CHEMICAL INFORMATION AND COMPUTATION

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2018, NUMBER TWO 256th ACS National Meeting, Boston, MA, Fall, 2018
2018, NUMBER ONE, 255th ACS National Meeting, New Orleans, LA, Spring, 2018
2017, NUMBER TWO, 254th ACS National Meeting, Washington, DC, Fall, 2017
2017, NUMBER ONE, 253rd ACS National Meeting, San Francisco, CA, Spring, 2017
2016, NUMBER TWO, 252nd ACS National Meeting, Philadelphia, PA, Fall, 2016
2016, NUMBER ONE, 251st ACS National Meeting, San Diego, CA, Spring, 2016


Chemical Information and Computation 2018, Number Two.
256th ACS National Meeting and Exposition
Boston, MA, August 19-23, 2018

INTRODUCTION

NEWS AND NEW PRODUCTS

PEOPLE
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ACD/LABS
AMERICAN CHEMICAL SOCIETY
   ACS Publications
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BENEVOLENT AI
BIOSOLVEIT
BIOVIA
CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE (CCDC)
CERTARA
CHEMAXON
CHEMDIV
CLARIVATE ANALYTICS
COLLABORATIVE DRUG DISCOVERY
COMINNEX
COSMOLOGIC
CRESSET
CROSSREF
DIGITAL SCIENCE
DOTMATICS
DOUGLAS CONNECT
ELSEVIER
   Corporate
   Artificial intelligence
   Reaxys
   ScienceDirect
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EPA NATIONAL CENTER FOR COMPUTATIONAL TOXICOLOGY CHEMISTRY DASHBOARD
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IO INFORMATICS
JOHN WILEY & SONS
KNIME
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LHASA LIMITED
LINGUAMATICS
MEDCHEMICA
MELISSA
MOLECULAR CONNECTIONS
MONOCL
NEXTMOVE SOFTWARE
OPENEYE SCIENTIFIC SOFTWARE
OPTIBRIUM
ORCID
PERKINELMER INFORMATICS
PHARMACELERA
PISTOIA ALLIANCE
Q-CHEM
ROYAL SOCIETY OF CHEMISTRY
SCHRÖDINGER
SCIENCEOPEN
SCILLIGENCE
SILICON THERAPEUTICS
SIMULATIONS PLUS
SPRINGER NATURE
SYGNATURE DISCOVERY
TAYLOR & FRANCIS GROUP
THALESNANO
THE EDGE SOFTWARE CONSULTANCY
THIEME CHEMISTRY


CINF, COMP AND COMSCI TECHNICAL PROGRAMS

REVOLUTIONIZING CHEMISTRY WITH ARTIFICIAL INTELLIGENCE. AI FOR SMALL MOLECULES AND ORGANIC REACTIONS

"Found in Translation". A deeper analysis of neural machine translation models for chemical reaction prediction

REACTION ANALYTICS

Brief history of reaction analytics
Automatic discovery and enumeration of new tactical combinations
Retrosynthetic software for practicing chemists: novel and efficient in silico pathway design validated at the bench
Learning to plan chemical syntheses
Exploring the use of conditional generative adversarial networks (cGAN) to analyze chemical reactions via electron density fields
Machine learning and continuous flow. Detection and correction of flow-incompatible reaction conditions
Predicting reaction conditions for computer-generated SAVI reactions by machine learning from reaction databases
Using machine learning to recommend suitable conditions for organic reactions
Analyzing matched molecular pair transformations in drug discovery projects as a function of time and molecular environment
Regioselectivity: an application of expert systems and ontologies to chemical (named) reaction analysis
Representing organic reactions through InChI differences

ACS COMMITTEE ON SCIENCE (COMSCI) SYMPOSIUM. DEFENSE ADVANCED RESEARCH PROJECTS AGENCY (DARPA) MAKE-IT PROGRAM: AUTOMATING SMALL MOLECULE ROUTE DESIGN, OPTIMIZATION AND SYNTHESIS

SynRoute, synthetic route planning software that combines rapid search and machine learning
Edited (short) abstracts of the talks in this symposium

MOVE AWAY FROM THE LAMPOST AND FIND DRUGGABLE TARGETS

Open targets: an innovative public-private partnership to deliver more sustainable target selection for drug discovery
Computational methods help find chemical matter to uncover novel biology

