CHEMICAL INFORMATION AND COMPUTATION

2016, NUMBER TWO, 252nd ACS National Meeting, Philadelphia, PA, Fall, 2016
2016, NUMBER ONE, 251st ACS National Meeting, San Diego, CA, Spring, 2016
2015, NUMBER TWO, 250th ACS National Meeting, Boston, MA, Fall, 2015
2015, NUMBER ONE, 249th ACS National Meeting, Denver, CO, Spring, 2015
2014, NUMBER TWO, 248th ACS National Meeting, San Francisco, CA, Fall, 2014
2014, NUMBER ONE, 247th ACS National Meeting, Dallas, TX, Spring, 2014
2013, NUMBER TWO, 246th ACS National Meeting, Indianapolis, IN, Fall, 2013
2013, NUMBER ONE, 245th ACS National Meeting, New Orleans, LA, Spring, 2013
Click here for past reports (2009-2012)


CHEMICAL INFORMATION AND COMPUTATION 2016 NUMBER TWO;
252nd ACS NATIONAL MEETING AND EXPOSITION
PHILADELPHIA, PA, AUGUST 21-25, 2016

INTRODUCTION

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MOLSOFT
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OPEN PHACTS
OPTIBRIUM
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PISTOIA ALLIANCE
PUBCHEM
Q-CHEM
ROYAL SOCIETY OF CHEMISTRY
SCHRÖDINGER
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SCILLIGENCE
SIMULATIONS PLUS
SPRINGER NATURE
SYGNATURE DISCOVERY
TAYLOR & FRANCIS GROUP
THE EDGE SOFTWARE CONSULTANCY
THIEME CHEMISTRY
THOMSON REUTERS

CINF AND COMP TECHNICAL PROGRAMS

SHARING PHARMACEUTICAL INDUSTRY DATA: OUTLOOK AND OPPORTUNITIES

New momentum in pre- and post-competitive pharma data sharing; getting the right data to drive the science
Data sharing and beyond. Lessons learned from the life sciences industry
ChEMBL database. Experiences as a data broker
D3R. “Leveraging” datasets to drive progress in protein-ligand modeling for computer-aided drug design
Rapid, accurate and reproducible binding affinity calculation for drug discovery. A retrospective analysis of the Pfizer Pan-Trk Program
Developing a community resource for the understudied kinome
Advancing quantitative biophysical predictions. What can be gained from industry-academic data sharing?
Beyond data sharing. Using real-world data for teaching real-world computational workflows and for benchmarking new methods

EFFECTIVELY HARNESSING THE WORLD’S LITERATURE TO INFORM RATIONAL COMPOUND DESIGN

Harnessing the world’s literature to provide a crystallographic perspective on compound design: federated pharmacophore searching as an example
GOSTAR and ChEMBL comparison; commercial versus open chemogenomics databases
Exploring available compound data with the Open PHACTS discovery platform and KNIME
NDEx, the Network Data Exchange: a resource for biological networks with application in informed compound design
Extracting and exploiting medicinal chemistry ADMET knowledge automatically from public and large pharma data
Extracting knowledge from large in vitro metabolic stability datasets using matched molecular pair analysis (MMPA)
Gravitational waves shaking the chemical universe: virtual chemistry 2.0
Network analytics of structured and unstructured data: an evolutionary solution
Integrative data science, semantics, knowledge graphs, and evidence paths in the service of molecular discovery

BRINGING CHEMINFORMATICS INTO THE COLLEGE CHEMISTRY CLASSROOM

Learning to find the right information. A survey of chemistry information literacy in the undergraduate classroom
Co-developing chemical information management and laboratory safety skills

MISCELLANEOUS PAPERS FROM OTHER MEETINGS

Artificial intelligence is the future of drug discovery
The addition of chemical search capabilities to PATENTSCOPE: turning a full-text search system into a chemistry database
“Beyond China”. Who are the rising stars in patent information?
Examining funding data to predict the future of research

APPENDIX ONE. HERMAN SKOLNIK AWARD SYMPOSIUM 2016. HONORING STEPHEN BRYANT AND EVAN BOLTON

Introduction
Developing databases and standards in chemistry
Two decades of open chemical data at the Developmental Therapeutics Program (DTP) at the National Cancer Institute (NCI)
Using InChI to manage data
Open chemistry resources provided by the NCI computer-aided drug design (CADD) group
Evolution of open chemical information
Open chemical information at the European Bioinformatics Institute
History and the future of tools and software components for working with public chemistry data
PubChem a resource for cognitive computing
SPL and openFDA resources of open substance data
Building a network of interoperable and independently produced linked and open biomedical data
Chemical structure representation in PubChem
iRAMP and PubChem: of the people, for the people
Open chemical information: where now and how?
Conclusion
References

