IMP Reference Guide
develop.714915d50b,2024/12/07
The Integrative Modeling Platform
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Specialized restraints for modeling the Nuclear Pore Complex. More...
Specialized restraints for modeling the Nuclear Pore Complex.
These restraints have been used to model the Nuclear Pore Complex (NPC) but may be useful for other applications too. They model the NPC as lying in the xy plane, centered at the origin. (Transport through the pore corresponds to movement along the z axis.) The surface of the nuclear membrane is represented as the surface of a half torus, also lying in the xy plane and centered at the origin. Individual proteins (or parts of proteins, such as the N- or C- termini) are then localized to different regions of the complex (e.g. near the membrane or pore, or on the nuclear or cytoplasmic side) by simple restraints on their Cartesian coordinates.
Classes | |
class | MembraneExclusionRestraint |
Keep protein away from a half torus in the xy plane. More... | |
class | MembraneSurfaceLocationConditionalRestraint |
Localize one protein on the surface of a half torus in the xy plane. More... | |
class | MembraneSurfaceLocationRestraint |
Localize protein on the surface of a half torus in the xy plane. More... | |
class | XYRadialPositionLowerRestraint |
Restrain a protein's distance from the z axis to above a lower bound. More... | |
class | XYRadialPositionRestraint |
Restrain a protein's distance from the z axis to within a given range. More... | |
class | XYRadialPositionUpperRestraint |
Restrain a protein's distance from the z axis to below an upper bound. More... | |
class | YAxialPositionLowerRestraint |
Restrain a protein's y coordinate to above a lower bound. More... | |
class | YAxialPositionRestraint |
Restrain a protein's y coordinate to within a given range. More... | |
class | YAxialPositionUpperRestraint |
Restrain a protein's y coordinate to below an upper bound. More... | |
class | ZAxialPositionLowerRestraint |
Restrain a protein's z coordinate to above a lower bound. More... | |
class | ZAxialPositionRestraint |
Restrain a protein's z coordinate to within a given range. More... | |
class | ZAxialPositionUpperRestraint |
Restrain a protein's z coordinate to below an upper bound. More... | |