Rapid atomic density methods for molecular shape characterization

Julie C. Mitchell; Rex Kerr; Lynn F. Ten Eyck

doi:10.1016/S1093-3263(00)00079-6

Rapid atomic density methods for molecular shape characterization

Julie C. Mitchell, Rex Kerr, Lynn F. Ten Eyck

Research output: Contribution to journal › Article › peer-review

53 Scopus citations

Abstract

Two methods for rapid characterization of molecular shape are presented. Both techniques are based on the density of atoms near the molecular surface. The Fast Atomic Density Evaluation (FADE) algorithm uses fast Fourier transforms to quickly estimate densities. The Pairwise Atomic Density Reverse Engineering (PADRE) method derives modified density measures from the relationship between atomic density and total potentials. While many shape-characterization techniques define shape relative to a surface, the descriptors returned by FADE and PADRE can measure local geometry from points within the three-dimensional space surrounding a molecule. The methods can be used to find crevices and protrusions near the surface of a molecule and to test shape complementarity at the interface between docking molecules.

Original language	English
Pages (from-to)	325-330
Number of pages	6
Journal	Journal of Molecular Graphics and Modelling
Volume	19
Issue number	3-4
DOIs	https://doi.org/10.1016/S1093-3263(00)00079-6
State	Published - 2001
Externally published	Yes

Funding

The authors thank the La Jolla Interfaces in Science Program, Burroughs-Wellcome Fund, the National Science Foundation (NSF DBI 9616115/9911196), and the Department of Energy (DOE/OER DE-FG03-096ER62262) for helping to support our research.

Funders	Funder number
La Jolla Interfaces in Science Program
National Science Foundation	DBI 9616115/9911196
U.S. Department of Energy	DOE/OER DE-FG03-096ER62262
Burroughs Wellcome Fund

Keywords

Atomic density
Fast Fourier transform
Molecular recognition
Molecular shape
Molecular surface
Protein binding site
Protein cavities
Shape complementarity

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10.1016/S1093-3263(00)00079-6

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title = "Rapid atomic density methods for molecular shape characterization",

abstract = "Two methods for rapid characterization of molecular shape are presented. Both techniques are based on the density of atoms near the molecular surface. The Fast Atomic Density Evaluation (FADE) algorithm uses fast Fourier transforms to quickly estimate densities. The Pairwise Atomic Density Reverse Engineering (PADRE) method derives modified density measures from the relationship between atomic density and total potentials. While many shape-characterization techniques define shape relative to a surface, the descriptors returned by FADE and PADRE can measure local geometry from points within the three-dimensional space surrounding a molecule. The methods can be used to find crevices and protrusions near the surface of a molecule and to test shape complementarity at the interface between docking molecules.",

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AU - Mitchell, Julie C.

AU - Kerr, Rex

AU - Ten Eyck, Lynn F.

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AB - Two methods for rapid characterization of molecular shape are presented. Both techniques are based on the density of atoms near the molecular surface. The Fast Atomic Density Evaluation (FADE) algorithm uses fast Fourier transforms to quickly estimate densities. The Pairwise Atomic Density Reverse Engineering (PADRE) method derives modified density measures from the relationship between atomic density and total potentials. While many shape-characterization techniques define shape relative to a surface, the descriptors returned by FADE and PADRE can measure local geometry from points within the three-dimensional space surrounding a molecule. The methods can be used to find crevices and protrusions near the surface of a molecule and to test shape complementarity at the interface between docking molecules.

KW - Atomic density

KW - Fast Fourier transform

KW - Molecular recognition

KW - Molecular shape

KW - Molecular surface

KW - Protein binding site

KW - Protein cavities

KW - Shape complementarity

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JF - Journal of Molecular Graphics and Modelling

IS - 3-4

ER -

Rapid atomic density methods for molecular shape characterization

Abstract

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Keywords

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