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VISTRAJ: exploring protein conformational space
J J Salama1, H J Feldman, C W Hogue
1MDS Proteomics Inc., 480 University Ave, Toronto, Ontario, Canada.
Bioinformatics (Oxford, England)
|October 9, 2001
Summary
VISTRAJ enables 3D visualization and editing of protein conformational space using trajectory distributions. This application, coupled with FOLDTRAJ, aids in protein structure sampling and homology modeling, including modified amino acids.
Area of Science:
- Computational biology
- Structural bioinformatics
- Protein dynamics
Background:
- VISTRAJ and FOLDTRAJ are computational tools for protein structure analysis.
- Available for non-profit use.
Purpose of the Study:
- To introduce VISTRAJ for 3D visualization, manipulation, and editing of protein conformational space.
- To enable protein structure sampling and homology modeling using FOLDTRAJ.
- To support the generation of protein structures with post-translationally modified amino acids.
Main Methods:
- Utilizes probabilistic maps called 'trajectory distributions' to represent protein conformational space.
- Employs FOLDTRAJ for sampling protein structures based on these distributions.
- Integrates VISTRAJ and FOLDTRAJ for homology model creation.
Main Results:
- VISTRAJ provides interactive 3D visualization and editing of protein conformational landscapes.
- FOLDTRAJ effectively samples protein structures from trajectory distributions.
- Homology models can be generated, incorporating post-translational modifications.
Conclusions:
- VISTRAJ and FOLDTRAJ offer a powerful integrated approach for protein structure analysis and modeling.
- The tools facilitate the exploration and manipulation of protein conformational space.
- Enables the creation of more complex and biologically relevant protein models.