APPENDIX TWO. SQUONK COMPUTATIONAL NOTEBOOK


CHEMICAL INFORMATION AND COMPUTATION 2016 NUMBER ONE;
251st ACS NATIONAL MEETING AND EXPOSITION,
SAN DIEGO, CA, MARCH 13-17, 2016

INTRODUCTION

NEWS AND NEW PRODUCTS

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COMPCHEM SOLUTIONS
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MOLSOFT
MONOCL
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NEXT MOVE SOFTWARE
OPENEYE SCIENTIFIC SOFTWARE
OPEN PHACTS
OPTIBRIUM
ORCID
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PROQUEST
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PUBCHEM AND NCBI
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THIEME CHEMISTRY
THOMSON REUTERS

CINF AND COMP TECHNICAL PROGRAMS

LINKING BIG DATA WITH CHEMISTRY: DATABASES CONNECTING GENOMICS, BIOLOGICAL PATHWAYS AND TARGETS TO CHEMISTRY

Connecting 3D chemical data with biological information
PubChem BioAssay: link chemical research to GenBank and beyond
Predicting adverse drug events using literature-based pathway analysis
Competitive intelligence workbench: getting access to information for decision making
Combining semantic triples across domains to identify new and novel relationships and knowledge

GLOBAL INITIATIVES IN RESEARCH DATA MANAGEMENT AND DISCOVERY

Open data is not enough: a look at the Research Data Alliance
Responses to the data revolution: CODATA on policy, data science, and capacity building
Moving research forward with persistent identifiers and services
Discoverability and reusability of FAIR chemistry research data as a key outcome of registering persistent identifiers and standardized metadata with DataCite
Surveying and tracking the biomedical data landscape
Data Observation Network for Earth: earth and environmental science data management and discovery
California Digital Library: advancing the digital transition of scholarly information
PubChem BioAssay: a decade’s practice for managing chemistry research data
Data infrastructural design for informing critical evaluation
Community-driven disciplinary data repositories: a case study
ICSU World Data System: trusted data services for global science
STRENDA and MIRAGE: examples of community-based data reporting standardization initiatives
Standardizing the description of nanomaterials: the CODATA uniform description system
Scientific units in the electronic age
Authoring tools to automate data sharing in scientific publishing
Facilitating the inclusion of analytical raw data in the submission and review process
Crystallography: a domain exemplar for chemistry data management
Are data management solutions developed for commercial organizations suitable for academic research?
Data sharing in life sciences R&D: pre-competitive collaboration through the Pistoia Alliance
The Royal Society of Chemistry and the data publication landscape
Digital IUPAC: the need for global representation of chemistry and chemical information in the digital age
DIG chemistry: establishing a research data interest group to address the many faces of chemical data management

CHEMISTRY, DATA AND THE SEMANTIC WEB: AN IMPORTANT TRIPLE TO ADVANCE SCIENCE

Combined structure and reaction retrieval in scientific content. What satisfied users in the past and what they demand for the future
Helping people navigate the changing seas of scientific information

APPENDIX ONE. CHEMAXON EUROPEAN ANNUAL MEETING, MAY 2016

INTRODUCTION

CHEMICAL DATA EXTRACTION

Questel partners with ChemAxon
Development of ChemAnalyser, a novel, large-scale patent search engine
"Leveraging" the value of the contents of documents: Plexus for agile dissemination of text- and data-mining results

DATA CAPTURE, STORAGE AND SEARCH IN THE BACK-END

Handling large volumes of chemical data in a scalable way and on a tight budget with the PostgreSQL
database and the JChem PostgreSQL Cartridge
Fast similarity searching: making the virtual real
BioScity: interfacing Biomolecule Toolkit with lab reality

CREATE AND DESIGN IN A COLLABORATIVE ENVIRONMENT

IDBS and ChemAxon: a 1:1 stoichiometry
Roaming though natural products space with JChem and KNIME
Marvin Live to facilitate structure-based drug design
ChemAxon tools at Gedeon Richter
Using Plexus Design to create chemical space for structure-based drug design

DATA MANAGEMENT, CHARACTERISATION, ANALYSIS AND REPORT

Instant JChem as a basis to construct a customised database to store biological activity data
Instant JChem in virtual high throughput screening and commercial compound selection
Rollout of Plexus Connect at GSK: a brief history and update