DATA TO DECISIONS

Mining clinical trials information using text mining and cheminformatics technologies
Accelerating problem solving and decision making in medicinal chemistry through visualization

REPORTING AND REPRODUCIBILITY OF CHEMISTRY RESEARCH DATA

Reaction networks analysis for algorithmic process development
International chemical identifier for reactions (RInChI): the key to managing reaction databases effectively
De facto standard or a free-for-all? A benchmark for reading SMILES
Blockchain for research

PUBLISHING CHEMICAL DATA

Open data in chemistry. The fast track to scientific content
SynOne. The use of an expert-defined, chemical compound class taxonomy to map organic synthesis articles from the chemistry literature


REFERENCES



APPENDIX ONE. HERMAN SKOLNIK AWARD SYMPOSIUM HONORING GISBERT SCHNEIDER. DE NOVO DESIGN



APPENDIX TWO. POSTERS

WINNERS OF CINF SCHOLARSHIP FOR SCIENTIFIC EXCELLENCE

Molecular modeling of differential ERK1/2-ligand dynamic interactions
Symmetry and chirality analysis of substituted ferrocenes
Data integration and scaffold analysis reveal important structural motifs for ligand selectivity among hepatic organic anion transporting polypeptides

CHEMAXON POSTERS

Chemical intelligence that makes hidden knowledge effortlessly reachable
Compound design process - to a better start
Finding answers from chemical space extremely fast. Moving beyond the limit of recognition
Chemicalize - cheminformatics in the cloud
Sprouting out new ideas from knowledge ground


CHEMICAL INFORMATION AND COMPUTATION 2018 NUMBER ONE;
255th ACS NATIONAL MEETING AND EXPOSITION,
NEW ORLEANS, LA, MARCH 18-22, 2018

INTRODUCTION

NEWS AND NEW PRODUCTS

PEOPLE
Access Innovations
ACD/Labs
American Chemical Society
   ACS Publications
   Chemical Abstracts Service (CAS)
Bio-Rad Laboratories Informatics Division
BioSolveIT
BIOVIA
Cambridge Crystallographic Data Centre (CCDC)
Certara
Charles River Laboratories
ChemAxon
ChEMBL
ChemDiv
Chemical Computing Group
ChemPass
Clarivate Analytics
Collaborative Drug Discovery
ComInnex
CompChem Solutions
Core Informatics
COSMOlogic
Cresset
Crossref
Digital Science
Discngine
Dotmatics
Elsevier
   Reaxys
   ScienceDirect
   Scopus and CiteScore
   SSRN
   Mendeley
   The Hive
EPA National Center for Computational Toxicology Chemistry Dashboard
Evotec
FIZ Karlsruhe and STN International
iChemLabs
InChI Trust
InfoChem
John Wiley & Sons
KNIME
Kudos
Lhasa Limited
Linguamatics
Molecular Connections
Molecular Materials Informatics
Monocl
NextMove Software
Numerate
OpenEye Scientific Software
OpenTox
Optibrium
PerkinElmer Informatics
Pharmacelera
Pistoia Alliance
PubChem
Q-Chem
Royal Society of Chemistry
Schrödinger
ScienceOpen
Scilligence
Silicon Therapeutics
Simulations Plus
Springer Nature
Taylor & Francis Group
ThalesNano
The Edge Software Consultancy
Thieme Chemistry


CINF AND COMP TECHNICAL PROGRAMS

Drug Discovery: Cheminformatics Approaches

Synthetically Accessible Virtual Inventory (SAVI). Next version; toward more needles and less haystack
BioTransformer. An accurate, freely available tool for predicting small molecule metabolism.
Applications in drug discovery
Making virtual REAL. Synthetically feasible compounds and their exploration in docking screens
Deep learning approaches for detecting high-throughput screening false positives.

