Protein Modeling
Experimental structure determination involves difficult methods that require a significant amount of expertise and resources. Protein Modeling on the other hand enables access to sensible structural models in much shorter periods of time. The major aim of protein modeling is the prediction of a protein's tertiary structure from its primary structure. To this end a diverse range of approaches have been developed comparative, de novo or ab initio structure prediction.
The protein modeling methods provided in Discovery Studio provide an extensive set of tools for the construction of molecular structures and analysis of their behavior.
Analysis Goals
Protein Modeling provides tools and protocols that allow you to:
Protein Modeling Tasks
The following table describes the basic tasks that are possible with the Protein Modeling methods in Discovery Studio.
| For a discussion of the following tasks | See the following topic(s) |
|---|---|
| Build and edit proteins or peptide. | Build and Edit Protein tools. |
| Modify protein structures (e.g., split structures into distinct molecules, clean protein structures) or generate reports on protein structures. | Protein Reports and Utilities tools. |
| Identify conserved residues which may be important for the protein function or structure integrity. | Evolutionary Trace tools. |
| Identify and report abnormalities in a protein structure | Protein Health tools. |
| Align a set of pre-aligned sequences to another set of pre-aligned protein structures using the MODELER program. | How to run the Align Sequence with Structure protocol. |
| Align multiple protein structures using the 3DMA program. | How to run the Align Structures protocol. |
| Align multiple protein structures using the MODELER program. | How to run the Align Structures (MODELER) protocol. |
| Build one or many homology models for a protein sequence based on template protein structure(s). | How to run the Build Homology Models protocol. |
| Mutate selected residues into the specified type(s) and optimize the local structure of the mutated residues and their neighbors using the MODELER program. | How to run the Build Mutants protocol. |
| Predict protein docking conformations using ZDOCK, a rigid docking algorithm. | How to run the Dock Proteins (ZDOCK) protocol. |
| Refine the docked complexes from the rigid docking output and score the poses using RDOCK energy. | How to run the Refine Docked Proteins (RDOCK) protocol. |
| Optimizes a user-defined loop region of a protein structure using the Looper algorithm. | How to run the Loop Refinement protocol. |
| Optimize one or more user-defined loop regions using the MODELER program. | How to run the Loop Refinement (MODELER) protocol. |
| Identify antibody hypervariable loops and create antibody models with the selected antibody loop templates. | How to run the Model Antibody Loops protocol. |
| Filter and cluster a set of docked protein poses from ZDOCK output. | How to run the Process Poses (ZDOCK) protocol. |
| Optimize selected side-chain conformations of a protein structure using ChiRotor algorithm. | How to run the Side-Chain Refinement protocol. |
| Evaluates the fitness of a protein sequence in its current 3D environment. | How to run the Verify Protein (Profiles 3D) protocol. |
| Compare variable conformations of a protein. | How to run the Verify Protein (MODELER) protocol. |
Further information