#240 - Technical Sessions

ACS National Meeting
August 22-26, 2010
Boston, MA

SUNDAY MORNING

Session A

Semantic Web in Chemistry RDF & Computation
BCEC 156 A
Organized by: Martin Braendle, Egon Willighagen
Presiding: Egon Willighagen
co-sponsored with COMP
8:45   Introductory Remarks
8:55 1 Semantic envelopment of cheminformatics resources with SADI
Leonid L Chepelev Egon Willighagen, Michel Dumontier - Abstract
9:40 2 RESTful RDF web services for predictive toxicology
J. R. Garritano- Abstract - PDF
10:10   Intermission
10:25 3 Linking the resource description framework to cheminformatics and proteochemometrics
Dr. Egon L. Willighagen Prof. Jarl E.S. Wikberg - Abstract - PDF
10:55 4 Chemical e-Science Information Cloud (ChemCloud): A semantic web based eScience infrastructure
Stephan Heineke Prof. Dr. Adrian Paschke PhD - Abstract
11:25 5 Use of semantic web services to access small molecule ligand database
Anay P Tamhankar Aniket S Ausekar - Abstract

SUNDAY MORNING

Session B

Assessing Collections and Information Resources in Science and Technology
BCEC 155
Erja Kajosalo, Organizer and Presiding
co-sponsored with SLA
9:00   Introductory Remarks
9:05 6 Usage metrics: Tools for evaluating science monograph collections
Michelle M Foss Dr. Vernon Kisling, Ms. Stephanie Haas - Abstract - PDF
9:30 7 Happily ever after or not: E-book collection usage analysis and assessment at USCLibrary
Norah Xiao - Abstract - PDF
9:55 8 From Chemical Abstracts to SciFinder: Transitioning to SciFinder and assessing customer usage
Susan Makar, Stacy Bruss - Abstract - PDF
10:20   Intermission
10:35 9 Using Web of Knowledge to identify publishing andcitation patterns of campus researchers at the University of Arkansas
Lutishoor Salisbury Jeremy S. Smith - Abstract - PDF
11:00 10 Don't forget the qualitative: Including focus groups in the collection assessment process
Teri M. Vogel Susan Shepherd - Abstract - PDF
11:25   Lunch
2:00 19 Data-driven development: How ACS Publications uses data toenhance products and services, and respond to customer needs
Sara Rouhi Melissa Blaney - Abstract - PDF
2:25 20 Objective collections evaluation using statistics at the MIT Libraries
Mathew Willmott Erja Kajosalo - Abstract - PDF
2:50 21 Getting the biggest bang for your buck: Methods and strategies for managing journal collections
Grace Baysinger - Abstract - PDF
3:15 22 Taking a collection down to its elements: Using various assessment techniques to revitalize a library
Leah Solla - Abstract - PDF
3:40   Panel Discussion

SUNDAY AFTERNOON

Data-Intensive Drug Design
BCEC 156 A
John Van Drie, Organizer
co-sponsored with COMP
1:45   Introductory Remarks
11:40   Lunch Break
1:50 11 Strategies for the identification and generation of informative compound sets
Michael S Lajiness - Abstract
2:15 12 Public-domain data resources at the European Bioinformatics Institute and their use in drug discovery
Christoph Steinbeck - Abstract
2:40 13 Decision making in the face of complicated drug discovery data using the Novartis system for virtual medicinal chemistry (FOCUS)
Donovan Chin - Abstract
3:05 14 Integrating chemical and biological data: Insights from 10 years of VERDI
Susan Roberts W. Patrick Walters, Ryan McLoughlin, Philppe Gabriel, Jonathan Willis, Trevor Kramer - Abstract
3:30   Intermission
3:45 15 Collaborative database and computational models for tuberculosis drug discovery decision making
Dr. Sean Ekins PhD Dr Justin Bradford PhD, Krishna Dole, Anna Spektor, Kellan Gregory, David Blondeau, Dr Moses Hohman PhD, Dr Barry A Bunin - Abstract
4:10 16 Data drive life sciences: The Pyramids meet the Tower of Babel
Dr. Rajarshi Guha - Abstract
4:35 17 Design principles for diversity-oriented synthesis: Facilitating downstream discovery with upfront design
Lisa Marcaurelle - Abstract
5:00 18 Overview: Data-intensive drug design
John H Van Drie - Abstract - PDF

