EFMC-ISMC 2014

Company Worskhops

MONDAY, September 8 | 17:30-19:30

ChemDraw / SciFinder Workshop: Less time at the computer, more time for your research.

Presenter: Pierre Morieux & Miriam Plana

The ChemDraw suite of software applicationsis an industry leader in chemical drawing programs and provides an up-to-date collection of scientifically intelligent applications for chemical structure drawing and analysis combined with biological pathway drawing. The latest ChemBioDraw Ultra 14.0 suite now empowers scientists with a direct structure/reaction search link to SciFinder.

The first part of the workshop will be focused on the newest features of ChemDraw such as querying chemical reactions drawn within the application directly into SciFinder. Several drawing tips & tricks of ChemDraw will also be covered to help users draw molecules and reactions faster. Specifically, the users will be able to:

  • See how SciFinder and ChemDraw interact and work together
  • Learn time-saving shortcuts and tips
  • Learn how to customize and define their own hotkeys and labels
  • Learn how generic structures and R-group lists can help them to quickly generate multiple structures

By the end of the session, the participants should be able to save time drawing accurate and publication-grade chemical drawing figures.

 

The second part of the workshop will focus on SciFinder functionality and getting the most from your research. Only SciFinder provides medicinal chemists access to the world’s scientific journal and patent literature, including MEDLINE®, and covers more than 100 years of information. CAS scientists identify disclosed small molecules and disease-related terminology in the published literature. This includes names of targets, genes, proteins, enzymes and other biological entities. Using data-mining technologies, compounds have been related to indicators of diseases and targets to facilitate further analysis and refine larger answer sets.

  • Topics discussed by CAS and Perkin Elmer during this workshop will include:
  • How medicinal chemists can explore the chemistry space, potential applications and synthetic routes for preparing  compounds. 
  • How to efficiently visualize projects, design a synthesis plan, and easily manage and organize search results using SciPlanner’s interactive workspace.
  • How to find the most relevant substances, link directly to commercial sources and full text articles.
  • Benefits of using ChemDraw as part of your SciFinder search


At the conclusion scientists should feel confident they are making their vital decisions using the most reliable source of publically disclosed information.

 

MONDAY, September 8 | 17:30-19:30

Presenter: Olivier Barberan

Data driven approaches in Medicinal Chemistry : How to take advantages of Medicinal chemistry large scale data to support drug discovery?
The way of understanding drug discovery and consequently medicinal chemistry is evolving. The increasing rate of data generation in Medicinal Chemistry and related disciplines is a great opportunity for scientists to change the way of doing research. Data driven approaches in Medicinal chemistry will enable researchers to uncover hidden relationships in large scale data allowing them to improve decision making in drug discovery process. Consequently, wet scientists are embracing the new role of ‘data scientist’. How to manage and explore data has appeared more important as the perception grows that data are produced at a faster rate than the capacity to analyze and interpret them. Data driven approaches are consequently dependent on how medicinal synthetic chemists and computational chemists are dealing with the huge amount of data generated internally but also available externally in large scale repositories.
Having access to a large amount of data is one facet but quality, comprehensiveness and biological data access are other ones and unfortunately they are most of the time negatively correlated. Even if Chemical Abstract Service has the goal to ‘find, collect and organize all publicly disclosed chemical substances’ related biological data are not recorded. However, until now neither public (Pubchem, ChEMBL) nor private initiatives (GoSTAR, Integrity, Wombat) aim to curate biological and chemical data in a way that guaranty high quality, comprehensiveness of data and allow scientists to uncover new relationships.
In order to fill the gap a completely new Medicinal chemistry repository was built in order to capture biological activities including in vitro efficacy, in vivo animal models, metabolism and transport, pharmacokinetics and toxicology experiments from Journals and Patents : Reaxys Medicinal Chemistry. Advantages of using Reaxys Medicinal Chemistry in the drug discovery process will be demonstrated through the following data driven approaches: in silico screening, Model building, Phenotypic screening, Off Target profiling and Selectivity profiling, Metabolism and PK data profiling.


BIOVIA Workshop

TUESDAY, September 9 | 16:30-18:30

Presenter: Tien Luu

Part 1 - Non-Bond Analysis: Understanding Interactions for Structure-Based Drug Design

The perception, rationalization and optimization of non-bonded interactions is one of the fundamental challenges in rational drug design. Advancing theory and new experimental evidence for molecular interactions beyond classical hydrogen bonds and hydrophobic effects have necessitated a more sophisticated and comprehensive analysis of the interactions involved in shaping and stabilizing protein conformations, protein-protein, and protein-small molecule interactions. Discovery Studio has fully re-engineered and expanded the perception of non-bond interactions, including favorable, unfavorable and unsatisfied interactions. Here we present new client visualization tools available to medicinal and computational chemists to quickly and easily capture and render non-bond interactions and server components to rapidly calculate non-bond interactions for post-processing, enrichment of screening results and interaction fingerprint analysis.

Part 2 - QSAR Workbench:  A Web Application to Capture and Deliver Robust Statistical Models

Here, we will present the QSAR Workbench, a comprehensive statistical modelling web application, that can rapidly help guide QSAR experts through all key stages of model development.  Based on Pipeline Pilot chemistry and data modelling collections, it provides functionality to handle data sets, calculate descriptors, learn from an exhaustive number of statistical models and validate them.  Furthermore, as a Pipeline Pilot protocol-based application, it is easy for experts to introduce new statistical methods and descriptors and to try new combinations of existing methods, which enables for much more rapid exploration of the statistical model space.  Successfully validated predictive models can be published as a web service and integrated with various desktop tools, enabling project teams to usefully exploit series- or project-specific within their existing medicinal chemistry applications.

 

Chemical Computing Group Workshop

TUESDAY, September 9 | 16:30-18:30

Designing Inhibitors with MOE Structure-Based Drug Design Tools
The course covers the application of in silico structure based drug design (SBDD) tools for the rational design of Tarceva-based EGFR kinase inhibitors. Starting with raw PDB protein-ligand 3D structures, all the steps required to initiate and advance a SBDD study are covered: preparing PDB structures for modeling, binding pocket visualization, protein-ligand contact analysis and the use of SAR for in situ modeling (modifying and optimizing ligands in the binding pocket) to design new compounds. Advanced topics such as pharmacophore query generation, protein-ligand docking, protein alignments for binding site comparison and in situ combinatorial synthesis will also be covered.


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