Stable isotope labeled organic molecules have various applications in the pharmaceutical industry. Deuterium was discovered in 1932 and is used to study reaction mechanisms through kinetic isotope effects. Replacing hydrogen with deuterium in drug molecules can alter their metabolism and pharmacokinetics, potentially improving properties. Stable isotopes are also used as reference standards in mass spectrometry to improve quantification of drugs and metabolites. The global market for stable isotope labeled compounds was estimated at $220 million in 2013, with the pharmaceutical industry as the largest segment due to increasing clinical trials and quantification techniques. Challenges include high costs, but availability of resources in countries like India may allow for lower costs.
IB Chemistry on ICT, 3D software, Jmol, Pymol, Rasmol and ACD for Internal As...Lawrence kok
The document discusses measuring properties of bonds such as length, angle, and strength using various 3D modeling software. It also covers using these programs to analyze protein and enzyme structures from the Protein Data Bank by inputting four-letter codes. Details are provided on tools for molecular modeling and 3D representation in Jmol, PyMol, RasMol, and ACD Labs. Spectroscopic and chemistry databases are listed for reference.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
1. The document discusses various molecular modeling software and databases that can be used to measure bond lengths, bond angles, bond strengths, and compare protein and DNA structures between different species.
2. It provides instructions on how to use modeling programs like Jmol, Pymol, Rasmol and ACD Labs to obtain 3D structures from the Protein Data Bank and measure various parameters.
3. The document suggests possible research questions focusing on how factors like element identity, bond type, substituents, and lone pair electrons affect bond angles and lengths based on data collected from both 3D modeling and databases.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
The document provides a tutorial on using various 3D molecular modeling software like Jmol, Pymol, Rasmol and ACD Lab. It discusses how to use these software to generate 3D structures from SMILES or PDB files, optimize structures, measure bond lengths, angles and distances. Possible research questions are outlined focusing on how factors like element identity, double bonds, substituents affect bond angles based on data collected from the software and databases. Limitations of using computational methods are also discussed.
IB Chemistry on ICT, 3D software, Jmol, Pymol and Rasmol for Internal AssessmentLawrence kok
1. The document discusses measuring bond lengths, angles, and strengths using molecular modeling software like Jmol, PyMol, RasMol, and ACD Lab.
2. It also discusses using these software and databases like PDB, NCBI, UCSC and Ensembl to collect data on hydrogen bond distances between DNA/RNA base pairs across different species and cell types.
3. Limitations of molecular modeling are considered, like using multiple programs to validate results and checking against reliable databases like CRC and NIST. Accuracy of predicted structures from simulations alone is questioned.
The document describes the design and synthesis of tweezer peptide mimics of the estrogen receptor for screening endocrine disrupting chemicals. Key points:
- The project aims to design an artificial receptor to mimic the hormone binding domain of the estrogen receptor (ER) in order to screen for endocrine disrupting chemicals (EDCs).
- Three types of tweezer peptide mimics (Types A, B, and C) were designed based on selected amino acids known to interact with EDCs in the binding pocket of the natural ER.
- Type A mimics were synthesized using linear solid phase peptide synthesis. Types B and C used circular solid phase peptide synthesis and a combination of linear and click chemistry
CINF 35: Structure searching for patent information: The need for speedNextMove Software
Chemical databases grow larger every year. Without investing in additional hardware or improved software, the time to search these databases will in turn grow longer annually. With an ever-increasing number of pharmaceutical patents, the amount of chemical data associated with these is growing at a rate with which hardware advances alone cannot keep up.
Using automated mining of U.S. and European patents, we have extracted large collections of structural data in the form of reactions, mixtures, and exemplified compounds. Additional information such as protein targets and diseases are also extracted from each patent and associated with the structural data. We will describe how this data can be queried with natural language phrases and how these phrases are interpreted as structural queries.
Through innovations in substructure and similarity search algorithms, it is possible to search and retrieve hundreds of millions of chemical records in fractions of a second. We will demonstrate how this is achieved on a regular desktop machine using just-in-time and ahead-of-time compilation techniques.
Stable isotope labeled organic molecules have various applications in the pharmaceutical industry. Deuterium was discovered in 1932 and is used to study reaction mechanisms through kinetic isotope effects. Replacing hydrogen with deuterium in drug molecules can alter their metabolism and pharmacokinetics, potentially improving properties. Stable isotopes are also used as reference standards in mass spectrometry to improve quantification of drugs and metabolites. The global market for stable isotope labeled compounds was estimated at $220 million in 2013, with the pharmaceutical industry as the largest segment due to increasing clinical trials and quantification techniques. Challenges include high costs, but availability of resources in countries like India may allow for lower costs.
IB Chemistry on ICT, 3D software, Jmol, Pymol, Rasmol and ACD for Internal As...Lawrence kok
The document discusses measuring properties of bonds such as length, angle, and strength using various 3D modeling software. It also covers using these programs to analyze protein and enzyme structures from the Protein Data Bank by inputting four-letter codes. Details are provided on tools for molecular modeling and 3D representation in Jmol, PyMol, RasMol, and ACD Labs. Spectroscopic and chemistry databases are listed for reference.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
1. The document discusses various molecular modeling software and databases that can be used to measure bond lengths, bond angles, bond strengths, and compare protein and DNA structures between different species.
