Technical Program | San Francisco |
8:25 AM - 3:30 PM, Moscone Convention Center - 122, Oral
Cyberinfrastructure in Chemistry, Information and Education: New Emerging Technologies
Organized by: Guenter Grethe
Presiding: Guenter Grethe
8:25 AM | Introductory Remarks | ||||||
8:30 AM | PubChem: An information resource linking chemistry and biology Evan Bolton | ||||||
9:00 AM | Mining chemical information from the literature: Finding the right stuff Debra L. Banville | ||||||
9:30 AM | Creating a virtual large research infrastruktur René Deplanque | ||||||
10:00 AM | SemanticEye: A semantic Web application to rationalise and enhance chemical electronic publishing Omer Casher Henry S. Rzepa | ||||||
10:30 AM | CombeChem - Semantic support for the chemical information lifecycle Jeremy G Frey | ||||||
11:00 AM | Technical and social aspects of collaboratively developed information systems Christoph Steinbeck | ||||||
11:30 AM | Growth of e-Chemistry Peter Murray-Rust |
Break for Lunch
1:30 PM | CHEMGAROO: A chemistry educational system Jost T. Bohlen | ||||||
2:00 PM | Guaranteed high-interest withdrawals: Creating a dynamic and usable chemical information instruction digital depository F. Bartow Culp Grace A. Baysinger, Susan Cardinal | ||||||
2:30 PM | New information services in Germany: GetInfo and vascoda Irina Sens | ||||||
3:00 PM | Impact of cyberinfrastructure on large research libraries Grace Baysinger |
9:00 AM - 4:30 PM, Moscone Convention Center - 125, Oral
Advances in Virtual High-Throughput Screening
Organized by: Osman F. Güner
Presiding: Osman F. Güner
9:00 AM | Bayesian modeling in Pipeline PilotTM: Application to structural analysis of CDK2 inhibitors Shikha Varma-O’Brien David Rogers | ||||||
9:30 AM | Virtual Ligand Screening with eHiTS David Reid Zsolt Zsoldos, Aniko Simon, Bashir S. Sadjad, A Peter Johnson | ||||||
10:00 AM | Advanced HTS data mining using web service workflows David Wild Gary Wiggins, Xiao Dong, Huijun Wang, Marlon Pierce, Jang H Lee, geoffrey fox | ||||||
10:30 AM | Similarity searching in large virtual chemistry spaces derived from synthetically accessible combinatorial libraries Markus Boehm Gregory A. Bakken, Alan M. Mathiowetz | ||||||
11:00 AM | Increasing the speed and accuracy of the virtual screening process Pascal Bonnet Eric Arnoult, Christophe Meyer |
Break for Lunch
1:30 PM | New tools for virtual high-throughput screening N. Sukumar Curt M. Breneman, C. Matthew Sundling | ||||||
2:00 PM | Consensus descriptor-subset selection for ensemble QSAR models Debojyoti Dutta Rajarshi Guha, Peter C. Jurs, Ting Chen | ||||||
2:30 PM | Neighbor voting: A method to improve confidence in docking poses Santosh Putta Paul Beroza, Komath Damodaran, Thomas Macke | ||||||
3:00 PM | Using physicochemical parameter models to screen for bioavailability and drug plasma concentration Pranas Japertas Alanas Petrauskas, Remigijus Didziapetris | ||||||
3:30 PM | Probabilistic pharmacophore matching Boris Klebansky | ||||||
4:00 PM | Using physicochemical parameter models to screen for bioavailability and drug plasma concentration Kristian Birchall Gavin Harper, Valerie J. Gillet, Stephen Pickett |
9:00 AM - 1:15 PM, Moscone Convention Center - 228/230, Oral
Careers for Computational Chemists in Pharma, Biotech, Patent Law, Software Vendors, National Labs, and the National Institutes of Health
Organized by: Wendy D. Cornell
9:00 AM | Introductory Remarks | ||||||
9:05 AM | Peer review at the National Institutes of Health George Chacko | ||||||
9:30 AM | Guiding health science – and having fun! Janna P. Wehrle | ||||||
9:55 AM | Intramural research at the National Center for Biotechnology Information Evan Bolton | ||||||
10:20 AM | Intermission | ||||||
10:35 AM | Academia or industry? Ramy Farid | ||||||
11:00 AM | Long and winding road as a computational chemist in biotech Erin K. Bradley | ||||||
11:25 AM | Putting science skills to work in the legal profession Michael Shuster | ||||||
11:50 AM | Computer assisted drug discovery in pharma: Catch that trade wind in your sails Veerabahu Shanmugasundaram | ||||||