Drug Design: QSAR and Docking

Hydrophobic similarity between molecules. Application to three-dimensional molecular overlays with PharmScreen

Enhance Discovery: Share Chemical Structures

Deposit chemical structures into PubChem, a public data repository
Supporting the community to share chemical structures
ChemAxon’s chemical structure file formats for better data storage and search
NCI/CADD cactus web server: tool for connecting chemical structures

Workflows and Cheminformatics

Diamond, XChem and CCP-CompMedChem: creating user-focused tools and workflows for structure-based drug design
How can you access PubChem programmatically?
Interactive and reproducible data analysis with the open-source KNIME Analytics Platform
Using Python to streamline access to the Cambridge Structural Database through new workflows Parallel, heterogeneous workflows on the cloud with Floe
Quality data to quality models
Automating matched molecular pair analysis of bioactivity and solubility data
Reaction and chemistry data blendings

Information Legacy of Eugene Garfield: from the Chicken Coop to the World Wide Web

Eugene Garfield: the man and his legacy
From the Index Chemicus Registry System to SciFinder and beyond
Eugene Garfield: the father of chemical text mining and artificial intelligence (AI) in cheminformatics
Eugene Garfield’s legacy and its impact on the culture of research
Beyond citations. What are new ways to assess content that will extend the assessment toolbox?
Novel research and its scientific and technological impact
Clarivate Analytics. Building on the Garfield legacy with Web of Science


Appendix One. ChemAxon European User Meeting, Budapest, March 20-22, 2018

Introduction

Dealing with New Molecules

Marvin Live deployed at Boehringer Ingelheim
Preclinical data management. From RS3 to ChemAxon compound registration
Screener - Compound Registration - Mosaic use case

Keynote Talk

Driving efficiency and innovation in R&D

World of Macromolecules

HELM-driven tools for peptide-based drug design using the ChemAxon Biomolecule Toolkit
Macromolecules in E-Workbook

Creating and Searching Structures

Scientific data management platform for specialty chemicals R&D
Integrating ChemAxon software in an inventory and ELN
ChemAxon’s technology in Reaxys
Rhea, a curated knowledgebase of biochemical reactions

Chemical Data Management

Getting the best out of the JChem PostgreSQL cartridge
How to use IJC as a lab notebook
Software tools in the academic HTS workflow
A user experience of ChemAxon software at GSK
JChem for Office goes online

Knowledge Extraction

ChemAxon’s naming technology to accelerate extraction of chemical information from unstructured data
Patent application management using ChemCurator and Marvin Live at Sprint Bioscience
ChemAxon’s technology integration for efficient patent searches and intellectual property (IP) landscape analyses

Partner Session

Conclusion


APPENDIX TWO. POSTERS

Winners of CINF Scholarship for Scientific Excellence

BioTransformer. A tool for small molecule metabolism prediction and metabolite identification.
Designing CDK2 inhibitors using the molecular chimera approach
Triangulation of repurposing candidates for orphan disease

NextMove Software Poster

Can we agree on the structure represented by a SMILES string?

ChemAxon Posters

Finding answers from chemical space extremely fast
Japanese and Chinese support for Chemicalize

Cresset Posters

Can I make this into a macrocycle? Effective methods for fragment growing, joining and cyclization
Rapid and accessible in silico macrocycle design: application to BRD4
Selectivity profiles in Activity Atlas
Adding pharmacophores to shape and electrostatics: too much of a good thing?
Deciphering kinase SAR using electrostatics


References


CHEMICAL INFORMATION AND COMPUTATION 2017 NUMBER TWO;
254th ACS NATIONAL MEETING AND EXPOSITION,
WASHINGTON, DC, AUGUST 20-24, 2017

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
CHARLES RIVER LABORATORIES
CHEMAXON
CHEMDIV
CLARIVATE ANALYTICS
COLLABORATIVE DRUG DISCOVERY
COSMOLOGIC
CRESSET
CROSSREF
DIGITAL SCIENCE
DISCNGINE
DOTMATICS
ELSEVIER
   Reaxys
   ScienceDirect
   Scopus and CiteScore
   SSRN: ChemRN
   Cell Press
EPA NATIONAL CENTER FOR COMPUTATIONAL TOXICOLOGY
EVOTEC
FIZ KARLSRUHE AND STN INTERNATIONAL
ICHEMLABS
IDBS
INCHI TRUST
INFOCHEM
INTEGRATED CHEMISTRY DESIGN
JOHN WILEY & SONS
KNIME
KUDOS
LHASA LIMITED
LINGUAMATICS
MEDCHEMICA
MOLECULAR CONNECTIONS
MOLECULAR MATERIALS INFORMATICS
MOLSOFT
MONOCL
NEXTMOVE SOFTWARE
NUMERATE
OPENEYE SCIENTIFIC SOFTWARE
OPENTOX
OPTIBRIUM
ORCID
OXFORD DRUG DESIGN
PERKINELMER INFORMATICS
PISTOIA ALLIANCE
PUBCHEM
Q-CHEM
ROYAL SOCIETY OF CHEMISTRY
SCHRÖDINGER
SCIENCEOPEN
SCILLIGENCE
SILICON THERAPEUTICS
SIMULATIONS PLUS
SPECS
SPRINGER NATURE
SYGNATURE DISCOVERY
TAYLOR & FRANCIS GROUP
THE EDGE SOFTWARE CONSULTANCY
THALESNANO
THIEME CHEMISTRY
XEMISTRY