2. It provides instructions on how to use modeling programs like Jmol, Pymol, Rasmol and ACD Labs to obtain 3D structures from the Protein Data Bank and measure various parameters.
3. The document suggests possible research questions focusing on how factors like element identity, bond type, substituents, and lone pair electrons affect bond angles and lengths based on data collected from both 3D modeling and databases.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
The document provides a tutorial on using various 3D molecular modeling software like Jmol, Pymol, Rasmol and ACD Lab. It discusses how to use these software to generate 3D structures from SMILES or PDB files, optimize structures, measure bond lengths, angles and distances. Possible research questions are outlined focusing on how factors like element identity, double bonds, substituents affect bond angles based on data collected from the software and databases. Limitations of using computational methods are also discussed.
IB Chemistry on ICT, 3D software, Jmol, Pymol and Rasmol for Internal AssessmentLawrence kok
1. The document discusses measuring bond lengths, angles, and strengths using molecular modeling software like Jmol, PyMol, RasMol, and ACD Lab.
2. It also discusses using these software and databases like PDB, NCBI, UCSC and Ensembl to collect data on hydrogen bond distances between DNA/RNA base pairs across different species and cell types.
3. Limitations of molecular modeling are considered, like using multiple programs to validate results and checking against reliable databases like CRC and NIST. Accuracy of predicted structures from simulations alone is questioned.
The document describes the design and synthesis of tweezer peptide mimics of the estrogen receptor for screening endocrine disrupting chemicals. Key points:
- The project aims to design an artificial receptor to mimic the hormone binding domain of the estrogen receptor (ER) in order to screen for endocrine disrupting chemicals (EDCs).
- Three types of tweezer peptide mimics (Types A, B, and C) were designed based on selected amino acids known to interact with EDCs in the binding pocket of the natural ER.
- Type A mimics were synthesized using linear solid phase peptide synthesis. Types B and C used circular solid phase peptide synthesis and a combination of linear and click chemistry
CINF 35: Structure searching for patent information: The need for speedNextMove Software
Chemical databases grow larger every year. Without investing in additional hardware or improved software, the time to search these databases will in turn grow longer annually. With an ever-increasing number of pharmaceutical patents, the amount of chemical data associated with these is growing at a rate with which hardware advances alone cannot keep up.
Using automated mining of U.S. and European patents, we have extracted large collections of structural data in the form of reactions, mixtures, and exemplified compounds. Additional information such as protein targets and diseases are also extracted from each patent and associated with the structural data. We will describe how this data can be queried with natural language phrases and how these phrases are interpreted as structural queries.
Through innovations in substructure and similarity search algorithms, it is possible to search and retrieve hundreds of millions of chemical records in fractions of a second. We will demonstrate how this is achieved on a regular desktop machine using just-in-time and ahead-of-time compilation techniques.
Dry needling is generally very safe, though some minor side effects can occur in a small percentage of patients. Temporary pain during treatment occurs in 60-70% of cases, while minor bleeding or bruising occurs in 15-20% of treatments and is considered normal. Drowsiness, tiredness or dizziness may occur in 1-3% of patients. Fainting can occur in 0.3% of patients, especially with needling of the head or neck. Serious side effects are extremely rare, occurring in less than 0.01% of treatments, and may include damage to small nerves or blood vessels, usually resulting in temporary numbness, tingling or pain. Dry needling aims to stimulate the
Datos abiertos y participacion ciudadana - Conferencia Universidad VeracruzanaHiriam Eduardo Perez Vidal
Se presentan casos de estudio de portales de datos abiertos en el mundo, en tres ellos el Banco Interamericano de Desarrollo, Banco Mundial, Naciones Unidas, Reino Unido, y el caso de Mexico.
Se muestran también aplicaciones para la industria y el gobierno que emplean los Datos Abiertos, y como la participación ciudadana puede ser potencializada.
El documento resume las principales tendencias del mercado de marketing y publicidad identificadas en el festival Cannes Lions de 2016, incluyendo la multiplicidad de funcionalidades y dispositivos móviles, la importancia de las experiencias personalizadas a lo largo del recorrido del consumidor utilizando datos y realidad virtual, y la necesidad de enfocarse en ideas grandes con resultados medibles, transparencia y empatía con los clientes.
This is a diagram of some of the forces that have had an influence on me. It's a graphical diagrammatic CV (resume) with lots of additional information that CVs don't usually show.
This is also an attempt at the Most Confusing Powerpoint Slide of 2016. The final slide has lots of layers of graphical complexity. But because I built it up line by line, you should be able to understand the final slide by the time you reach it.
You may use this presentation in any way you want, but please tell me that you used it, and if you make any money by using it I want a share.
Consumer Technology - Social Listening in a Rapidly Changing IndustryBrandwatch
The document analyzes social media conversations about leading consumer technology brands. It finds that while brands generate most of the online content, audiences drive over 95% of conversations through sharing, replies and mentions of brands. The report also evaluates brands across several metrics to create a Consumer Technology Social Index, finding Lenovo ranked highest overall. It examines topics like the language used to discuss brands, products and features as well as differences in audiences by gender and profession.
Acuril 2016: Transition to customer focused Information servicesGO opleidingen
During Acuril2016 in Haiti GO | School for Information conducted a workshop on Customer Focused Information Services for Caribean Information Specialists.