12:15 PM | Panel Discussion |
8:00 AM - 5:00 PM, Moscone Convention Center - 122, Oral
Challenges in Structure Searching
Organized by: Jan Williams
Presiding: Jan Williams
8:00 AM | Structure Searching Concepts at Chemical Abstract Service: Past, Present, and Future (?) W. Fisanick Karen Lucas, Tommy Ebe | ||||||
8:30 AM | Weaving tools and techniques to create a tapestry of substance-oriented information from CAS Linda S. Toler Kathleen D. Schmidt | ||||||
9:00 AM | Combining text and structural search in the chemical literature John G. Cleary Nicholas T. Goncharoff | ||||||
9:30 AM | Compound Selection and Library Analysis at Bayer Healthcare AG Jens Schamberger | ||||||
10:00 AM | Intermission | ||||||
10:15 AM | Substructure searching of Markush structures and its uses John M. Barnard Anthony P. F. Cook, Geoff M. Downs, Annette von Scholley-Pfab, Daniel G. Thomas, P. Matthew Wright, Jimmy Chung, Gavin Harper, Stephen Pickett | ||||||
10:45 AM | A new look at the Merged Markush Service Joseph M. Terlizzi | ||||||
11:15 AM | Towards Markush: First steps to turn a chemistry database engine into a Markush device Szabolcs Csepregi Nóra Máté, Szilárd Dóránt, Andras Volford, György Pirok, Ferenc Csizmadia |
Break for Lunch
1:00 PM | Think like a database: Substructure searching in the classroom Judith N. Currano | ||||||
1:30 PM | Comparison of structure searching between SciFinder Scholar and MDL CrossFire Commander Bing Wang | ||||||
2:00 PM | Advantages of multi-file chemical structure searching Bob Stewart | ||||||
2:30 PM | Multi-host, multi-file chemical structure patent searching Donald Walter | ||||||
3:00 PM | Advances in chemical reaction searching Jim Nourse William Lingran Chen, Bradley D. Christie, David L. Grier, Burton A. Leland | ||||||
3:30 PM | Rapid structure lookup and distributed substructure searches in very large databases Marc C. Nicklaus Markus Sitzmann, Igor V. Filippov, Wolf-Dietrich Ihlenfeldt | ||||||
4:00 PM | Intermission | ||||||
4:30 PM | Open Meeting. CINF Division | ||||||
5:00 PM | Intermission | ||||||
5:30 PM | Open Meeting. Committees on Publications and Chemical Abstracts Service. |
8:30 AM - 12:05 PM, Moscone Convention Center - 125, Oral
Library Watch: New Hot Areas in Chemistry
Organized by: Leah R. Solla, Andrea B. Twiss-Brooks
8:30 AM | Introductory Remarks | ||||||
8:35 AM | Catalyzing sustainability: Emerging fields in green chemistry Kathryn E. Parent Jennifer L. Young, Julie B. Manley, Paul T. Anastas | ||||||
9:05 AM | Soft Matter: Where hard science gets soft and squishy Carol Stanier | ||||||
9:35 AM | Brief introduction to materials science for the information professional Meghan Lafferty | ||||||
10:05 AM | Trends in Chinese chemical research DingFei Lui Song Yu, Dani Xu | ||||||
10:35 AM | Is it chemistry or biology – or both? Sarah Thomas | ||||||
11:05 AM | Bioinformatics: an instructional opportunity for academic science and engineering libraries Erja Kajosalo | ||||||
11:35 AM | The art and science of information dissemination Sarah Tegen Adam Chesler |
8:30 AM - 11:30 AM, Marriott - Salon 11, Oral
Chemical Information and Chemical Information Education in the Electronic Age
Organized by: F. Bartow Culp
Presiding: F. Bartow Culp
8:30 AM | Introductory Remarks | ||||||
8:35 AM | Beyond Google®: Goals for chemical information instruction in the electronic age Adrienne W. Kozlowski F. Bartow Culp | ||||||
9:00 AM | Exploring chemistry through the chemical literature co Allan K. Hovland | ||||||
9:25 AM | Teaching students how to use patent databases Lawton Shaw Margy MacMillan | ||||||
9:50 AM | Intermission | ||||||
10:00 AM | From standards to practice: Incorporating chemical information literacy standards into the classroom Carrie L. Newsom | ||||||
10:25 AM | Teaching chemical principles using the Cambridge Structural Database Gary M Battle Ian Bruno | ||||||
11:05 AM | Chemical information instruction in the age of Google® Charles F. Huber |
1:30 PM - 4:30 PM, Moscone Convention Center - 125, Oral
Entepreneurship in Chemical Informatics
Organized by: Alan Engel, Terry Wright