SUNDAY EVENING

2010 CNF Scholarship for Scientific Excellence
BCEC Hall C
Guenter Grethe, Organizer
Sponsored by FIZ Chemie Berlin
6:30pm 23 Predicting specific inhibition of cyclophilins A and B using docking, growing, and free energy perturbation calculations
Somisetti V Sambasivarao Orlando Acevedo - Abstract
6:30pm 24 Using aggregative web services for drug discovery
Dr. Qian Zhu PhD Dr. Michael S. Lajiness PhD, Dr. David J. Wild PhD - Abstract
6:30pm 25 Semantifying polymer science using ontologies
Dr. Edward O. Cannon PhD Dr. Adams Nico, Prof. Peter Murray-Rust - Abstract
6:30pm 26 Toxicity reference database (ToxRefDB) to develop predictive toxicity models and prioritize compounds for future toxicity testing
Hao Tang Hao Zhu PhD, Liying Zhang, Alexander Sedykh PhD, Ann Richard PhD, Ivan Rusyn MD, PhD, Prof. Alexander Tropsha PhD - Abstract
6:30pm 27 OrbDB: A database of molecular orbital interactions
Matthew A. Kayala Chloe A. Azencott, Dr. Jonathan H. Chen PhD, Prof. Pierre F. Baldi PhD - Abstract
6:30pm 28 Novel approach to drug discovery integrating chemogenomics and QSAR modeling: Applications to anti-Alzheimer's agents
Rima Hajjo Dr. Simon Wang PhD, Prof. Bryan L. Roth MD, PhD, Prof. Alexander Tropsha PhD - Abstract
6:30pm 29 Cheminformatics improvements by combining semantic web technologies, cheminformatical representations, and chemometrics for statistical modeling and pattern recognition
Dr. Egon L. Willighagen - Abstract
6:30pm 30 Prediction of consistent water networks in uncomplexed protein binding sites based on knowledge-based potentials
Michael Betz Gerd Neudert, Gerhard Klebe - Abstract
6:30pm 31 Functional binders for non-specific binding: Evaluation of virtual screening methods for the elucidation of novel transthyretin amyloid inhibitors
Carlos J.V. Simões Trishna Mukherjee, Prof. Richard M. Jackson PhD, Prof. Rui M.M. Brito PhD - Abstract

MONDAY MORNING

Session B

Semantic Web in Chemistry OWL Chemical Ontologies
BCEC 155
Martin Braendle, Egon Willighagen, Organizers; Martin Braendle, Presiding
Co-sponsored by COMP
8:30 32 Using the oreChemexperiments ontology: Planning and enacting chemistry
Prof Jeremy G Frey Mark I Borkum, Prof Carl Lagoze, Dr. Simon J Coles - Abstract
9:15 33 CHEMINF: Community-developed ontology of chemical information and algorithms
Leonid L Chepelev Janna Hastings, Egon Willighagen, Nico Adams, Christoph Steinbeck, Peter Murray-Rust, Michel Dumontier - Abstract
9:45   Intermission
10:00 34 Chemical entity semantic specification: Knowledge representation for efficient semantic cheminformatics and facile data integration
Leonid L Chepelev Michel Dumontier - Abstract
10:30 35 Semantic assistant for lipidomics researchers
Alexandre Kouznetsov Rene Witte, Christopher J.O. Baker - Abstract
11:00 36 ChemicalTagger:A tool for semantic text-mining in chemistry
Dr Lezan Hawizy Dave M Jessop, Professor Peter Murray-Rust - Abstract
11:30   Lunch Break

