Protein Preparation and Refinement

This category contains 10 nodes.


Search a protein sequence database using BLAST

Induced Fit Docking 

Set up a sequence of jobs in which ligands are docked with Glide, then Prime Refinement is used to allow the receptor to relax, and the ligands are […]

Prime Build Homology Model 

Build homology models

Prime Energy 

Evaluate the energy and its components for one or more proteins

Prime Minimization 

Minimize molecules using Prime

Prime Refine Loops 

Refine the structure of loops in the input protein

Prime Side Chain Sampling 

Refines protein structures via side chain prediction

Protein Assignment 

Assign chi angles in residues and orientation of waters.

Protein Preparation Workflow 

Set up and run the protein preparation.

Residue Scanning 

Bioluminate residue scanning: Mutates and refines residues and proteins