Presiding: Alan Engel, Terry Wright
1:30 PM | Produce, purchase, or partner? An informatics business development case study Gregory M. Banik Kevin Scully | ||||||
2:00 PM | Strategic analysis of discovery research informatics in the pharmaceutical Industry Richard Kho Hugo O. Villar | ||||||
2:30 PM | Nothing ventured, nothing gained Wendy A Warr | ||||||
3:00 PM | Freedom to use and barriers to entry for the informatics entrepreneur Gianna Arnold | ||||||
3:30 PM | Crossing the Pacific: Relocating a small patent information business Alan Engel | ||||||
4:00 PM | Time for a global patent database Gregory Aharonian |
8:00 PM - 10:00 PM, Moscone Convention Center - Hall D, Poster
Sci-Mix Poster Session
8:00 PM | Optimizing CoMFA setttings Shane D. Peterson Wesley Schaal, Torbjörn Lundstedt, Anders Karlén | ||||||
8:00 PM | A procedure for modeling induced fit effects in receptor-ligand complexes Florian Raubacher | ||||||
8:00 PM | Addressing the speed/accuracy dilemma of the virtual screening process Christophe Meyer Pascal Bonnet, Eric Arnoult | ||||||
8:00 PM | eHiTS_Score: A new statistically derived empirical scoring function Darryl Reid Zsolt Zsoldos, Aniko Simon, Bashir S. Sadjad, A Peter Johnson | ||||||
8:00 PM | Fragmental QSAR model for the prediction of AMES genotoxicity Kiril Lanevskij Pranas Japertas, Remigijus Didziapetris, Alanas Petrauskas | ||||||
8:00 PM | Identification of unique and redundant scaffolds in chemical databases Mark R. Hansen Jason Hodges | ||||||
8:00 PM | In silico technology for identification of potentially toxic compounds in drug discovery Alanas Petrauskas Pranas Japertas, Remigijus Didziapetris | ||||||
8:00 PM | Maximum common substructure search in focused set profiling and in library analysis Ferenc Csizmadia Miklos Vargyas, Szabolcs Csepregi, Peter Vadasz | ||||||
8:00 PM | Mechanistic, ionization-specific model of human intestinal absorption Pranas Japertas Alanas Petrauskas, Remigijus Didziapetris | ||||||
8:00 PM | MDL® CMC database used to a seek SARS cure Pieder Caduff Hualiang Jiang | ||||||
8:00 PM | Normalizing ionic resonance structures Markus Sitzmann Wolf-Dietrich Ihlenfeldt, Marc C. Nicklaus | ||||||
8:00 PM | ZINC: Molecular representation is important for virtual screening John J Irwin Brian K. Shoichet | ||||||
8:00 PM | Prediction of hERG liability using a novel approach Max Leong | ||||||
8:00 PM | Predictive data mining system to build models based on customized training sets and adding knowledge Guangyu Sun Chihae Yang, Kevin P. Cross, Jared Archer | ||||||
8:00 PM | Quantitative structure and activity relationships study on the Ah receptor binding affinities of polybrominated diphenyl ethers using a support vector machine Gang Zheng Man Xiao, Xiaohua Lu | ||||||
8:00 PM | Quantum mechanical energy-based screening of combinatorially generated library of tautomers Maciej Haranczyk Maciej Gutowski | ||||||
8:00 PM | R-NN curves: A method for diversity analysis and cluster identification Rajarshi Guha Debojyoti Dutta, Peter C. Jurs, Ting Chen | ||||||
8:00 PM | Sources of information on chemical industry statistics for chemical engineering students Bing Wang | ||||||
8:00 PM | Standardizer: Molecular cosmetics for cheminformatics Ferenc Csizmadia György Pirok, Nóra Máté, István Cseh, Szilárd Dóránt, Péter Kovács, Szabolcs Csepregi | ||||||
8:00 PM | Studying the effects of individual interaction energies in a variety of protein-ligand complexes Sally Mardikian Valerie J. Gillet, Richard M. Jackson, David R. Westhead | ||||||
8:00 PM | Understanding stereoselectivity: Molecular modeling to inform organic synthesis Robert S. Paton Jonathan M. Goodman | ||||||
8:00 PM | Multivariate analysis of pyranone based HIV protease inhibitors: Cheminformatics approach Barun Bhhatarai Rajni Garg |
8:30 AM - 5:50 PM, Moscone Convention Center - 122, Oral
Herman Skolnik Award Symposium
Organized by: Hugo Kubinyi
Presiding: Osman F. Güner
8:30 AM | Do MedChem rules stand up to validation? Yvonne C. Martin | ||||||
8:55 AM | Exploiting QSAR models for effective lead optimization Richard A. Lewis | ||||||