CHEMAXON PRESENTATIONS

PARTNER SESSION

CONCLUSION


CHEMICAL INFORMATION AND COMPUTATION 2015, NUMBER TWO;
250th ACS NATIONAL MEETING AND EXPOSITION;
BOSTON, MA, AUGUST 16-20, 2015

INTRODUCTION

NEWS AND NEW PRODUCTS

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CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE (CCDC)
CERTARA
CHARLES RIVER
CHEMAXON
CHEMBL
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CLC DRUG DISCOVERY WORKBENCH
COLLABORATIVE DRUG DISCOVERY
COMINNEX
COMPCHEM SOLUTIONS
CORE INFORMATICS
COSMOLOGIC
CRESSET
CROSSREF
DATACITE
DEEP WEB TECHNOLOGIES
DIGITAL SCIENCE
DISCNGINE
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MINER3D
MOLECULAR MATERIALS INFORMATICS
NCI CADD GROUP CACTUS
NEXTMOVE SOFTWARE
OPENEYE SCIENTIFIC SOFTWARE
OPEN PHACTS
OPEN SPECTRAL DATABASE
OPTIBRIUM
ORCID
PISTOIA ALLIANCE
PROQUEST
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ROYAL SOCIETY OF CHEMISTRY (RSC)
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SPECS
SPRINGER NATURE
TAYLOR & FRANCIS GROUP
TEMIS
THIEME CHEMISTRY
THOMSON REUTERS

CINF AND COMP TECHNICAL PROGRAMMES

VISUALIZING CHEMISTRY DATA TO GUIDE OPTIMIZATION

Integrating data visualization into the drug discovery workflow
Data visualization: new directions or just familiar routes?
Reaction discovery and optimization tools for visualizing chemistry data
Visualization of structure-activity relationship patterns and compound design using the SAR Matrix method
Extraction of structure-activity relationship information from activity cliff clusters
Visualization and manipulation of matched molecular series for decision support
Design and characterization of chemical space networks
Compact models for compact devices: visualization of SAR data using mobile apps


RETROSYNTHESIS, SYNTHESIS PLANNING, REACTION PREDICTION: WHEN WILL COMPUTERS MEET THE NEEDS OF THE SYNTHETIC CHEMIST?

What are the next steps in your synthesis? The Reaxys experience
Green chemistry in synthesis planning systems: a role for biocatalysis data and sustainability metrics?
Synthetically accessible virtual inventory (SAVI)
Analyzing success rates of supposedly "easy" reactions
Computer-inspired organic synthesis: building on success
Using reaction driven de novo design as a “retrosynthetic” analysis tool
SynTree, chemical synthesis on a PC
Empowering chemists in synthesis planning. Lessons from the evolution of ARChem
Computer-aided synthesis design (CASD) and forward reaction prediction tools for both idea generation in new synthesis route planning and for de novo molecule design
Chematica, the Deep Blue of chemistry
Reaction mining with condensed graphs of reactions: problems and perspectives
Assessment of optimal conditions for selective deprotection reactions resulting from analysis of a large reaction database


HERMAN SKOLNIK AWARD SYMPOSIUM 2015, HONORING JÜRGEN BAJORATH

Introduction
Receptor-independent ligand activity models and receptor-dependent activity models
Non-specificity of drug-target interactions
Molecular similarity approaches in cheminformatics
Generative topographic mapping
Development of a knowledge-generating platform from drug discovery through to production
Enabling drug discovery by computational molecular design
Integrating public data sources into the drug discovery workflow
"Close-in" analogue prioritization using SAR matrices
Graphical analysis of analogue series and associated SAR information
Various ways to define molecular similarity
Could “inactive” compounds be good starting points for drug discovery?
Complexity and heterogeneity of data for chemical information science
Conclusion
References


CHEMICAL INFORMATION AND COMPUTATION 2015, NUMBER ONE;
249th ACS NATIONAL MEETING AND EXPOSITION;
DENVER, CO, MARCH 22-26, 2015