MONDAY

The Journal of Chemical Information and Modeling's 50th Anniversary Symposium
BCEC AM: 156 A, PM: 157 C
William Jorgensen, Organizer & Presiding
Co-sponsored with COMP
8:45   Introductory Remarks
8:55 37 From canonical numbering to the analysis of enzyme-catalyzed reactions: 32 years of publishing in JCIM (JCICS)
Prof. Johann Gasteiger
9:25 38 Fifteen years of JCICS
Dr. George W MilneAbstract
9:55 39 Fifteen years in chemical informatics: Lessons from the past, ideas for the future
Dimitris Agrafiotis PhD - Abstract
10:25   Intermission
10:40 40 Applications of wavelets in virtual screening
Prof Val Gillet PhD Mr Richard Martin, Dr Eleanor Gardiner, Dr Stefan Senger - Abstract
11:10 41 Privileged substructures revisited: Target community-selective scaffolds
Jürgen Bajorath - Abstract - PPT
11:40 42 Automated retrosynthetic analysis: An old flame rekindled
Prof Peter Johnson PhD Anthony P Cook, James Law, Mahdi Mirzazadeh, Dr Aniko Simon PhD - Abstract
12:10   Lunch
1:30   Introductory Remarks
1:40 139 Configurational entropy and mechanical stress in molecular recognition
Prof. Michael K. Gilson M.D., Ph.D. - Abstract
2:10 140 Advancing anthrax toxin countermeasures using topomeric searching and virtual screening methodologies
Prof. Elizabeth A Amin PhD Dr. Ting-Lan Chiu PhD, Dr. Derek J Hook PhD, Dr. Michael A Walters PhD, Prof. Barry C Finzel PhD, Jonathan Solberg, Satish Patil, Dr. Todd W Geders PhD, Dr. Subhashree Rangarajan PhD, Dr. Rawle Francis PhD, Xia Zhang - Abstract
2:40 141 Model-free drug-like filters
Prof. Tudor I. Oprea MD, PhD Dr Oleg Ursu, Dr Cristian G. Bologa - Abstract
3:10   Intermission
3:25 142 Chemocentric informatics: Enabling bioactive compound discovery through structural hypothesis fusion
Prof. Alexander Tropsha - Abstract
3:55 143 Computers and drug discovery: From duds to $5B drugs
Prof. Robert C Glen PhD - Abstract
4:25 144 Weighting and fusion methods for similarity-based virtual screening
Prof. Peter Willett Shereen Arif, Dr John Holliday, Nurul Malim, Christoph Mueller - Abstract

MONDAY AFTERNOON

Session B

Wheres the Good Stuff? Consumer Health Information, and Social Networking Resources and Services
BCEC 155
Andrea Twiss-Brooks, Organizer & Presiding
1:00 43 Dietary supplements: Free evidence-based resources for the cautious consumer
Brian Erb MLS - Abstract - PDF
1:25 44 What lessons learned can we generalize from evaluation and usability of a health website designed for lower literacy consumers?
Mary J Moore PhD Randolph G. Bias PhD - Abstract
1:50 45 National Library of Medicine resources for consumer health information
Michelle Eberle - Abstract
2:15 46 Better prescription for information: Dietary supplements online
Gail Y. Hendler MLS - Abstract - PDF

MONDAY AFTERNOON

Semantic Web in Chemistry RDF/OWL Applications
BCEC 156 A
Martin Braendle, Egon Willighagen, Organizers; Egon Willighagen, Presiding
1:15 47 Overview of the linking open drug data task
Eric Prudhommeaux Egon Willighagen, Susie Stephens - Abstract
2:00 48 Control, monitoring, analysis and dissemination of laboratory physical chemistry experiments using semantic web and broker technologies
Prof Jeremy G Frey Stephen Wilson - Abstract
2:30   Intermission
2:45 49 Semantic analysis of chemical patents
Dave M Jessop Dr Lezan Hawizy, Prof. Peter Murray-Rust, Professor Robert C Glen - Abstract
3:15 50 Data mining and querying of integrated chemical and biological information using Chem2Bio2RDF
Dr David J Wild Bin Chen, Dr Ying Ding, Xiao Dong, Huijun Wang, Dazhi Jiao, Dr Qian Zhu, Madhuvanti Sankaranarayanan - Abstract
3:45 51 Mining and visualizing chemical compound-specific chemical-gene/disease/pathway/literature relationships
Dr. Qian Zhu Prajakta Purohit, Jong Youl Choi, Seung-Hee Bae, Dr. Judy Qiu, Prof. Ying Ding, Prof. David Wild - Abstract
4:15   Intermission
4:20   CINF Open Meeting
4:30   Open Meeting. Committees on Publications and Chemical Abstracts Service

MONDAY AFTERNOON

CINFlash: Can You Present Faster Than a Femtosecond Laser?
BCEC 155
Rajarshi Guha, Organizer
Co-sponsored with COMP
2:45   Panel Discussion

