Interfaces in molecular docking

Julie C. Mitchell; Sharokina Shahbaz; Lynn F. Ten Eyck

doi:10.1080/0892702031000152217

Interfaces in molecular docking

Julie C. Mitchell, Sharokina Shahbaz, Lynn F. Ten Eyck

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

4 Scopus citations

Abstract

The Fast Atomic Density Evaluation (FADE) program analyzes shape complementarity using atomic density methods and fast Fourier transforms (FFT). Statistical results for 184 protein-protein and protein-DNA complexes are presented. Almost all of the interfaces studies were found to be complementary, and the average FADE complementarity score highlighted systems known to have strong shape complementarity at the binding interfaces. Also given is a detailed analysis of the interfaces for Fasciculin-Acetylcholinesterase and Barnase-Barstar to show how shape complementarity relates to site mutagenesis experiments. For these two cases, there was good agreement between interface points of highest complementarity and the location of residues known to be important for binding.

Original language	English
Pages (from-to)	97-106
Number of pages	10
Journal	Molecular Simulation
Volume	30
Issue number	2-3
DOIs	https://doi.org/10.1080/0892702031000152217
State	Published - Feb 15 2004
Externally published	Yes

Keywords

Barnase-Barstar
Fasciculin- acetylcholinesterase
Fast Atomic Density Evaluation
Fast Fourier transforms
Mutagenesis experiments

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10.1080/0892702031000152217

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title = "Interfaces in molecular docking",

abstract = "The Fast Atomic Density Evaluation (FADE) program analyzes shape complementarity using atomic density methods and fast Fourier transforms (FFT). Statistical results for 184 protein-protein and protein-DNA complexes are presented. Almost all of the interfaces studies were found to be complementary, and the average FADE complementarity score highlighted systems known to have strong shape complementarity at the binding interfaces. Also given is a detailed analysis of the interfaces for Fasciculin-Acetylcholinesterase and Barnase-Barstar to show how shape complementarity relates to site mutagenesis experiments. For these two cases, there was good agreement between interface points of highest complementarity and the location of residues known to be important for binding.",

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AU - Shahbaz, Sharokina

AU - Ten Eyck, Lynn F.

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AB - The Fast Atomic Density Evaluation (FADE) program analyzes shape complementarity using atomic density methods and fast Fourier transforms (FFT). Statistical results for 184 protein-protein and protein-DNA complexes are presented. Almost all of the interfaces studies were found to be complementary, and the average FADE complementarity score highlighted systems known to have strong shape complementarity at the binding interfaces. Also given is a detailed analysis of the interfaces for Fasciculin-Acetylcholinesterase and Barnase-Barstar to show how shape complementarity relates to site mutagenesis experiments. For these two cases, there was good agreement between interface points of highest complementarity and the location of residues known to be important for binding.

KW - Barnase-Barstar

KW - Fasciculin- acetylcholinesterase

KW - Fast Atomic Density Evaluation

KW - Fast Fourier transforms

KW - Mutagenesis experiments

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EP - 106

JO - Molecular Simulation

JF - Molecular Simulation

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Interfaces in molecular docking

Abstract

Keywords

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