Stunning Entries From Sony World Photography Awards 2017maditabalnco
This document contains 20 photos submitted for a photography contest across various categories such as nature, architecture, motion, travel, wildlife, street photography, portraits, and culture. The photos were taken in locations around the world including Portugal, Abu Dhabi, Rio de Janeiro, China, Australia, Brazil, Indonesia, Greece, Lebanon, France, Turkey, Italy, and Russia. They showcase landscapes, cityscapes, animals, people, and cultural events.
Thank you to everyone who participated in the #OfficeAnywhere photo contest! We received a lot of great submissions, and narrowing down the top 10 finalist was a challenge for our team. Check out our picks!
En esta presentación muy personal del congreso #DMD16 Galicia te voy a contar mis inicios con el blog y cómo he decidido salir de la zona de confort para ganarme la vida con aquello que más me apasiona.
The document summarizes key aspects of the Spanish education system. It describes the socioeconomic context of Spain and Catalonia. It then outlines the political and competencial organization between the state and autonomous communities in Spain. Finally, it provides details on the structure and organization of the Spanish education system from early childhood education through higher education. It also describes the school calendar and timetable as well as characteristics of the specific Escola L’Estel school.
Whether you're a pro-driver or not, still, there are a lot of safety precautions that need to be followed and these include driving at night.
For a safe night driving, bearing these simple tips will surely make your night driving at ease!
Plotly is a data visualization tool that is good for data journalists and bloggers. It allows creation of web figures, shows exact values, allows data sharing, and streaming of data. The Plotly Julia API allows access to Plotly's functionality from the Julia programming language. Some example visualizations created with Plotly include network diagrams, tax rates vs income levels, healthcare spending vs life expectancy, and a chocolate bar chart. Plotly has a Facebook group and Mashup Award for visualizations created with the tool.
Becoming a New Manager - Todd DeLuca - STC Summit 2015Todd DeLuca, MTSC
Becoming a New Manager - Todd DeLuca - STC Summit 2015
Have you wondered how to transition from a sole contributor to a manager? What if there are few opportunities to advance? How do others recognize your potential? Maybe you’ve just been thinking about that ‘leap’ but don’t know if leading others is for you.
If you’re not sure where to start, then review this informative session and learn from someone who has been there. Todd DeLuca outlines his experience of being a lone writer to leading a Technical Communications department. More specifically, he describes activities and actions that helped him demonstrate his capability to decision makers that helped him stand out as a potential leader (to get the job) !
Everyone’s leadership path follows its own course. After viewing this session, you’ll have pointers on how to pave your own path and receive some ‘newbie’ advice on what you should do when you reach your destination.
Jack D Ryger: A Journey Through The Beautiful Seasons Of Central ParkJack D. Ryger
Central Park offers scenic beauty throughout the four seasons - in summer one can sunbathe on the Great Lawn or enjoy a picnic by the lake, fall brings paddle boat rides and vibrant foliage, winter features ice skating on the frozen lake, and spring allows one to admire blooming cherry blossoms in the conservatory garden. The document encourages visiting Central Park anytime to experience its natural attractions and seasonal changes.
Seminário 04 - Prática Escolar: do erro como fonte de castigo ao erro como fo...Cosmo Matias Gomes
O documento discute a avaliação da aprendizagem escolar, comparando abordagens que veem o erro como fonte de castigo versus fonte de virtude. Defende que o erro não deve ser punido, mas sim usado para melhorar a aprendizagem. Também trata da avaliação como um ato de acolhimento para apoiar o estudante.
Axway Introduction & Digital Business (by Jo Van Audenhove & Rogier van Boxtel)ACA IT-Solutions
This document provides an agenda and introduction for an Axway & ACA IT-Solutions seminar on accelerating digital transformation. The agenda includes presentations on Axway's offering and positioning of Appcelerator, how to transform business with Appcelerator, and a customer testimonial. Axway provides digital business solutions to connect people, processes, and things while governing data flows. Appcelerator is a mobile and web development platform that enables speed, simplicity, and ease of use for developers.
Impacto de las tics en la cultura de l mediacion a distancia para la educacio...rosa zambrano
El documento discute el impacto de las tecnologías de la información y la comunicación (TICS) en la educación superior a distancia en Ecuador. Señala que las TICS pueden servir como mediadores culturales para desarrollar un nuevo modelo educativo comunitario siempre que haya un cambio de mentalidad. También destaca la necesidad de capacitar continuamente a las personas involucradas en el proceso y de fusionar las herramientas tecnológicas con las interacciones entre estudiantes de una manera dialéctica e interpretativa. Finalmente, concluye que la univers
Chemical Text Mining for Current Awareness of Pharmaceutical PatentsNextMove Software
This document summarizes a presentation given at the ACS National Meeting in Philadelphia on August 19th, 2012 about chemical text mining of pharmaceutical patents. The presentation discussed trends in US patent applications for pharmaceuticals from 2002-2012, workflows for extracting and analyzing information from patent texts, and tools like LeadMine and PatFetch that can recognize chemical entities and access patent texts programmatically.
