Services

Make the most of your investment in BIOVIA solutions with lab-to-plant process consulting, onsite implementation, expert training and superior support

Protein Based Modeling

Protein Homology Modeling

The course will provide an overview of protein homology modeling in Discovery Studio, starting from a target protein sequence through to optimizing and refining complete structures.

The course will cover the following topics:

  • Search methods to identify proteins homologous to the target sequence
  • Analysis and identification of suitable template(s)
  • Performing sequence and structure alignments to determine target-template similarity
  • Generating high-quality homology models using MODELER
  • Validation and analysis of models
  • Further refinement and analysis

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

Antibody Modeling

This course will provide an overview of the workflow to model antibody structures in Discovery Studio, starting from the light and heavy chain antibody sequences to optimizing and refining complete structures.

The course guides users through the steps to build high-quality antibody models and will cover the following topics:

  • Introduction to antibodies
  • Fab antibody modeling
    • Structure template identification
    • Framework model generation
    • Analysis and selection of framework models
    • CDR loop refinement
    • De novo loop modeling
  • Full length antibody modeling
  • Further refinement and analysis

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

Protein-Protein Docking

This course covers protein-protein docking in Discovery Studio, detailing the automated algorithms (ZDOCK and RDOCK) and how they are used to generate, analyze and refine protein-protein complexes.

The course will cover the following topics:

  • Rigid-body protein-protein docking with ZDOCK
  • Clustering and filtering of poses using biological information where available
  • Visualization and analysis of docked protein complex poses
  • Refinement of selected docked protein poses with RDOCK

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

Simulations

A general overview in the proper use of:

  • Energy calculations
  • Manual and automatic atom potential typing
  • Energy minimization
  • Molecular dynamics
  • Constraints
  • Solvation models
  • Trajectory analysis
  • Force field-based docking
  • Electrostatic calculations

Focus is on working through the following Discovery Studio interfaces:

  • CHARMm
  • DelPhi
  • CDOCKER

Duration: 2 x 3 hours on-line, 2 days on-site

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

QM/MM

The course will provide an overview of quantum mechanics, molecular mechanics and their combination in QM/MM calculations within Discovery Studio.

The course will cover the following topics:

  • When to use QM/MM methods
  • Overview of density functional theory and its implementation in DMol3
  • Overview of molecular mechanics calculations with CHARMm
  • Considerations for the preparation and setup of QM/MM systems
  • Performing QM/MM calculations in Discovery Studio

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

Browse By:

Resource Center