INTRODUCTION

NEWS AND NEW PRODUCTS

PEOPLE
ACCESS INNOVATIONS
ACD/LABS
AMERICAN CHEMICAL SOCIETY
   ACS Publications
   Chemical Abstracts Service (CAS)
BIOSOLVEIT
BIOVIA
CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE (CCDC)
CERTARA
CHEMAXON
CHEMBL
CHEMDIV
CHEMICAL COMPUTING GROUP (CCG)
CHEMICAL SEMANTICS
COLLABORATIVE DRUG DISCOVERY
COMINNEX
COMPCHEM SOLUTIONS
CORE INFORMATICS
COSMOLOGIC
CRESSET
CROSSREF
DATACITE
DIGITAL SCIENCE
DOTMATICS
ELSEVIER
   Reaxys
   ScienceDirect
   Elsevier Research Intelligence
   Pathway Studio
   PharmaPendium
EVOTEC
F1000RESEARCH CHEMICAL INFORMATION SCIENCE CHANNEL
FIZ KARLSRUHE AND STN INTERNATIONAL
ICHEMLABS
IDBS
INCHI TRUST
INFOCHEM
IO INFORMATICS
JOHN WILEY & SONS
KNIME
KUDOS
LHASA LIMITED
LINGUAMATICS
MINER3D
MOLECULAR MATERIALS INFORMATICS
MOLECULAR NETWORKS
MOLSOFT
NEXTMOVE SOFTWARE
OPENEYE SCIENTIFIC SOFTWARE
OPEN PHACTS
OPTIBRIUM
PERKINELMER INFORMATICS
PISTOIA ALLIANCE
PROQUEST
PROUS INSTITUTE
PUBCHEM
ROYAL SOCIETY OF CHEMISTRY (RSC)
   RSC Publishing
   ChemSpider
SCHRÖDINGER
SCIENCEOPEN
SCIENTIFIC UPDATE
SCILLIGENCE
SIMULATIONS PLUS
SPECS
SPRINGER NATURE
SPRINGER SCIENCE+BUSINESS MEDIA
TAYLOR & FRANCIS GROUP
TEMIS
THERMO FISHER SCIENTIFIC
THIEME CHEMISTRY
THOMSON REUTERS
   Pharma and Life Sciences
   Research Analytics
WIKIPEDIA SUBSTRUCTURE SEARCH

CINF AND COMP TECHNICAL PROGRAMMES

DRUG DISCOVERY

Small molecule crystal structures in drug discovery and development
QSAR modelling independent of input tautomers
General applicability of template CoMFA to prospective bioactivity prediction

MOLECULAR AND STRUCTURAL 2D AND 3D CHEMICAL FINGERPRINTING: COMPUTATIONAL STORING, SEARCHING AND COMPARING MOLECULAR AND CHEMICAL STRUCTURES

Insights into molecular similarity from crystal structures
Do chiral fingerprints and descriptors work?
Similarity to SAR - interactive navigation of similarity relationships to guide optimisation
Database fingerprint clustering methods using KNIME
Highly visual representation methods for comparison of chemical structures and related properties


GETTING TO THE BEST REACTION: TOOLS FOR FINDING A NEEDLE IN A HAYSTACK

Automated design of realistic organometallic complexes and catalysts
Different needles for different tailors. How specialised reaction search algorithms support scientists working in various research areas
Mining electronic lab notebooks for synthetic needles (or gems)


DEFINING “VALUE” IN SCHOLARLY COMMUNICATIONS: EVOLVING WAYS OF EVALUATING IMPACT ON SCIENCE

Impact of crystal structures over the last, and next, 50 years

RESEARCH RESULTS: REPRODUCIBILITY, REPORTING, SHARING AND PLAGIARISM

Addressing researcher incentives for “publishability” over accuracy
Ethics in publishing: editorial and related experiences
Data management and the research record in research misconduct investigations
Irreproducibility in the scientific literature. How often do scientists tell the truth, the whole truth and nothing but the truth?
Interplay of prior information and new data in high-throughput small-molecule studies
STRENDA – proposing minimum information for reporting functional enzymology data
Reproducibility in organic synthesis
Data and models, models and data
Reproducibility and the quality of chemical probes
Reporting and reuse of crystal structure data and knowledge
Sharing and reproducibility/replication. An NIH view
Globalisation of Big Data. Access, integration, and quality control issues
Flagging and curating erroneous chemical and biological records using cheminformatics to ensure data reproducibility
Increasing open communication to facilitate reproducibility


DEVELOPMENT AND USE OF DATA FORMAT STANDARDS FOR CHEMINFORMATICS

Standard data format for computational chemistry: CSX
Development of an ontology specific to computational chemistry


CHEMICAL INFORMATION AND COMPUTATION 2014, NUMBER TWO;
248th ACS NATIONAL MEETING AND EXPOSITION;
SAN FRANCISCO, CA, AUGUST 10-14, 2014