CINF AND COMP TECHNICAL PROGRAMS

WHAT DO SYNTHETIC CHEMISTS WANT FROM THEIR REACTION SYSTEMS?

Applying machine learning to synthesis design. Prediction of organic reaction outcomes
Retrosynthesis and reaction prediction with deep neural networks
International Chemical Identifier for Reactions (RInChI): What is RInChI and how does it revolutionize the handling of reaction databases?
Better synthesis for the next molecule
Pistachio: search and faceting of large reaction databases
Computational approach to the history of chemical reactivity. Exploring the Reaxys database
From search tool to research partner. Changing the role of computers in chemical development
Supporting synthetic research with SciFindern
Renaissance of reaction classification and visualization. History, definition and new use cases
ReaxysTree for reactions
Analyzing reaction pathways in Reaxys
Any electron withdrawing group will do. Introducing specific ambiguity into reaction searches

MARKUSH 360. CURRENT AND FUTURE OF GENERIC STRUCTURES IN CHEMICAL PATENT CREATION, SEARCH & ANALYSIS

Understanding linguistic Markush expressions in chemical patents
Everlasting challenge. Markush indexing, searching and display in modern retrieval systems
Advanced Markush technologies. Automatic generation, non-hit visualization and overlap analysis
Challenges and successes in machine interpretation of Markush descriptions
Challenges in extracting Markush structure data from structure depictions and related text
MARPAT: CAS’s database of Markush structures


APPENDIX ONE. HERMAN SKOLNIK AWARD SYMPOSIUM 2017. HONORING DAVID WINKLER

Introduction
Approaching reality: simulating electronic devices
Applications of machine learning to materials and chemical property prediction
A nanoinformatics platform for environmental impact assessment of manufactured nanomaterials
Accurate and interpretable nano-QSAR models from genetic programming-based decision tree construction approaches
Self-organizing neural networks in chemistry
Understudied proteins. Time to shift the paradigm
Sparse QSAR modeling methods for therapeutic and regenerative medicine
Conclusion


APPENDIX TWO. POSTER

Merck AcceSSible InVentory (MASSIV): in silico synthesis guided by chemical transforms obtained through bootstrapping reaction databases.


REFERENCES


CHEMICAL INFORMATION AND COMPUTATION 2017 NUMBER ONE;
253rd ACS NATIONAL MEETING AND EXPOSITION,
SAN FRANCISCO, CA, APRIL 2-6, 2017

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
CHARLES RIVER LABORATORIES
CHEMATICA
CHEMAXON
CHEMBL
CHEMDIV
CHEMICAL COMPUTING GROUP
CLARIVATE ANALYTICS
COLLABORATIVE DRUG DISCOVERY
COMPCHEM SOLUTIONS
CORE INFORMATICS
COSMOLOGIC
CRESSET
DIGITAL SCIENCE
DOTMATICS
ELSEVIER
   Corporate
   Reaxys
   ScienceDirect
   Scopus and CiteScore
   SSRN: BioRN
   PharmaPendium
EPA NATIONAL CENTER FOR COMPUTATIONAL TOXICOLOGY
EVOTEC
FIZ KARLSRUHE AND STN INTERNATIONAL
ICHEMLABS
IDBS
INCHI TRUST
INFOCHEM
JOHN WILEY & SONS
KNIME
KUDOS
LHASA LIMITED
LINGUAMATICS
MOLSOFT
MONOCL
NEXTMOVE SOFTWARE
NUMERATE
OPENEYE SCIENTIFIC SOFTWARE
OPEN PHACTS
OPTIBRIUM
ORCID
PERKINELMER INFORMATICS
PISTOIA ALLIANCE
PROUS INSTITUE
Q-CHEM
ROYAL SOCIETY OF CHEMISTRY
SCHRÖDINGER
SCIENCEOPEN
SCILLIGENCE
SILICON THERAPEUTICS
SIMULATIONS PLUS
SPRINGER NATURE
SYGNATURE DISCOVERY
TAYLOR & FRANCIS GROUP
THALESNANO
THE EDGE SOFTWARE CONSULTANCY
THIEME CHEMISTRY


CINF AND COMP TECHNICAL PROGRAMS

SHOULD I MOVE MY COMPUTATIONAL CHEMISTRY OR INFORMATICS TOOLS TO THE CLOUD?