MONDAY EVENING

Sci-Mix
BCEC Hall C
Rajarshi Guha, Organizer
8:00pm 2 RESTful RDF web services for predictive toxicology
Dr. Nina Jeliazkova PhD - Abstract - PDF
8:00pm 6 Usage metrics: Tools for evaluating science monograph collections
Michelle M Foss Dr. Vernon Kisling, Ms. Stephanie Haas - Abstract - PDF
8:00pm 20 Objective collections evaluation using statistics at the MIT Libraries
Mathew Willmott Erja Kajosalo - Abstract - PDF
8:00pm 28 Novel approach to drug discovery integrating chemogenomics and QSAR modeling: Applications to anti-Alzheimer's agents
Rima Hajjo Dr. Simon Wang PhD, Prof. Bryan L. Roth MD, PhD, Prof. Alexander Tropsha PhD - Abstract
8:00pm 31 Functional binders for non-specific binding: Evaluation of virtual screening methods for the elucidation of novel transthyretin amyloid inhibitors
Carlos J.V. Simões Trishna Mukherjee, Prof. Richard M. Jackson PhD, Prof. Rui M.M. Brito PhD - Abstract
8:00pm 78 Prediction of solvent physical properties using the hierarchical clustering method
Dr. Todd M Martin Dr. Douglas M Young - Abstract
8:00pm 91 SAR and the role of active-site waters in blood coagulating serine proteases: A thermodynamic analysis of ligand-protein binding
Dr. Noeris K Salam Dr. Woody Sherman, Dr. Robert Abel - Abstract

TUESDAY

Herman Skolnik Award Symposium: The Marriage, or at Least Dating, of Molecular Simulation and Modeling with QSAR Analysis AM: Exploring Chemometric Methods
BCEC 156 A
Organized by: Anton Hopfinger, Emilio X. Esposito
Presiding: AM: Anton Hopfinger, PM: Emilio X. Esposito
8:15   Introductory Remarks
8:30 52 What makes polyphenols good antioxidants? Alton Brown, you should take notes...
Emilio Xavier Esposito PhD - Abstract
9:15 53 Engineering and 3D protein-ligand interaction scaling of 2D fingerprints
Jürgen Bajorath - Abstract - PDF
10:00   Intermission
10:15 54 In silico binary QSAR models based on4D-fingerprints and MOE descriptors for prediction of hERG blockage
Prof. Y. Jane Tseng PhD - Abstract - PPT - MP3
11:00 55 Telling the good from the bad and the ugly: The challenge of evaluating pharmacophore model performance
Robert D. Clark PhD - Abstract
12:00   CINF Luncheon (ticketed)
2:00 56 Creative application of ligand-based methods to solve structure-based problems: Using QSAR approaches to learn from protein crystalstructures
Prof. Curt M Breneman Dr. Sourav Das, Dr. Matt Sundling, Mr. Mike Krein, Prof. Steven Cramer, Prof. Kristin P Bennett, Dr. Charles Bergeron, Mr. Jed Zaretzki - Abstract
2:45 57 Computer-aided drug discovery
Prof. William L Jorgensen - Abstract
3:40   Intermission
3:45 58 Structure-based discovery and QSAR methods: A marriage of convenience
Jose S Duca - Abstract
4:30 59 Extending the QSAR Paradigm using molecular modeling and simulation
Professor Anton J Hopfinger Ph.D. - Abstract
5:15   Presentation of Award

WEDNESDAY

Section A

The Emerging Concepts of Activity Landscapes and Activity Cliffs and Their Role in Drug Research
BCEC 156 A
Organized by: Gerald Maggiora, Jurgen Bajorath, Michael Lajiness
Presiding: AM: Jurgen Bajorath, PM: Gerald Maggiora
Co-sponsored by COMP, MEDI
8:50   Introductory Remarks
9:00 60 Overview of activity landscapes and activity cliffs: Prospects and problems
Prof Gerald M Maggiora - Abstract
9:30 61 Exploring and exploiting the potential of structure-activitycliffs
Michael S Lajiness Dr Gerald M Maggiora PhD - Abstract
10:00 62 What makes a good structure activity landscape? Network metrics and structure representations as a way of exploring activity landscapes
Dr. Rajarshi Guha - Abstract
10:30   Intermission
10:45 63 Consensus model of activity landscapes and consensus activity cliffs
Jose L Medina-Franco Karina Martinez-Mayorga, Fabian Lopez-Vallejo - Abstract
11:15 64 R-Cliffs: Activity cliffs within a single analog series
Dimitris Agrafiotis PhD - Abstract
11:45   Lunch
2:00 70 Analysis of activity landscapes, activity cliffs, and selectivity cliffs
Jürgen Bajorath - Abstract - PDF
2:30 71 Using Activity Cliff Information in structure-based design approaches
Birte Seebeck, Prof. Dr. Matthias Rarey Markus Wagener - Abstract
3:00 72 Exploring activity cliffs using large scale semantic analysis of PubChem
Dr David J Wild Bin Chen, Qian Zhu - Abstract
3:30 73 Quantifying the usefulness of a model of a structure-activity relationship: The SALI Curve Integral
John H Van Drie Rajarshi Guha - Abstract
4:00   Concluding Remarks