INTRODUCTION

NEWS AND NEW PRODUCTS

People
Accelrys
Access Innovations
ACD/Labs
American Chemical Society
   ACS Publications
   Chemical Abstracts Service (CAS)
BioSolveIT
BIOVIA
Cambridge Crystallographic Data Centre (CCDC)
Certara
ChemAxon
ChEMBL
Chemical Computing Group (CCG)
Collaborative Drug Discovery
ComInnex
CompChem Solutions
COSMOlogic
Cresset
CrossRef
DataCite
Digital Chemistry
Dotmatics
Drug Design Data Resource (D3R)
Elsevier
   Reaxys
   ScienceDirect
   Elsevier Research Intelligence
   Pathway Studio
   PharmaPendium
Evotec
FIZ Karlsruhe and STN International
iChemLabs
IDBS
InfoChem
Infotrieve
John Wiley & Sons
KNIME
Kudos
Lhasa Limited
Linguamatics
Molecular Connections
Molecular Materials Informatics
Molecular Networks
Molsoft
Nature Publishing Group and Digital Science
NextMove Software
OpenEye Scientific Software
Open PHACTS
Optibrium
PerkinElmer Informatics
Pistoia Alliance
Prestwick Chemical
ProQuest
PubChem
Q-Chem
Royal Society of Chemistry (RSC)
   RSC Publishing
   ChemSpider
Schrödinger
ScienceOpen
Scilligence
Sigma Aldrich
Simulations Plus
Specs
Springer Science+Business Media Taylor & Francis Group
TEMIS
The Edge Software Consultancy
Thieme Chemistry
Thomson Reuters
   Pharma and Life Sciences
   Research Analytics
   EndNote
ToxBank
Wavefunction
WorldWideScience.org

CINF AND COMP TECHNICAL PROGRAMMES

Drug Discovery: ADME/Tox

Predicting drug bioavailability using physiologically-based pharmacokinetic modelling and global sensitivity analysis to identify sensitive parameters
CypRules: a rule-based P450 inhibition prediction server
Improving the chance of success when an outcome cannot be predicted
Looking beyond a few hard cut-offs in assessing ADMET risk


Drug Discovery: Informatics

Chiral and isotopic matched pair identification and data analysis on physicochemical and in vitro endpoints for drug discovery
Modelling a crowdsourced definition of molecular complexity
RegMol: registration and assay database for biologics and small molecules from Scilligence
PubChem BioAssay, a public information resource for drug discovery: a bibliometric analysis on PubChem application
Collaborative sharing of molecules and data in the mobile age


Drug Discovery. Ligand-based Drug Design

Complementarity between PubChem 2D and 3D neighbours

Hunting for Hidden Treasures: Chemistry Text Mining in Patents and Other Documents

Teach Document-to-Structure to be trilingual: extract, display, and search chemical information within English, Chinese, and Japanese patents
Recent enhancements in the accuracy of the CLiDE tool for extracting chemical structure data from patents and other documents
Structure Clipper: an interactive tool for extracting chemical structures from patents
Computer-assisted Markush structure curation from patent documents
Use of reverse text-mining to establish whether indexing and classification of chemical patents is still necessary
Extraction of chemical reactions from full text documents: from n-tuples of value attribute pairs toward the automated construction of reaction databases
Knowledge mining by structure search
Toward extracting analytical science metrics from the RSC archives
SureChEMBL: an open system for exploration of patent chemistry space
Computer analysis of the scientific literature
Using the biorelations and intelligence network (BRAIN) for knowledge discovery


Herman Skolnik Award Symposium 2014 Honouring Engelbert Zass

Introduction
Evolution and transformation of journals in a digital environment
End user behaviour
Panel discussion on information literacy
Chemical publications revisited
CAS keeps pace with the worldwide growth in disclosed chemistry
InChI and the information chain
Virtual communities and beyond
Reaxys: a digital transformation
Award address
Conclusion
References


CHEMICAL INFORMATION AND COMPUTATION 2014, NUMBER ONE;
247th ACS NATIONAL MEETING AND EXPOSITION;
DALLAS, TX, MARCH 16-20, 2014

