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Ligand Based Design Training

Pharmacophore Modeling in Discovery Studio

This course provides an introduction to pharmacophore modeling in Discovery Studio, overviewing the diverse applications of these tools in drug discovery and design.

The course provides the foundations for subsequent pharmacophore courses and will cover the following topics:

  • Pharmacophore definition and features
  • Pharmacophore application in drug discovery
  • Ligand-pharmacophore scoring and mapping
  • Ligand perception
    • Conformation generation
    • Multi-conformer databases

Duration: 2.5 hours on-line, 1 day on-site

Email the Accelrys Training team to arrange on-line or on-site training for this course

Common Feature Pharmacophore Generation

This course covers the generation of qualitative pharmacophores in Discovery Studio, detailing the automated algorithms (HipHop/HipHopRefine) and the applications of these models in drug discovery and design.

The course will cover the following topics:

  • Creating common feature pharmacophores from active ligand training sets
  • Generating pharmacophore-derived alignments of ligands
  • Using data from inactive ligands to add excluded volumes to pharmacophores to reduce false positives
  • Analysis and application of qualitative pharmacophores

Duration: 2 hours on-line, 0.5 day on-site

Email the Accelrys Training team to arrange on-line or on-site training for this course

3D QSAR Pharmacophore Generation

This course covers the generation of quantitative pharmacophores in Discovery Studio, detailing the automated algorithms (HypoGen/HypoGenRefine) and the applications of these models in drug discovery and design.

The course will cover the following topics:

  • Creating 3D QSAR pharmacophores from activity data training sets
  • Refining pharmacophores with excluded volumes using data from inactive ligands
  • Analysis and application of quantitative pharmacophores

Duration: 2 hours on-line, 0.5 day on-site

Email the Accelrys Training team to arrange on-line or on-site training for this course

Receptor-Based Pharmacophores

This course provides an overview of the approaches to deriving pharmacophores from receptor structures and presents their applications in diverse molecular modeling workflows.

The course guides users through the steps to create receptor-based pharmacophore models in Discovery Studio and will cover the following topics:

  • Automated protein-ligand pharmacophore generation
  • Multiple ligands alignment-based pharmacophores
  • Fragment-based pharmacophores for lead optimisation
  • Structure-based pharmacophores from interactions maps
  • Validation and analysis of receptor-based pharmacophores

Duration: 2 hours on-line, 0.5 day on-site

Email the Accelrys Training team to arrange on-line or on-site training for this course

Fragment Based Drug Design in Discovery Studio

This course provides an overview to the fragment-based modeling methods in Discovery Studio and presents their applications in lead identification and optimization.

The course guides users step-by-step through the generation of potential libraries with different fragment based modeling techniques and will cover the following topics:

  • Fragment docking using Multiple Copy Simultaneous Search (MCSS)
  • Scaffold screening to identify fragment leads (LUDI)
  • Optimizing lead compounds from a scaffold with a reaction-based in situ enumeration (GROW)
  • Scaffold hopping to identify replacement fragments for lead optimization (REPLACE)

Duration: 3 hours on-line, 1 day on-site

Email the Accelrys Training team to arrange on-line or on-site training for this course

QSAR

This course covers an introduction to the QSAR tools available in Discovery Studio to give an overview of the various different descriptors which can be calculated within the application.

The course also describes the available regression methods and highlight the main parameters affecting each algorithm as well as providing a comparison of the various techniques.

The course will cover the following topics:

  • Introduction to QSAR
  • Working with descriptors
    • available descriptors
    • how to calculate them
    • how to use them
  • Regression techniques
    • Available methods
      • Advantages and applicability
  • Modern methods
    • Available methods
    • Advantages and applicability
  • Example workflow
    • How to apply the generated models

Duration: 3 hours on-line, 1 day on-site

Email the Accelrys Training team to arrange on-line or on-site training for this course

Library Design and Analysis

This course covers the library design and optimization methods in Discovery Studio which form a versatile and multipurpose toolkit of functionality to guide optimal library design.

The course will cover the following topics:

  • Library enumeration (reaction-based and R-group/Markush)
  • Diversity selection and clustering
  • Similarity selection
  • Compound selection optimizing multiple molecular properties simultaneously using Pareto methods
  • Selection of subset libraries to complement and augment existing libraries
  • Comparison of libraries

Duration: 3 hours on-line, 1 day on-site

Email the Accelrys Training team to arrange on-line or on-site training for this course

Structure-Based Design - Docking

This course provides an overview of the different classical docking methods in Discovery Studio and presents the applications of virtual screening in drug discovery and design.

The course will cover the following topics:

  • High through-put virtual screening with LIBDOCK
  • Simulated annealing docking refinement with CDOCKER
  • Flexible protein docking
  • Visualization and charting of protein ligand interactions
  • Using scoring functions to facilitate the ranking of docked ligands
  • Calculation of enrichment hit-rate plots and ROC curves

Duration: 3 hours on-line, 1 day on-site

Email the Accelrys Training team to arrange on-line or on-site training for this course

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