings of the Adaptive Computing in Design and Manufacture Conference (ACDM08), entitled "Combined Interactive and Automated Adaptive Search for Molecular Design". See the publications page (http://www.pharma-it.net/publications.html) for a PDF of the poster and the extended abstract. d) The work "Evolutionary Algorithms for automated drug design towards target molecule properties" has been accepted as a full paper for the Genetic and Evolutionary Computation (GECCO) Conference 2008 (http://www.sigevo.org/gecco-2008/) to be published in the ACM series 2. New Collaborators a) Prof Herman van Vlijmen, Director of Computational Virology and Chem/Bio-Informatics at Tibotec in Mechelen, Belgium, has been appointed as a full professor at Leiden University. He will collaborate closely with Prof Ad IJzerman on various aspects of computer-aided drug design and also be involved with ongoing projects in the Pharma-IT Platform. Prof van Vlijmen was working in the CADD division of Biogen in Cambridge/MA for several years before returning to Europe. Information about his previous work can be found here: http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&cmd=Search&term=van%20vlijmen%20h[au] b) An expert in modeling ion channels will join the Pharma-IT Platform on 1 June 2008 to work on the TI Pharma Cardiotoxicity Project on hERG modeling, Dr Munikumarreddy Doddareddy. Dr Doddareddy obtained his PhD from the Korean Institute of Science and Technology (KIST) in Seoul, South Korea, and published extensively on both ligand-based and target based ion channel activity models. For a list of his previous work please have a look here: http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&cmd=Search&term=doddareddy%20mr[au] c) Eric Faddiev, master student in the bioinformatics program of TU Delft and Leiden University, joined the Pharma-IT Plaform for his master thesis to work on the design of ligands for isoforms of the 14-3-3 protein. A warm welcome to Prof van Vlijmen, Dr Doddareddy and Eric Faddiev and we are looking forward to a fruitful period of joint research in the group! 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 various conferences in the coming months with poster and/or oral presentations: a) Annual Meeting of the KNCV, with a poster on "The ‘Pharma-IT Platform’: An Initiative by Leiden University to Analyze Life Science Data Using Computer Science Methods", 17 April, Ede, The Netherlands (http://www.voorjaarsbijeenkomst.kncv.nl/) b) Bio-IT World Conference & Expo 2008, with an oral presentation on "Merging High-Content Screening and in silico Approaches for Compound Profiling and Mode-of-Action Analysis", 28 - 30 April 2008, Boston, USA (http://www.bio-itworldexpo.com/) c) Adaptive Computing in Design and Manufacture Conference (ACDM08), with a poster on "Combined Interactive and Automated Adaptive Search for Molecular Design", 29 April - 1 May 2008, Bristol, UK (http://www.ad-comtech.co.uk/ACDM08/) d) International Conference on Chemical Structures (ICCS), with an oral presentation on "Merging High-Content Screening and in silico Approaches for Compound Profiling and Mode-of-Action Analysis", 1 - 5 June 2008, Noordwijkerhout, The Netherlands (http://www.int-conf-chem-structures.org/) 4. Personal News Andreas Bender, member of the Academic Leadership Team of the Pharma-IT Platform and Assistant Professor for Cheminformatics and Pharmaceutical IT with Leiden University, will be the AstraZeneca Visiting Fellow with the Institute for Bioinformatics and Applied Biotechnology (IBAB) Bangalore (http://www.ibab.ac.in) from June to September 2008. He will be involved in teaching as well as research modules of the newly designed cheminformatics course at IBAB, which has just been awarded 'Centre of Excellence' status for research and training in the field of Bioinformatics from the Department of Information Technology of the Ministry of Communication and IT of the Government of India. 5. Events a) On Tuesday, 13th of May, at 2pm our 2nd Pharma IT Interaction Meeting will take place. Location will be room C06 of the Gorlaeus Laboratoria (Map http://tinyurl.com/4xuow6). Firstly, Hendrik Blockeel from KU Leuven will give a presentation on his current work on "Inductive Logic Programming and its applications in drug discovery", including a short demo of the Chemistry Assistant software developed by the spin-off company PharmaDM. This will be followed by coffee, an update of the Pharma-IT activities and socializing. You are very welcome to attend the event and/or to forward the information to a colleage. b) Save the date! On 10 September the Pharma-IT Workshop on Cheminformatics and Systems Biology will take place. More information on http://www.pharma-it.net and in our next newsletter. Best wishes, 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 every 3 months.