INTRODUCTION

NEWS AND NEW PRODUCTS

People
Accelrys
Access Innovations
ACD/Labs
American Chemical Society
   ACS Publications
   Chemical Abstracts Service (CAS)
Argenta
BioFocus
Bio-Rad Laboratories Informatics Division
BioSolveIT
Cambridge Crystallographic Data Centre (CCDC)
CARLSBAD
Certara
ChemAxon
ChEMBL
Chemical Computing Group (CCG)
CLC bio (Molegro)
Collaborative Drug Discovery
CompChem Solutions
COSMOlogic
Cresset
CrossRef
Digital Chemistry
Dotmatics
Eidogen-Sertanty
Elsevier
   Reaxys
   ScienceDirect
   Scopus
   SciVal
   Pathway Studio
   PharmaPendium
Evotec
FIZ Karlsruhe and STN International
GGA Software Services
iChemLabs
IDBS
InfoChem
John Wiley & Sons
KNIME
Kudos
Lhasa Limited
Linguamatics
Molecular Connections
Molecular Materials Informatics
Molsoft
Nature Publishing Group and Digital Science
NextMove Software
OpenEye Scientific Software
Open PHACTS
Optibrium
PerkinElmer Informatics
Pistoia Alliance
ProQuest
PubChem
Q-Chem
Questel
Royal Society of Chemistry (RSC)
   RSC Publishing
   ChemSpider
Schrödinger
ScienceOpen
Scilligence
Scitegrity
SimBioSys
Simulations Plus
Specs
Springer Science+Business Media
Taylor & Francis Group
TEMIS
ThalesNano
Thieme Chemistry
Thomson Reuters
   Cortellis
   Web of Science
   EndNote

CINF AND COMP TECHNICAL PROGRAMMES

ACS Award for Computers in Chemical and Pharmaceutical Research: Symposium in Honour of Martin Stahl

The evolving role of modelling and informatics in drug discovery
Drug discovery and development by design: using the knowledge from every organic crystal structure ever published


Drug Discovery

Advances in multi-parameter optimisation: targeting the "best" profile for your project’s objectives
Predictive application of bioisostere transformations to identify novel high quality compound ideas


Keeping the Thrill Alive: Research Data and Electronic Notebooks

Dark reaction project: archiving and deriving value from unreported “failed” hydrothermal synthesis reactions
Factors to consider when choosing the right ELN for capturing and collaborating with your research data
Royal Society of Chemistry activities to develop a data repository for chemistry-specific data
Eureka research workbench: an open source eScience laboratory notebook
PubChem: a platform to archive and share scientific information
Keeping the thrill alive: data on demand
Building a mobile reaction lab notebook
Creating context for the experiment record: user-defined metadata
Generating metadata for an experiment: using a tablet ELN
Mining ELN based structured test and chemical property data to optimise catalyst development
Sample management with the LabTrove ELN
Digital data repositories in chemistry and their integration with journals and electronic laboratory notebooks
Data exchange between electronic lab notebooks and data repositories
Standardised representations of ELN reactions for categorisation and duplicate/variation identification
Extracting data, information, and knowledge from an ELN


New Models in Substance Discovery

New approaches to search interfaces in PubChem
From searching to finding: new developments for managing large datasets
Search and navigation functionality for a major reference work online: SOS 4.0
Chemical most common denominator: use of chemical structures for semantic enrichment and interlinking of scientific information
Representation and display of non-standard peptides using semi-systematic amino acid monomer naming
New structure search capabilities for accessing CAS content


CHEMICAL INFORMATION AND COMPUTATION 2013, NUMBER TWO;
246th ACS NATIONAL MEETING AND EXPOSITION
INDIANAPOLIS, IN, SEPTEMBER 8-12, 2013