Extraction, Analysis, Atom Mapping, Classification and Naming of Reactions fr...NextMove Software
The document discusses extracting reaction information from pharmaceutical electronic laboratory notebooks (ELNs) and some of the challenges involved. It describes exporting data from the complex database schemas of ELNs, converting file formats like sketches to standard reaction formats, standardizing reactions, determining reaction identity when reactions are duplicated, and classifying reactions into an ontology. The goal is to make the synthetic knowledge contained in ELNs accessible for applications like yield prediction, retrosynthesis, and reducing costs through more efficient routes.
Dry needling is generally very safe, though some minor side effects can occur in a small percentage of patients. Temporary pain during treatment occurs in 60-70% of cases, while minor bleeding or bruising occurs in 15-20% of treatments and is considered normal. Drowsiness, tiredness or dizziness may occur in 1-3% of patients. Fainting can occur in 0.3% of patients, especially with needling of the head or neck. Serious side effects are extremely rare, occurring in less than 0.01% of treatments, and may include damage to small nerves or blood vessels, usually resulting in temporary numbness, tingling or pain. Dry needling aims to stimulate the
Datos abiertos y participacion ciudadana - Conferencia Universidad VeracruzanaHiriam Eduardo Perez Vidal
Se presentan casos de estudio de portales de datos abiertos en el mundo, en tres ellos el Banco Interamericano de Desarrollo, Banco Mundial, Naciones Unidas, Reino Unido, y el caso de Mexico.
Se muestran también aplicaciones para la industria y el gobierno que emplean los Datos Abiertos, y como la participación ciudadana puede ser potencializada.
El documento resume las principales tendencias del mercado de marketing y publicidad identificadas en el festival Cannes Lions de 2016, incluyendo la multiplicidad de funcionalidades y dispositivos móviles, la importancia de las experiencias personalizadas a lo largo del recorrido del consumidor utilizando datos y realidad virtual, y la necesidad de enfocarse en ideas grandes con resultados medibles, transparencia y empatía con los clientes.
This is a diagram of some of the forces that have had an influence on me. It's a graphical diagrammatic CV (resume) with lots of additional information that CVs don't usually show.
This is also an attempt at the Most Confusing Powerpoint Slide of 2016. The final slide has lots of layers of graphical complexity. But because I built it up line by line, you should be able to understand the final slide by the time you reach it.
You may use this presentation in any way you want, but please tell me that you used it, and if you make any money by using it I want a share.
Consumer Technology - Social Listening in a Rapidly Changing IndustryBrandwatch
The document analyzes social media conversations about leading consumer technology brands. It finds that while brands generate most of the online content, audiences drive over 95% of conversations through sharing, replies and mentions of brands. The report also evaluates brands across several metrics to create a Consumer Technology Social Index, finding Lenovo ranked highest overall. It examines topics like the language used to discuss brands, products and features as well as differences in audiences by gender and profession.
Acuril 2016: Transition to customer focused Information servicesGO opleidingen
During Acuril2016 in Haiti GO | School for Information conducted a workshop on Customer Focused Information Services for Caribean Information Specialists.
Stunning Entries From Sony World Photography Awards 2017maditabalnco
This document contains 20 photos submitted for a photography contest across various categories such as nature, architecture, motion, travel, wildlife, street photography, portraits, and culture. The photos were taken in locations around the world including Portugal, Abu Dhabi, Rio de Janeiro, China, Australia, Brazil, Indonesia, Greece, Lebanon, France, Turkey, Italy, and Russia. They showcase landscapes, cityscapes, animals, people, and cultural events.
Thank you to everyone who participated in the #OfficeAnywhere photo contest! We received a lot of great submissions, and narrowing down the top 10 finalist was a challenge for our team. Check out our picks!
En esta presentación muy personal del congreso #DMD16 Galicia te voy a contar mis inicios con el blog y cómo he decidido salir de la zona de confort para ganarme la vida con aquello que más me apasiona.
The document summarizes key aspects of the Spanish education system. It describes the socioeconomic context of Spain and Catalonia. It then outlines the political and competencial organization between the state and autonomous communities in Spain. Finally, it provides details on the structure and organization of the Spanish education system from early childhood education through higher education. It also describes the school calendar and timetable as well as characteristics of the specific Escola L’Estel school.
Whether you're a pro-driver or not, still, there are a lot of safety precautions that need to be followed and these include driving at night.
For a safe night driving, bearing these simple tips will surely make your night driving at ease!
Plotly is a data visualization tool that is good for data journalists and bloggers. It allows creation of web figures, shows exact values, allows data sharing, and streaming of data. The Plotly Julia API allows access to Plotly's functionality from the Julia programming language. Some example visualizations created with Plotly include network diagrams, tax rates vs income levels, healthcare spending vs life expectancy, and a chocolate bar chart. Plotly has a Facebook group and Mashup Award for visualizations created with the tool.
Becoming a New Manager - Todd DeLuca - STC Summit 2015Todd DeLuca, MTSC
Becoming a New Manager - Todd DeLuca - STC Summit 2015
Have you wondered how to transition from a sole contributor to a manager? What if there are few opportunities to advance? How do others recognize your potential? Maybe you’ve just been thinking about that ‘leap’ but don’t know if leading others is for you.
If you’re not sure where to start, then review this informative session and learn from someone who has been there. Todd DeLuca outlines his experience of being a lone writer to leading a Technical Communications department. More specifically, he describes activities and actions that helped him demonstrate his capability to decision makers that helped him stand out as a potential leader (to get the job) !