Computational and data sciences in the cloud. To be or not to be
Lessons learned in using “cloud big compute” to transform computational chemistry research
Getting our heads into the cloud: GSK experiences using cloud computing for structure based drug design
Practical lessons learned on a long and winding road to the cloud
“Design Anywhere”. A mobile app for drug design
Accelerating discovery in the cloud. A cohesive workflow for the virtual screening and refinement of computationally-intensive libraries
Cloud first strategy that accelerates informatics and computations in drug discovery
High performance and/or cloud computing for free energy prediction using molecular dynamics simulations?
Lessons learned in developing and delivering a secure, multi-tenant environment for drug discovery R&D informatics
What's with all this GPU-accelerated cloud computing stuff?
Cloud is the only place for computational chemistry. Why this is a once-in-a-lifetime opportunity for the field to leap forward
Enhancing internal computational capabilities with the cloud
Steps to getting science in the cloud at Merck
Deploying large-scale binding-affinity calculations to the cloud
Virtual screening in the cloud with Pharmit
Research informatics. Get ready for the cloud!

TEXT MINING AND NATURAL LANGUAGE PROCESSING FOR CHEMICAL INFORMATION: FROM DOCUMENTS TO KNOWLEDGE

Making the old new again: modern technology provides access to historical chemical information
Evolution of SciFinder to meet the changing needs for scientific information
The addition of chemical search capabilities to PATENTSCOPE: turning a full-text search system into a chemistry database

PUBLIC-PRIVATE PARTNERSHIPS. FOSTERING DRUG DISCOVERY AND DATA SHARING

CCDC: a public-private research partnership
PubChem’s literature and patent information for drug discovery
Selection of cross-docking candidates and comparison of evaluation metrics in Continuous Evaluation of Ligand Pose Prediction (CELPP)
Synthetically accessible virtual inventory (SAVI)
Extracting and exploiting medicinal chemistry ADMET knowledge automatically from public and large pharma data

THE USE OF SCIENTIFIC INFORMATION IN IP-RELATED MATTERS

Your next breakthrough starts here. CAS content and solutions foster discovery and innovation

THE LATEST ADVANCES FROM CAS

The latest advances from CAS: SciFindern

LINKS TO SUMMARIES OF OTHER CINF SYMPOSIA

MISCELLANEOUS PAPERS FROM OTHER MEETINGS

Using data science techniques to put molecules in context
Chemical structure representation of inorganic salts and mixtures of gases


APPENDIX ONE. POSTER

Similarity implicated exploration of the fragment galaxy


APPENDIX TWO. POSTER

Estimating Predictive Uncertainty for Artificial Neural Net Ensembles


APPENDIX THREE. CHEMAXON US USER MEETING, SAN FRANCISCO, APRIL 10-11, 2017

INTRODUCTION
CHEMICAL CALCULATIONS AND DRAWING
Structure and reaction querying in Reaxys
Predicting off-target toxicities
DATA MANAGEMENT
ChemAxon solutions
Consultancy use cases
BIOMOLECULES
Biomolecules in R&D informatics
A chemical workbench for biopolymers
Managing the process of biologics registration
BACK END: STORE AND SEARCH
JChem engines
The PostgreSQL cartridge at Dart Neuroscience
Migrating the eMolecules chemical search engine to ChemAxon
MadFast similarity search
PARTNER SESSION
CONCLUSION


