Modeling
Overview
Evolution subproject
Evaluation subproject
Methods
Rosetta Ligand Docking
Overview
Methods
Algorithm
- 1) starting position is chosen randomly or defined an .xml file
- 2) placement of the ligand is modified by a random translation of a distance of 0.1 A in each direction and 0.05° around each axis
- 3) rigid body orientation and side-chain angles of the ligand are optimized using the gradient based Davidson–Fletcher–Powell algorithm. Afterwards, the corresponding energy function is calculate daccording to the Monte-Carlo method.
P= min (1, exp(-(Estart-Efinal)/kT). This move is accepted if the energy function decreases.
Figure (1): Flowchart Ligand Docking Protocol
Modeller
Overview
Method
Rosetta EnzymeDesign
Overview
Method
Figure (2): Flowchart Enzym Design Protocol