Everyone’s leadership path follows its own course. After viewing this session, you’ll have pointers on how to pave your own path and receive some ‘newbie’ advice on what you should do when you reach your destination.
Jack D Ryger: A Journey Through The Beautiful Seasons Of Central ParkJack D. Ryger
Central Park offers scenic beauty throughout the four seasons - in summer one can sunbathe on the Great Lawn or enjoy a picnic by the lake, fall brings paddle boat rides and vibrant foliage, winter features ice skating on the frozen lake, and spring allows one to admire blooming cherry blossoms in the conservatory garden. The document encourages visiting Central Park anytime to experience its natural attractions and seasonal changes.
Seminário 04 - Prática Escolar: do erro como fonte de castigo ao erro como fo...Cosmo Matias Gomes
O documento discute a avaliação da aprendizagem escolar, comparando abordagens que veem o erro como fonte de castigo versus fonte de virtude. Defende que o erro não deve ser punido, mas sim usado para melhorar a aprendizagem. Também trata da avaliação como um ato de acolhimento para apoiar o estudante.
Axway Introduction & Digital Business (by Jo Van Audenhove & Rogier van Boxtel)ACA IT-Solutions
This document provides an agenda and introduction for an Axway & ACA IT-Solutions seminar on accelerating digital transformation. The agenda includes presentations on Axway's offering and positioning of Appcelerator, how to transform business with Appcelerator, and a customer testimonial. Axway provides digital business solutions to connect people, processes, and things while governing data flows. Appcelerator is a mobile and web development platform that enables speed, simplicity, and ease of use for developers.
Impacto de las tics en la cultura de l mediacion a distancia para la educacio...rosa zambrano
El documento discute el impacto de las tecnologías de la información y la comunicación (TICS) en la educación superior a distancia en Ecuador. Señala que las TICS pueden servir como mediadores culturales para desarrollar un nuevo modelo educativo comunitario siempre que haya un cambio de mentalidad. También destaca la necesidad de capacitar continuamente a las personas involucradas en el proceso y de fusionar las herramientas tecnológicas con las interacciones entre estudiantes de una manera dialéctica e interpretativa. Finalmente, concluye que la univers
Chemical Text Mining for Current Awareness of Pharmaceutical PatentsNextMove Software
This document summarizes a presentation given at the ACS National Meeting in Philadelphia on August 19th, 2012 about chemical text mining of pharmaceutical patents. The presentation discussed trends in US patent applications for pharmaceuticals from 2002-2012, workflows for extracting and analyzing information from patent texts, and tools like LeadMine and PatFetch that can recognize chemical entities and access patent texts programmatically.
Extraction, Analysis, Atom Mapping, Classification and Naming of Reactions fr...NextMove Software
The document discusses extracting reaction information from pharmaceutical electronic laboratory notebooks (ELNs) and some of the challenges involved. It describes exporting data from the complex database schemas of ELNs, converting file formats like sketches to standard reaction formats, standardizing reactions, determining reaction identity when reactions are duplicated, and classifying reactions into an ontology. The goal is to make the synthetic knowledge contained in ELNs accessible for applications like yield prediction, retrosynthesis, and reducing costs through more efficient routes.
Presented by Antoinette Azevedo, e-SubmissionsSolutions.com at Documentation and Training Life Sciences, June 23-26, 2008 in Indianapolis.
Life sciences regulatory authorities in North America, Europe and Japan have been developing standards for drug and biologic registration submissions in electronic format for over ten years. The current version of the format—electronic Common Technical Document (eCTD)—has been the recommended format since 2005 and is on the way to becoming mandatory. This presentation will provide an overview of best practices to enable a sponsor to prepare a compliant eCTD for regulatory authority review.
A California biotech submitted an eCTD to the US FDA in summer 2005. This company used commercial-off-the-shelf publishing software, experienced consultants, and in-house staff to compile this eCTD. This drug was the biotechs first candidate for commercialization. The biotech was partnered with big Pharma to assist with sales and marketing after the FDA authorized the drug for marketing. The biotech hired a sales force of nearly 200 in anticipation of FDA approval.
The FDA issued a refuse-to-file on this eCTD in fall 2005, due to problems with the PDF files and navigability of the content of the submission. The company’s market capitalization dropped 50% overnight. The company had to recompile the submission, by reworking the source files and rebuilding the XML backbone. The new version of the eCTD was resubmitted in early 2006. The FDA accepted the resubmission for review.
However, in May 2006 the FDA issued an approvable letter, that meant the drug could be approved in the future if certain conditions were met (meaning yet another delay in being able to market the product, plus additional expense to conduct further clinical studies). In June, 2006, the big pharma company terminated the partnership with the biotech. In July 2006, the biotech laid off their sales force. In August, 2006, the biotech laid off 100 more employees. In September 2006, the biotech had a meeting with FDA to discuss what additional studies and analysis was needed. Finally, in January 2007, the biotech announced plans to resubmit its NDA by end of second quarter 2007.