9:20 AM | The more things change, the more they stay the same: Issues in data analysis from QSAR to HTS David Rogers | ||||||
9:45 AM | Intermission | ||||||
10:00 AM | What's a drug designer to do? Robert D. Clark | ||||||
10:25 AM | Identifying the optimal energy window in pharmacophore discovery John H. van Drie | ||||||
10:50 AM | High strain energies of bound ligands: What is going on? Paul Labute | ||||||
11:15 AM | “Fuzzy” pharmacophores for virtual screening and library design Gisbert Schneider |
Break for Lunch
2:00 PM | Structure-based 3D pharmacophores as a tool for efficient virtual screening Gerhard Wolber | ||||||
2:25 PM | Recent advances in molecular docking Christian Lemmen, Holger Claußen, Marcus Gastreich | ||||||
2:50 PM | Understanding decoys and hits in molecular docking Brian K. Shoichet | ||||||
3:15 PM | Intermission | ||||||
3:30 PM | Modeling chemical reactions in drug design Johann Gasteiger | ||||||
3:55 PM | Oncology: Targeting the Hedgehog Signaling Pathway with small molecules Alex S. Kiselyov Sergey Tkachenko, Sergei Malarchuk, Ilya Okun | ||||||
4:20 PM | Design and synthesis of tailor-made compound libraries via a knowledge-based approach: A case study Wibke E. Diederich Christof Gerlach, Andreas Blum, Jark Boettcher, Sascha Brass, Torsten Luksch, Gerhard Klebe | ||||||
4:45 PM | Intermission | ||||||
5:00 PM | Herman Skolnik Award Lecture: Why models fail Hugo Kubinyi | ||||||
5:25 PM | Award Presentation |
9:00 AM - 4:30 PM, Moscone Convention Center - 122, Oral
Rediscovery of Older Information
Organized by: C. Huber, Jan Williams
9:00 AM | The past illuminates the future Philip Abrahams | ||||||
9:30 AM | Cooperation between Canadian university chemistry departments, the Chemical Institute of Canada, and publisher: Archiving the Canadian Journal of Chemistry, issues 1951 through 1997 Brian Maurice Lynch Lai Im Lancaster | ||||||
10:00 AM | A remembrance (and retrieval) of information past: Finding older information in CAS databases Jan Williams Ida L. Copenhaver | ||||||
10:30 AM | Backfile journals and indexes: Impact and issues for researchers and research institutions Gary Ives | ||||||
11:00 AM | An analysis of citations in scientific and patent literature to historical research from the first half of the 20th century and the relationship to the accessibility of these works on electronic archives Simon M Pratt, Robert A Stembridge |
Break for Lunch
2:00 PM | Effects of electronic indexes and journals on citation patterns in chemical information Beth Thomsett-Scott | ||||||
2:30 PM | If you build it, will they come? Experience with journal backfiles at HighWire Press Helen Barsky Atkins | ||||||
3:00 PM | Looking back, moving forward: Examining the impact of digitizing the ACS archive David P Martinsen Adam Chesler | ||||||
3:30 PM | Recent advances in the phlogiston theory: Mining the *really* old literature F. Bartow Culp | ||||||
4:00 PM | Reviving analytical data of the past with open submission databases and text mining tools Christoph Steinbeck Sam Adams, Stefan Kuhn, Peter Murray-Rust, Joe A Townsend, Christopher A. Waudby |
8:30 AM - 12:00 PM, Moscone Convention Center - 125, Oral
Materials Informatics
Organized by: Laurel A. Harmon, Mitchell A. Miller
8:30 AM | Cell-Surface Informatics (CSI): A platform for quantifying effects of biomaterial surface features on cells J. Carson Meredith Jing Su | ||||||
9:00 AM | Evolving an informatics environment for materials discovery and research Charles P. McGonegal Joseph F. Schaaf, J. W. Adriaan Sachtler | ||||||
9:30 AM | High-throughput sensor-based solvent-resistance mapping of copolymers and determination of quantitative structure-property relationships Radislav A. Potyrailo Ronald J. Wroczynski | ||||||
10:00 AM | Informatics for a high-throughput liquid formulations workflow Dave Rothman Tom Boomgaard, Bruce Wilson, Mary Beth Seasholtz | ||||||
10:30 AM | Using integrative analytics for on-line optimization of catalyst libraries Francois Gilardoni David Farrusseng | ||||||
