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Protein Modeling and Sequence Analysis Training

Protein Homology Modeling

Overview - Protein Homology Modeling in Discovery Studio Training

The course will provide an overview of protein homology modeling in Discovery Studio starting from a complete sequence alignment. This workshop follows on from the Sequence Analysis for Homology Modeling Workshop.

On completion of the workshop the user will have covered:

  • Construction of a homology model using MODELER
  • Validation and analysis of models using MODELER PDF energies and DOPE scores
  • Validation and analysis of models using Profiles-3D and Evolutionary Trace
  • Modeling loop regions in the homology model using MODELER and LOOPER
  • Overall model refinement including side chain placement using ChiRotor
  • Special cases - Modeling transmembrane protein structures

Duration: 1 day

Protein Protein Docking

Understanding the characteristics of protein-protein interfaces and the role of computational protein docking methods.

Understanding the physical principles underlying the ZDOCK method and the RDOCK refinement.

Setting up a ZDOCK run and using the tools to display and analyze docked protein complex structures.

Understanding how to perform clustering of the docked protein poses.

Be able to apply biochemical and biological information to facilitate the analysis of docking predictions.

Duration: 1 day

Sequence Analysis

Performing BLAST, PSI-BLAST protein sequence similarity searches with local or NCBI databases to identify potential homologues.

Using an input sequence alignment to search against a database of sequence profiles and output significant alignment hits.

Performing multiple sequence alignments, multiple structure alignments, and profile-profile alignments.

UsingEvolutionary Trace Analysis tools to analyze protein sequences and identify conserved residues based on sequence clustering.

Duration: 1 day

QM/MM

Duration: 1 day

Antibody Modeling

Duration: 1 day

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