This presentation will describe:
* Regulatory and business drivers behind the eCTD format
* Technical components of an eCTD
* Practical implications of collecting documents and data over the discovery, development, application review, and post-marketing lifecycle phases of a drug or biological product
* Global picture for adoption of the eCTD format
* Future direction for the eCTD format
* Role of electronic document management in the eCTD lifecycle
* Top 12 Issues FDA Has with eCTD and how to avoid them
* Preparing submission-ready source documents and data for submission in eCTD
* Whether to purchase an eCTD publishing system or to outsource.
* How to prepare for the technical challenges of eCTD
ChemSpider is an online database of over 20 million chemical structures assembled from well over a hundred data sources including chemical and screening library vendors, publicly accessible databases and resources, commercial databases and Open Access literature articles. Such a public resource provides a rich source of ligands for the purpose of virtual screening experiments. These can take many forms. This work will present results from two specific types of studies: 1) Quantitative Structure Activity Relationship (QSAR) based analyses and 2) In-silico docking into protein receptor sites. We will review results from the application of both approaches to a number of specific examples. QSAR analyses utilizing the ChemModLab environment for assessing quantitative structure-activity relationships will and screening using a molecular surface descriptor model.
The document describes several web services and resources provided by the National Cancer Institute's (NCI) Computer-Aided Drug Design (CADD) Group for accessing chemical structure and compound information. The key services and databases mentioned include the Chemical Identifier Resolver, which allows conversion between various chemical structure representations and identifiers, and the NCI/CADD Chemical Structure Database, which contains over 100 million chemical structures and structure identifiers.
CAS Solutions is developing new solutions to help researchers address challenges in their work. They are improving workflow efficiency and providing targeted solutions beyond organic chemistry. CAS has added approximately 75 million new substances to their database over the last 10 years. Their new PatentPak tool allows scientists to directly access chemistry information in patents, saving time compared to searching individual patent websites. A new solution currently in development will focus on supporting researchers in making discoveries work.
5th Meeting on U.S. Government Chemical Databases and Open Chemistry TalkMarkus Sitzmann
The document describes the NCI/CADD Chemical Identifier Resolver, which works as a resolver for different chemical structure identifiers. It allows the conversion of a given structure identifier into another representation or identifier. The resolver indexes over 150 chemical structure databases containing over 120 million structures. It is accessible via a web API that detects the identifier type and performs the requested conversion via calculation or database lookup.
We’re all SMILES! Building Chemical Semantic Web Services with SADI, ChEBI, a...Michel Dumontier
This document summarizes a presentation about building chemical semantic web services using SADI, ChEBI, and CHEMINF. It discusses how SADI allows services to be discovered and composed to answer queries by reasoning over chemical ontologies. As an example, it describes how a SPARQL query engine could discover and invoke web services to determine if caffeine is a drug-like molecule according to the Lipinski rule of five.
This was a presentation I gave to an audience at Nature Publishing Group in New York on May 7th 2009. It's a long presentation and over an hour in length. Not much new here relative to other presentations...just a knitting together of many of the others on here.
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with an increasing number of Open Source software programs we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 190 separate data sources, ChemSpider has taken on the task of both robotically and manually integrating and curating publicly available data sources. ChemSpider has also provided an environment for users to deposit, curate and annotate chemistry-related information. This has allowed the community to enhance ChemSpider by adding analytical data, associating synthetic pathways and publications and connecting to social networking resources. I will discuss how ChemSpider is fast becoming the premier curated platform and centralized hub for resourcing information about chemical entities and how the platform provides the foundation data for services allowing the analysis of analytical data and collaborative science.
This document summarizes advances in automatic chemical spelling correction. It discusses using edit distances and dynamic programming to correct spelling errors. Examples are given of correcting errors in chemical names, CAS registry numbers, and protein target names. Benchmarking on patent data shows automatic correction improves recall of chemical entity recognition by around 20-40%. The techniques allow fuzzy matching of chemical structures and nomenclature rules.
Overview of the SureChEMBL system and web interface.
https://www.surechembl.org/search/
SureChEMBL is a freely available web resource for chemistry patent searching. It is based on a fully automatic and dynamic text and image mining pipeline.
1. The document discusses cheminformatics topics including substructure searching using SMARTS, calculation of topological polar surface area, quantitative structure-activity relationships (QSAR) modeling, and Lipinski's rule of five.
2. It provides an example of using SMARTS to search for functional groups known to cause toxicological problems.
3. QSAR modeling involves using molecular descriptors and regression techniques to develop mathematical models that correlate molecular structure to properties or biological activities.
Automated Extraction of Reactions from the Patent Literaturedan2097
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Ivanti’s Patch Tuesday breakdown goes beyond patching your applications and brings you the intelligence and guidance needed to prioritize where to focus your attention first. Catch early analysis on our Ivanti blog, then join industry expert Chris Goettl for the Patch Tuesday Webinar Event. There we’ll do a deep dive into each of the bulletins and give guidance on the risks associated with the newly-identified vulnerabilities.
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A Comprehensive Guide to DeFi Development Services in 2024Intelisync
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5th LF Energy Power Grid Model Meet-up SlidesDanBrown980551
5th Power Grid Model Meet-up
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Chemical Text Mining for Current Awareness of Pharmaceutical Patents
1. Chemical Text Mining for Current
Awareness of Pharmaceutical
Patents
Daniel Lowe and Roger Sayle
NextMove Software
Cambridge, UK
ACS National Meeting, Philadelphia, USA 19th August 2012
2. US patent applications by year
35000
30000
25000
Patent applications per year
20000
Pharma
15000 C07D
10000
5000
0
2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012*
*2012 includes patent applications published on or before 9th August 2012.
