Supercharge.hh File Reference

This protocol supercharges the surface of an input pdb with either positive or negatively charged residues. More...

#include <protocols/design_opt/Supercharge.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <core/types.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/tag/XMLSchemaGeneration.fwd.hh>
#include <utility/vector1.hh>
#include <set>

Classes
class	protocols::design_opt::Supercharge
	Adds charged residues to a protein surface. More...

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::design_opt

Detailed Description

This protocol supercharges the surface of an input pdb with either positive or negatively charged residues.

There are two modes for supercharging. The first is called AvNAPSA developed by the David Liu lab at Harvard. In this approach, surface residues are defined by the Average # Neighbor Atoms Per Sidechain Atom (AvNAPSA value), with a cutoff of 150. I think 100 is a safer cutoff. Arg, Lys, Asp, Glu, Asn, Gln are the only residues allowed to mutated. Lys is always chosen for positive, Glu is always chosen for negative, unless the native is Asn, then Asp is chosen. Thus, the sequence is deterministic. If one desires a particular net charge, the residues would be sorted from low to high AvNAPSA value and mutated one at a time until the target charge is achieved - this ignores the ceiling of 150 or 100. The second approach uses the Rosetta score function to guide the surface mutagenesis. The user must specifiy if Arg, Lys, or Asp, Glu are desired, and what the reference weights are. Alternatively, the user can specify a target net charge, and the reference weights of the charged residues will be incremented/decremented until the net charge is reached.

Author

Bryan Der

Rocco Moretti (rmore.nosp@m.ttia.nosp@m.se@gm.nosp@m.ail..nosp@m.com) (Moverization)