Protein-Protein Docking

Protein–protein docking is the computational prediction of protein complex structure as it would occur in a living organism, given the individually solved component protein structures. Profacgen makes use of state-of-the-art docking software tools to find the relative transformation and conformation of two proteins that result in a stable (energetically favorable) complex. The docking process is composed of two main steps: 1) Generating a set of configurations which reliably includes at least one nearly correct one, and 2) reliably distinguishing nearly correct configurations from the others with a scoring function. Our procedure starts with rigid body global search based on the Fast Fourier Transform (FFT) correlation approach that samples rotational and translational space of one protein while fixing the other. If binding sites are known, this information can be used to reduce the search space. The generated conformations are then scored and ranked based on shape-complementarity, electrostatic and desolvation contributions. Results are clustered to find highly populated low-energy conformations. The representative complexed structure(s) can be further refined by energy minimization.

		From	To	From	To	From	To
Monday	Open
Tuesday	Open
Wednesday	Open
Thursday	Open
Friday	Open
Saturday	Open
Sunday	Open