“Pharma” is defined as IPC codes C07*, A61K, A61P and A01N.
ACS National Meeting, Philadelphia, USA 19th August 2012
6. SGml (2001 grants)
• Uses different tags to Red Book documents
• May contain unclosed tags:
<PCIT>
<DOC><DNUM><PDAT>5154857</PDAT></DNUM>
<DATE><PDAT>19921000</PDAT></DATE></DOC>
<PARTY-US>
<NAM><SNM><STEXT><PDAT>Goto et al.</PDAT></STEXT></SNM></NAM>
</PARTY-US>
<PNC><PDAT>25229963</PDAT></PNC></PCIT><CITED-BY-EXAMINER>
ACS National Meeting, Philadelphia, USA 19th August 2012
7. Red Book (2002 – present)
<heading id="h-0082" level="1">Example 30</heading>
<heading id="h-0083" level="1">Preparation of (E)-2-amino-N-(3-(2-(2,6,6-
trimethylcyclohex-1-enyl)vinyl)phenyl)acetamide</heading>
<p id="p-0883" num="1052"><chemistry id="CHEM-US-00235" num="00235">
<img id="EMI-C00235" he="20.07mm" wi="57.57mm" file="US20090170841A1-
20090702-C00235.TIF" img-content="chem" img-format="tif"/>
</chemistry>
</p>
<p id="p-0884" num="1053">(E)-2-amino-N-(3-(2-(2,6,6-trimethylcyclohex-1-
enyl)vinyl)phenyl)acetamide was prepared following the method used in
Example 15.</p>
<p id="p-0885" num="1054">Step 1: Coupling of Wittig reagent 24 with 3-
nitrobenzaldehyde gave 1-nitro-3-(2-(2,6,6-trimethylcyclohex-1-
enyl)vinyl)benzene as a light yellow oil. Yield (0.639 g, 95%), isomer ratio
4:1 ratio trans:cis.</p>
<p id="p-0886" num="1055">trans-isomer: <sup>1</sup>H NMR (300 MHz, CDCl<sub>3</sub>)
δ 8.24 (t, J=1.9 Hz, 1H), 8.04 (m, 1H), 7.69 (d, J=7.7 Hz, 1H), 7.47 (t, J=8.0 Hz, 1H), 6.83 (dd,
J=16.3, 0.85 Hz, 1H), 6.40 (d, J=16.3 Hz, 1H), 2.06 (t, J=6.2 Hz, 2H), 1.81 (s, 3H), 1.65 (m, 2H), 1.52 (m,
2H), 1.08 (s, 6H);</p>
ACS National Meeting, Philadelphia, USA 19th August 2012
8. Html generated from red book
ACS National Meeting, Philadelphia, USA 19th August 2012
9. Benefits of clean Input
• Patent feed text:
Cis-2,3,6,7,12,12a-hexahydro-2-benzyl6-(4-methoxyphenyl)-pyrazino0x9b 2',1':6,1
!pyrido0x9b 3,4-b!indole-1,4-dione
New line in
• Extracted from USPTO source: middle of name!
Cis-2,3,6,7,12,12a-hexahydro-2-benzyl6-(4-methoxyphenyl)-
pyrazino[2',1':6,1]pyrido[3,4-b]indole-1,4-dione
• LeadMine entity:
Cis-2,3,6,7,12,12a-hexahydro-2-benzyl-6-(4-methoxyphenyl)-
pyrazino[2',1':6,1]pyrido[3,4-b]indole-1,4-dione
ACS National Meeting, Philadelphia, USA 19th August 2012
10. leadMine 2.0
• Dictionary and grammar based general entity
recogniser
• Tokenization determined by the terms to be
recognised
ACS National Meeting, Philadelphia, USA 19th August 2012
11. Default Dictionaries
Dictionary Example Size
Molecule benzoic acid Infinite
Dictionary ranitidine 11,201
Registry # GW-409544 Large but finite
CAS Number 7732-18-5 Large but finite
Element gold 185
Fragment phenyl Infinite
Atom Fragment chloro 11
Polymer polystyrene 74
Generic alkane 362
Noise formal 16
ACS National Meeting, Philadelphia, USA 19th August 2012
12. LeadMine 2.0
• Dictionaries to be used are configurable e.g.
protein targets, genes, diseases, reaction
names etc.
• Matching speed is independent of dictionary
size
• Any dictionary can be used with spelling
correction to match lexically close entities
ACS National Meeting, Philadelphia, USA 19th August 2012
13. LeadMine 2.0 Configuration
#A company registry number for a compound
[dictionary]
location CFDictR.cfx
Multiple dictionaries
entityType R
htmlColor #90b0ff
can map to the same
caseSensitive false
useSpellingCorrection false
entity type
#A molecule e.g. 2-methylpyridine
[dictionary]
location CFDictM.cfx
entityType M
htmlColor violet
enforceBracketing true
Spelling correction can
caseSensitive false
useSpellingCorrection true
be adjusted on a per
minimumCorrectedEntityLength 9
maxCorrectionDistance 1
dictionary basis
ACS National Meeting, Philadelphia, USA 19th August 2012
14. Building Dictionaries
• Uses Daciuk/Mihov’s algorithm to allow building
dictionaries with millions of entities in linear time
• Extremely large dictionaries are often smaller when
compiled than the original input
• 54 million synonyms from PubChem can be compiled
to a dictionary slightly less than 1gb in 17 minutes
and 20 seconds!