WEDNESDAY

Section B

Recent Progress in Chemical Structure Representation AM: Applications and Tools
BCEC 155
Richard Apodaca, Organizer & Presiding
9:00   Introductory Remarks
9:05 65 Chemical structure representation in the DuPont Chemical Information Management Solutions database: Challenges posed by complex materials in a diversified science company
Dr. Mark A Andrews Dr. Edward S. Wilks - Abstract - PDF
9:35 66 From deposition to application: Technologies for storing and exploiting crystal structure data
Dr Colin R Groom Dr Jason Cole, Dr Simon Bowden, Dr Tjelvar Olsson - Abstract
10:05 67 Recent IUPAC recommendations for chemical structure representation: An overview
Mr. Jonathan Brecher - Abstract
10:35   Intermission
10:50 68 Orbital development kit
Dr. Egon L. Willighagen - Abstract - PDF
11:20 69 Line notations as unique identifiers
Krisztina Boda PhD - Abstract
11:50   Lunch
2:00 74 Status of the InChI and InChIKey algorithms
D. J. Wild - Abstract - PDF
2:30 75 Self-contained sequence representation (SCSR): Bridging the gap between bioinformatics and cheminformatics
Dr Keith T Taylor Dr William L Chen, Brad D Christie, Joe L Durant, David L Grier, Burt A Leland, Jim G Nourse - Abstract - PDF
3:00   Intermission
3:15 76 Representation of Markush structures: From molecules toward patents
Szabolcs Csepregi Nóra Máté, Róbert Wágner, Tamás Csizmazia, Szilárd Dóránt, Erika Bíró, Tim Dudgeon, Ali Baharev, Ferenc Csizmadia - Abstract - PDF
3:45 77 CSRML: A new markup language definition for chemical substructure representation
Dr. Christof H. Schwab Dr. Bruno Bienfait, Dr. Johann Gasteiger, Dr. Thomas Kleinoeder, Dr. Joerg Marucszyk, Dr. Oliver Sacher, Dr. Aleksey Tarkhov, Dr. Lothar Terfloth, Dr. Chihae Yang - Abstract - PDF

THURSDAY

General Papers AM: Characterization and Prediction
BCEC 156 A
Rajarshi Guha, Organizer; Presiding: Rajarshi Guha, PM; Xiang Wang, AM
8:45 78 Prediction of solvent physical properties using the hierarchical clustering method
Dr. Todd M Martin Dr. Douglas M Young - Abstract
9:10 79 Scaffold diversity analysis using scaffold retrieval curves and an entropy-based measure
Jose L Medina-Franco PhD Karina Martinez-Mayorga, Andreas Bender PhD, Thomas Scior PhD - Abstract
9:35 80 Nonsubjective clustering scheme for multiconformer databases
Dr. Austin B. Yongye Dr. Andreas Bender, Dr. Karina Martinez-Mayorga - Abstract
10:00   Intermission
10:10 81 Finding drug discovery "rules of thumb" with bump hunting
Mr. Tatsunori Hashimoto Dr. Matthew Segall PhD - Abstract
10:35 82 Machine learning in discovery research: Polypharmacology predictions as a use case
Nikil Wale PhD Kevin McConnell PhD, Eric M Gifford PhD - Abstract
11:00 83 Interpretable correlation descriptors for quantitative structure-activity relationships
Prof. Jonathan D. Hirst - Abstract
11:25   Lunch
1:30 84 Chemistry in your hand: Using mobile devices to access public chemistry compound data
Dr Antony J Williams PhD Valery Tkachenko - Abstract
1:55 85 Feature analysis of ToxCast(TM) compounds
Patra Volarath Stephen Little, Chihae Yang, Matt Martin, David Reif, Ann Richard - Abstract
2:20 86 Extracting information from the IUPAC Green Book
Prof Jeremy G Frey Mark I Borkum - Abstract
2:45 87 Biologics and biosimilars: One and the same?
Roger Schenck - Abstract
3:10   Intermission
3:20 88 Intelligent mining of drug information resources
Rashmi Jain Anay Tamhankar, Aniket Ausekar, Yuthika Dixit - Abstract
3:45 89 Cheminformatics semantic grid for neglected diseases
Paul J Kowalczyk PhD - Abstract
4:10 90 Extraction and integration of chemical information from documents
Dr Hugo O Villar Dr. Juan Betancort, Dr Mark R Hansen - Abstract
4:35 91 SAR and the role of active-site waters in blood coagulating serine proteases: A thermodynamic analysis of ligand-protein binding
Dr. Noeris K Salam Dr. Woody Sherman, Dr. Robert Abel - Abstract

 

 

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