molecular surface
分子的表面
molecular surface (分子的表面)
分子的表面 (molecular surface)
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2018-12-25
Molecular Surfaces
Molecular Surfaces
Source (資訊來源):
http://www.msg.ucsf.edu/local/programs/moloc/surface.html
Info cited on 2018-12-25-WD2 (資訊引用於 中華民國107年12月25日) by 湯偉晉 (WeiJin Tang)
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Molecular Surfaces
Types of Surfaces
The most obvious surface type of a molecular structure is the van der Waals surface which separates the inner space, the points, which lie within the van der Waals sphere of any of the molecules atoms, from the outer space.
If the effect of solvent is also considered, two other types of surface are also commonly used. For these the solvent molecules are considered to be spherical particles. For water a solvent radius of 1.4 A is frequently used.
The Lee-Richards surface (J.Mol.Biol. 55, 379 (1971)) is defined in analogy to the van der Walls surface, but the van der Waals radii are augmented by the solvent radius. Thus, the outer space consists of the points at which a solvent molecule can be placed without overlapping with the structure. A solvent radius of zero yields the van der Waals surface.
The Connolly surface (J.Appl.Cryst. 16, 548-558 (1983)) consist of all the points of the van der Walls surface at which a solvent sphere can touch it. However, the points which cannot be reached by a solvent sphere are replaced by the so called reentrant surface, which consists of points of the solvent van der Walls surface in geometries where the solvent touches more than one atom of the structure simultaneously. In other words, for every point of the Connolly surface there exists a position of a solvent sphere such that the point also belongs to the surface of the sphere. However, no solvent position may exists, which would make the point an inner point of the solvent sphere. This property makes Connolly surfaces very intuitive and popular.
These two surface types are termed solvent-accessible surfaces, with the difference that either solvent-center or solvent-surface are considered the accessing elements.
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2018-12-25
Molecular Surfaces
Molecular Surfaces
Source (資訊來源):
http://www.msg.ucsf.edu/local/programs/moloc/surface.html
Info cited on 2018-12-25-WD2 (資訊引用於 中華民國107年12月25日) by 湯偉晉 (WeiJin Tang)
#
- - - - - - - -
Molecular Surfaces
Types of Surfaces
The most obvious surface type of a molecular structure is the van der Waals surface which separates the inner space, the points, which lie within the van der Waals sphere of any of the molecules atoms, from the outer space.
If the effect of solvent is also considered, two other types of surface are also commonly used. For these the solvent molecules are considered to be spherical particles. For water a solvent radius of 1.4 A is frequently used.
The Lee-Richards surface (J.Mol.Biol. 55, 379 (1971)) is defined in analogy to the van der Walls surface, but the van der Waals radii are augmented by the solvent radius. Thus, the outer space consists of the points at which a solvent molecule can be placed without overlapping with the structure. A solvent radius of zero yields the van der Waals surface.
The Connolly surface (J.Appl.Cryst. 16, 548-558 (1983)) consist of all the points of the van der Walls surface at which a solvent sphere can touch it. However, the points which cannot be reached by a solvent sphere are replaced by the so called reentrant surface, which consists of points of the solvent van der Walls surface in geometries where the solvent touches more than one atom of the structure simultaneously. In other words, for every point of the Connolly surface there exists a position of a solvent sphere such that the point also belongs to the surface of the sphere. However, no solvent position may exists, which would make the point an inner point of the solvent sphere. This property makes Connolly surfaces very intuitive and popular.
These two surface types are termed solvent-accessible surfaces, with the difference that either solvent-center or solvent-surface are considered the accessing elements.
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