Daciuk, J.; Mihov, S.; Watson, B. W.; Watson, R. E. Incremental
construction of minimal acyclic finite-state automata.
Computational linguistics 2000, 26, 3–16.
ACS National Meeting, Philadelphia, USA 19th August 2012
15. Foreign Language Support
• Chinese and Japanese chemical names may be
rapidly converted to English as a pre-
processing step
“Translating IUPAC-like chemical nomenclature to and from
simplified Chinese” 9:10 am, Wednesday, Global Opportunities
in Chemical Information
ACS National Meeting, Philadelphia, USA 19th August 2012
18. BRAT (brat rapid annotation tool)
T1 M 25 44 4-hydroxypiperidine
T2 M 78 95 dimethylformamide
T3 M 121 153 1-(bromomethyl)-4-methoxybenzene
T4 M 178 191 triethylamine
T5 M 404 417 ethyl acetate
T6 N 439 444 water
T7 G 457 462 brine
T8 M 495 509 sodium sulfate
T9 G 658 668 silica gel
T10 M 675 683 methanol
T11 M 684 702 methylene chloride
T12 M 714 747 1-(4-methoxybenzyl)piperidin-4-ol
ACS National Meeting, Philadelphia, USA 19th August 2012
19. BRAT (brat rapid annotation tool)
ACS National Meeting, Philadelphia, USA 19th August 2012
22. PatfetcH-cont.
• Recognises common USPTO grant/application
number variants e.g. 6356863/US
6356863/006356863/US 6,356,863 B1
• Allows all USPTO patent grant/applications to
be accessed as text or html from simple URLs
e.g. patfetch/patents/6356863.html
ACS National Meeting, Philadelphia, USA 19th August 2012
23. “Macroscopic” analysis
• Having all patents available allows for analysis
that spans the entire corpus rather than being
limited to a single patent
• Example use cases
– Identifying the key compounds in a patent
– Finding the first instance of a molecule in the
patent literature
– Identify patents containing novel chemistry
ACS National Meeting, Philadelphia, USA 19th August 2012
24. Filtering irrelevant patents
• Most irrelevant patents can be excluded by
IPC codes. These are assigned by the USPTO to
classify each patent.
• Typical pharmaceutical IPC codes
– CO7 (Organic Chemistry)
– A61K (Preparations for medical, dental or toilet purposes)
– A61P (Specific therapeutic activity of chemical compounds
or medicinal preparations)
– AO1N (Preservation of bodies of humans or animals or
plants or parts thereof)
ACS National Meeting, Philadelphia, USA 19th August 2012
25. Finding the first mention of a
compound
• Trivial names of compound often won’t be present in
the first patent synthesising a compound
• Brand name Fabior, approved May 11, 2012
• Generic name Tazarotene
• First mentioned in US05023341
ACS National Meeting, Philadelphia, USA 19th August 2012
26. Finding the first mention of a
compound
• Brand name Erivedge, approved January 30, 2012
• Generic name Vismodegib
• First mentioned in US20060063779A1
ACS National Meeting, Philadelphia, USA 19th August 2012
27. Novel compounds per patent
ACS National Meeting, Philadelphia, USA 19th August 2012
28. Novel compounds per patent
ACS National Meeting, Philadelphia, USA 19th August 2012
29. Awareness of novel scaffolds
Pitt, W. R.; Parry, D. M.; Perry, B. G.; Groom, C. R. Heteroaromatic rings of
the future. Journal of medicinal chemistry 2009, 52, 2952–2963.
ACS National Meeting, Philadelphia, USA 19th August 2012
30. Awareness of novel scaffolds
US46041346, 1983
ACS National Meeting, Philadelphia, USA 19th August 2012
31. Awareness of novel scaffolds
US20040038959A1
ACS National Meeting, Philadelphia, USA 19th August 2012
32. Rate of novel scaffold discovery
600
500
Novel scaffolds per year
400
300
6 atom ring fused to 5 atom ring
6 atom ring fused to 6 atom ring
200
100
0
*year not yet complete
ACS National Meeting, Philadelphia, USA 19th August 2012
33. Solvent Occurrences
Extracted from reactions in 2008-2011 USPTO patent applications
ACS National Meeting, Philadelphia, USA 19th August 2012
34. Conclusions
• Getting clean text from patents is an
important starting point
• LeadMine offers a highly configurable
environment for performing entity extraction
• Comprehensive coverage of the patent
literature can assist in identifying the
interesting aspects of a new patent
ACS National Meeting, Philadelphia, USA 19th August 2012
35. acknowledgements
• Sorel Muresan and Paul Hongxing Xie, AstraZeneca.
• Nicko Goncheroff, SureChem/Digital Science.
• Colin Batchelor, Royal Society of Chemistry.
• Peter Loew and Heinz Saller, InfoChem.
• Pat Walters, Vertex Pharmaceuticals.
• Thank you for your time.
ACS National Meeting, Philadelphia, USA 20th August 2012