11:00 AM | Materials informatics for materials chemistry Krishna Rajan | ||||||
11:30 AM | Experimental strategies for combinatorial and high throughput materials development James N. Cawse |
1:10 PM - 5:00 PM, Moscone Convention Center - 125, Oral
Chemical Information and Organic Chemistry: The Road Ahead
Organized by: Martin G. Hicks, Guenter Grethe
Presiding: Guenter Grethe
1:10 PM | Introductory Remarks | ||||||
1:15 PM | Chemical ontologies: Towards automated data mining and knowledge generation on chemical compounds Lutz Weber | ||||||
1:40 PM | Open-standards based IT integration in Life Science research: From present to future Carsten Stauffer Frank N. Penkert, Karsten Tittmann, Heinz Rakel | ||||||
2:05 PM | Classification of organic and bio-organic reactions with MOLMAP physicochemical descriptors Joao Aires-de-Sousa Sunil Gupta, Diogo A. R. S. Latino, Qing-You Zhang | ||||||
2:30 PM | Following the road step by step: A new reaction database-driven tool for stepwise retrosynthetic analysis Christof H. Schwab Bruno Bienfait, Johann Gasteiger | ||||||
2:55 PM | Introducing Route Designer v1.0 A Peter Johnson Zsolt Zsoldos, Aniko Simon, Darryl Reid, James Law, Yang Liu, Sing Yoong Khew, Howard Y. Ando | ||||||
3:20 PM | Organic chemistry in the ChemgaPedia encyclopaedia: Useful visualization tools for e-teaching and e-learning Torsten Winkler Rainer Herges | ||||||
3:45 PM | Libraries and librarians: Supporting chemists with information Andrea Twiss-Brooks | ||||||
4:10 PM | Chemical information instruction and support at ETH Zürich: Concept, realization, and trends Martin P. Braendle Engelbert Zass, Blanka Cartier, Arun Kumar | ||||||
4:35 PM | Beilstein Chemical Toolkit (BCT): A flexible framework for handling chemical structure drawing Jochen Zügge |
8:30 AM - 4:20 PM, Moscone Convention Center - 122, Oral
General Papers
Organized by: Terry Wright
8:30 AM | 2D and 3D Visualization of pharmacophoric ligand-receptor interaction Fabian Bendix Philipp Adaktylos, Gerhard Wolber, Thierry Langer | ||||||
8:55 AM | Designed visualizations for enabling medicinal chemistry Barry J. Wythoff | ||||||
9:20 AM | A novel interactive tool for multidimensional biological data analysis Zhaowen Luo Xuliang Jiang | ||||||
9:45 AM | Dynamic indexing of chemical metadata using open tools: Case study of Open Babel, CDK, and the Blue Obelisk Geoffrey R. Hutchison Tobias Helmus, Stefan Kuhn, Henry S. Rzepa, Christoph Steinbeck, Christopher J. Swain, Egon L. Willighagen | ||||||
10:10 AM | Chemical ontologies and safety intelligence networks Jürgen Harter | ||||||
10:35 AM | Chemical structure search engines in cyberspace Klaus Gubernator Craig A. James | ||||||
11:00 AM | Exploring the feasibility of a protein structure prediction metaserver based on the AMBER/PBSA scoring function Hai-Feng Chen MJ Hsieh, Ray Luo | ||||||
11:25 AM | Continuum polarizable force field Yuhong Tan Ray Luo |
Break for Lunch
1:00 PM | High-throughput and conventional experimentation coexistence: War of the worlds? Francois Gilardoni David Farrusseng | ||||||
1:25 PM | In silico compound activity reprofiling A. W. Edith Chan Richard J Fagan, John P Overington | ||||||
1:50 PM | Interplay of sequence and structure: Extending the limits of detectability of distantly-related proteins Gerald M Maggiora Nathalie Meurice, Daniel P. Vercauteren | ||||||
2:15 PM | Interpretable correlation descriptors for quantitative structure-activity relationships James L. Melville Jonathan D. Hirst | ||||||
2:40 PM | Local lazy regression: Making use of the neighborhood to improve QSAR predictions Rajarshi Guha Debojyoti Dutta, Peter C. Jurs, Ting Chen | ||||||
3:05 PM | MCDL: A new public domain chemical information toolkit Andrei A. Gakh Michael N. Burnett, Sergei V. Trepalin, Alexander V. Yarkov, Igor V. Pletnev | ||||||
3:30 PM | Perchlorate and the press: Reporting on ambiguity Margaret W. Batschelet, William H. Batschelet | ||||||
3:55 PM | UsefulChem project: Open source chemical research with blogs and wikis Jean Claude Bradley Khalid Mirza, Alicia Holsey, Brett Rosen, James Giammarco, Julimarie DeNicco |