INTRODUCTION

NEWS AND NEW PRODUCTS

PEOPLE
ACCELRYS
ACCESS INNOVATIONS
ACD/LABS
AMERICAN CHEMICAL SOCIETY
   ACS Publications
   Chemical Abstracts Service (CAS)
ARGENTA
BIOFOCUS
BIO-RAD LABORATORIES INFORMATICS DIVISION
BIOSOLVEIT
CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE (CCDC)
CERTARA
CHEMAXON
CHEMBL
CHEMDIV
CHEMICAL COMPUTING GROUP (CCG)
COMINNEX
COMPCHEM SOLUTIONS
COSMOLOGIC
CRESSET
CROSSREF
DELTASOFT
DOTMATICS
ELSEVIER
   Reaxys
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   Scopus
   SciVal
   Pathway Studio
EVOTEC
FIZ KARLSRUHE AND STN INTERNATIONAL
FQS POLAND (FUJITSU)
GGA SOFTWARE SERVICES
ICHEMLABS
INCHI TRUST
INFOCHEM
INHIBOX
JOHN WILEY & SONS
KNIME
KUDOS
LHASA LIMITED
LINGUAMATICS
METAMOLECULAR
MOLECULAR CONNECTIONS
MOLECULAR MATERIALS INFORMATICS
MOLECULAR NETWORKS
MOLSOFT
NATURE PUBLISHING GROUP AND DIGITAL SCIENCE
NEXTMOVE SOFTWARE
OPENEYE SCIENTIFIC SOFTWARE
OPEN PHACTS
OPTIBRIUM
PERKINELMER INFORMATICS
PISTOIA ALLIANCE
PROQUEST
Q-CHEM
ROYAL SOCIETY OF CHEMISTRY (RSC)
   RSC Publishing
   ChemSpider
SCHRÖDINGER
SCIENCEOPEN
SCILLIGENCE
SCITEGRITY
SIGMA ALDRICH
SILCSBIO
SIMULATIONS PLUS
SPECS
SPRINGER SCIENCE+BUSINESS MEDIA
TAYLOR & FRANCIS GROUP
TEMIS
THALESNANO
THE EDGE SOFTWARE CONSULTANCY
THIEME CHEMISTRY
THOMSON REUTERS
   Cortellis
   MetaCore and Integrity
   Thomson Innovation and IP Manager
   Web of Knowledge
WAVEFUNCTION

CINF AND COMP TECHNICAL PROGRAMMES

CURRENT CHALLENGES IN CHEMINFORMATICS: EXPLOITING INFORMATION AND KNOWLEDGE IN STRUCTURED AND UNSTRUCTURED ENVIRONMENTS

Scaffold-based reasoning approaches for cross-assay structure-activity relationship identification
Knowledge mining by structure search
Spaghetti seas and filter forests. Navigating Pipeline Pilot protocol creation with maintenance in mind
New frontier in reaction search. Dynamic mining of ELN based reaction methodology data in Spotfire
Plexus: a clean Web application for structural data analysis
Improving access to data. A distributed approach
Digital fractionation. Using NoSQL technology to extract biochemical data from big data repositories
Exploring interconnectivity of molecular biology databases and data mining tools
Caveats in the use of pharmaceutical drug discovery data
Extracting synthetic knowledge from reaction databases
Validation and characterisation of chemical structures derived from names and images in scientific documents
Tackling the difficult areas of chemical entity extraction: misspelt chemical names and unconventional entities
OPSIN. Taming the jungle of IUPAC chemical nomenclature
Pushing chemical biology data through the pipes. Architecting and extending the BARD API
QSAR modelling on the Web
Data curation and formal BioAssay Ontology (BAO)-based annotations of the DrugMatrix enable bioactivity-based target-relationship analysis and demonstrate incorporation of external datasets into the BioAssay Research Database (BARD)
Development of the BioAssay Research Database (BARD). A user-friendly perspective based on active participation from biologists and chemists
BADAPPLE promiscuity plugin for BARD: evidence-based promiscuity scores


SEMANTIC TECHNOLOGIES IN TRANSLATIONAL MEDICINE AND DRUG DISCOVERY

PubChemRDF. Towards a semantic description of PubChem
Enabling the translational medicine and drug discovery information workflow
Other papers in this symposium


EXCHANGEABLE MOLECULAR AND ANALYTICAL DATA FORMATS AND THEIR IMPORTANCE IN FACILITATING DATA EXCHANGE

Cheminformatics runs on molfiles and its siblings. There is a molfile for that
Reading and writing molecular file formats for data exchange of small molecules, biopolymers, and reactions
Facilitating accurate chemical data inter-conversion using Open Babel. The good, the bad, and the painful
Exchanging chemical structures and ELN data: CDX, CDXML, and other formats
Data exchange caveats and particulars. The devil is in the details


HERMAN SKOLNIK AWARD SYMPOSIUM 2013 HONOURING RICHARD D. (DICK) CRAMER

Introduction
CoMFA
More on QSAR
Drug discovery
Sabermetrics
Synthesis planning
Topomers
Conclusion
References


CHEMICAL INFORMATION AND COMPUTATION 2013 NUMBER ONE
245th ACS NATIONAL MEETING AND EXPOSITION
NEW ORLEANS, LA, APRIL 7-11, 2013

INTRODUCTION

NEWS AND NEW PRODUCTS

PEOPLE
ACCELRYS
ACCESS INNOVATIONS
ACD/LABS
AKOS CONSULTING & SOLUTIONS
AMERICAN CHEMICAL SOCIETY
   ACS Publications
   Chemical Abstracts Service (CAS)