APPENDIX FOUR, CHEMAXON EUROPEAN USER MEETING, BUDAPEST, MAY 9-11, 2017

CONTENTS
INTRODUCTION
KEYNOTE ADDRESS
Data for drugs
CHEMICAL DRAWING, CALCULATIONS AND DESIGN
Marvin JS in Discngine Decision
Marvin JS at the University of Chemistry and Technology, Prague
An integrated testing strategy for skin sensitization assessment
Does a 3D shape based method differ from a molecular descriptor based similarity method in its ability to predict biological activity?
MarvinLive at Sprint Bioscience
PLATFORM AND BACK END TOOLS
ChemAxon@Merck. Migration to ChemAxon technology. Our way into a new world
REGISTRATION AND MANAGEMENT OF CHEMICAL AND BIOLOGICAL DATA
Biology and chemistry in E-WorkBook
European Lead Factory Web portal
From library design to compound delivery
Development of compounds targeting resistant cancer
DATA EXTRACTION AND CURATION
Fast access to chemical data with ChemCurator
ChemAxon integration within Orbit Intellectual Property Business Intelligence (IPBI)
PARTNER SESSION
CHEMAXON UPDATE
CONCLUSION


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

INTRODUCTION

NEWS AND NEW PRODUCTS

PEOPLE
ACCESS INNOVATIONS
ACD/LABS
AMERICAN CHEMICAL SOCIETY
   ACS Publications
   Chemical Abstracts Service (CAS)
BIO-RAD LABORATORIES INFORMATICS DIVISION
BIOSOLVEIT
BIOVIA
CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE (CCDC)
CERTARA
CHARLES RIVER LABORATORIES
CHEMAXON
CHEMBL
CHEMDIV
CHEMICAL COMPUTING GROUP
CLARIVATE ANALYTICS
COLLABORATIVE DRUG DISCOVERY
COMPCHEM SOLUTIONS
CORE INFORMATICS
COSMOLOGIC
CRESSET
CROSSREF
DIGITAL SCIENCE
DISCNGINE
DOTMATICS
ELSEVIER
   Corporate
   Elsevier R&D Solutions
   Elsevier Research Platforms
   Elsevier Research Intelligence
EPA NATIONAL CENTER FOR COMPUTATIONAL TOXICOLOGY
EVOTEC
FIZ KARLSRUHE AND STN INTERNATIONAL
ICHEMLABS
IDBS
INFOCHEM
INTEGRATED CHEMISTRY DESIGN
INTE:LIGAND
IO INFORMATICS
JOHN WILEY & SONS
KNIME
KUDOS
LHASA LIMITED
LINGUAMATICS
MOLECULAR MATERIALS INFORMATICS
MOLSOFT
MONOCL
NEXTMOVE SOFTWARE
OPENEYE SCIENTIFIC SOFTWARE
OPEN PHACTS
OPTIBRIUM
ORCID
PERKINELMER INFORMATICS
PISTOIA ALLIANCE
PUBCHEM
Q-CHEM
ROYAL SOCIETY OF CHEMISTRY
SCHRÖDINGER
SCIENCEOPEN
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

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
COLLABORATIVE DRUG DISCOVERY
COMPCHEM SOLUTIONS
CORE INFORMATICS
COSMOLOGIC
CRESSET
DEEP WEB TECHNOLOGIES
DIGITAL SCIENCE
DISCNGINE
DOTMATICS
ELSEVIER
   Corporate
   Reaxys
   ScienceDirect
   Elsevier Research Intelligence
   Pathway Studio
   Cell Press
   Mendeley
EPA NATIONAL CENTER FOR COMPUTATIONAL TOXICOLOGY
EVOTEC
EXPERT SYSTEM
FIZ KARLSRUHE AND STN INTERNATIONAL
ICHEMLABS
IDBS
INFOCHEM
INTEGRATED CHEMISTRY DESIGN
IUCR JOURNALS
JOHN WILEY & SONS
KNIME
KUDOS
LHASA LIMITED
LINGUAMATICS
MOLECULAR MATERIALS INFORMATICS
MOLSOFT
MONOCL
NCI CADD GROUP CACTUS
NCI GENOMIC DATA COMMONS
NEXT MOVE SOFTWARE
OPENEYE SCIENTIFIC SOFTWARE
OPEN PHACTS
OPTIBRIUM
ORCID
PERKINELMER INFORMATICS
PISTOIA ALLIANCE
PROQUEST
PROUS INSTITUTE
PUBCHEM AND NCBI
Q-CHEM
SCHRÖDINGER
SCIENCEOPEN
SCILLIGENCE
SIMULATIONS PLUS
SPECS
SPRINGER NATURE
SYGNATURE DISCOVERY
TAYLOR & FRANCIS GROUP
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


This page last updated on 22nd August 2021.