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
Overview - QM/MM Modeling in Discovery Studio Training
The course will provide an overview of quantum mechanics, molecular mechanics and their combination in a QM/MM scheme within Discovery Studio. The details of the QM/MM scheme and different methods and protocols available will be covered.
Audience - QM/MM Modeling in Discovery Studio Training
This training is ideal for customers who use or plan to use the Discovery Studio QUANTUMm.
On completion of this course the user will have covered:
When and why QM/MM methods are important
The theoretical background for the DMol3 density functional method used in QUANTUMm
Performing DMol3 calculations in Discovery Studio
The theoretical background for the CHARMm molecular mechanics method used in QUANTUMm
Performing CHARMm calculations in Discovery Studio
Theoretical considerations for QM/MM methods
The ChemShell method used in QUANTUMm
Performing QM/MM calculations with QUANTUMm in Discovery Studio
Japanese
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