ARGENTA
BIOFOCUS
CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE (CCDC)
CERTARA
CHEMAXON
CHEMBL
CHEMDIV
CHEMICAL COMPUTING GROUP (CCG)
COMPCHEM SOLUTIONS
CRESSET
CROSSREF
DOTMATICS
EIDOGEN-SERTANTY
ELSEVIER
   Reaxys
   ScienceDirect
   Scopus
   SciVal
   Pathway Studio
   PharmaPendium

EVOTEC
FIZ KARLSRUHE AND STN INTERNATIONAL
GGA SOFTWARE SERVICES
ICHEMLABS
IDBS
INCHI TRUST
INFOCHEM
IO INFORMATICS
ISCIENCESEARCH
JOHN WILEY & SONS
KNIME
KUDOS
LHASA LIMITED
LINGUAMATICS
MINER3D
MOLECULAR CONNECTIONS
MOLECULAR MATERIALS INFORMATICS
MOLEGRO
NATURE PUBLISHING GROUP AND DIGITAL SCIENCE
NEXTMOVE SOFTWARE
NIH NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES (NCATS)
OPENEYE SCIENTIFIC SOFTWARE
OPEN PHACTS
OPTIBRIUM
PERKINELMER INFORMATICS
PISTOIA ALLIANCE
PROQUEST
PUBCHEM
Q-CHEM
ROYAL SOCIETY OF CHEMISTRY (RSC)
   RSC Publishing
   ChemSpider

SCHRÖDINGER
SCILLIGENCE
SIGMA ALDRICH
SIMULATIONS PLUS
SPRINGER SCIENCE+BUSINESS MEDIA
   Chemistry Central
TAYLOR & FRANCIS GROUP
TEMIS
THALESNANO
THE EDGE SOFTWARE CONSULTANCY
THOMSON REUTERS
   Cortellis
   Thomson Innovation and IP Manager
   Web of Knowledge
   EndNote

TIBCO SPOTFIRE

CINF AND COMP TECHNICAL PROGRAMMES

ADVANCES IN VISUALISING AND ANALYSING BIOMOLECULAR SCREENING DATA

Characterising the diversity and biological relevance of the MLPCN assay manifold and screening set
New ways to mine disparate screening data in PubChem
PubChem DataDicer. A data warehouse for rapid querying of bioassay data PubChem widgets
BioAssay Research Database: a platform to support the collection, management, and analysis of chemical biology data
Encoded Library Technology data analysis: finding the grain of sand you want without getting a sunburn
Exploring the chemical space of screening results
How to highlight hits: advances in visual data analytics tools for HTS data
Integrated cheminformatics software for visualising and analysing high-throughput screening data
Integrating design, analysis, and visualisation into the drug discovery workflow Other papers in this symposium


SCHOLARLY COMMUNICATION: NEW MODELS, NEW MEDIA, NEW METRICS

NIST-journal co-operation to improve the quality of published experimental data: pre-acceptance evaluation and online tools
Reproducibility in cheminformatics and computational chemistry research. Certainly we can do better than this
We?re not in Kansas anymore
Other papers in this symposium


FOODINFORMATICS: APPLICATIONS OF CHEMICAL INFORMATION TO FOOD CHEMISTRY

Reaxys as an information resource for food chemistry

LINKING BIOINFORMATIC DATA AND CHEMINFORMATIC DATA

About the impact of open access bioassay data on cheminformatic approaches
CAS? bioactivity and target indicators provide new insights for scientists working at the interface of chemistry and biology
Linking chemical biology information within PubChem
Other papers in this symposium


PUBLIC DATABASES SERVING THE CHEMISTRY COMMUNITY

Chemical science that underpins the Reaxys database
ChemReact: a free database containing more than 524,000 reactions available at your fingertips
Intuitive and integrated browsing of reactions, structures, and citations: the Roche experience
Universal SMILES. Finally, a canonical SMILES string?
One size fits all or how to find the needle in the haystack?
Other papers in this symposium


DRUG DISCOVERY. CHEMICAL AND STRUCTURAL INFORMATICS: INFORMATION IS POWER

Data are not sufficient. Making the difference in cross-functional project team decisions is the objective

ADVANCES IN VIRTUAL HIGH-THROUGHPUT SCREENING

PubChem3D: a virtual screening platform
Other papers in this symposium


This page last updated on 31st January 2017.