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MEGADOCK: An All-to-All Protein-Protein Interaction Prediction System Using Tertiary Structure Data
"... Abstract: The elucidation of protein-protein interaction (PPI) networks is important for understanding cellular structure and function and structure-based drug design. However, the development of an effective method to conduct exhaustive PPI screening represents a computational challenge. We have be ..."
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been investigating a protein docking approach based on shape complementarity and physicochemical properties. We describe here the development of the protein-protein docking software package “MEGADOCK ” that samples an extremely large number of protein dockings at high speed. MEGA-DOCK reduces
Capri/MR: Exploring Protein Databases from a Structural and Physicochemical Point of View
"... With the advent of high throughput systems to experimentally determine the three-dimensional (3-D) structure of proteins, molecular biologists are in urgent need of systems to automatically store, maintain and explore the vast structural databases that are thus being created. We have designed and im ..."
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and implemented the Capri/MR system which makes it possible to identify families of protein structures, as contained in such very large 3-D protein structure databases. Our system is able to automatically index and search a database of proteins by threedimensional shape, structural and/or physicochemical
RESEARCH ARTICLE Open Access
"... Prediction of protein-binding areas by smallworld residue networks and application to docking Carles Pons 1,2, Fabian Glaser 3 * and Juan Fernandez-Recio 1* Background: Protein-protein interactions are involved in most cellular processes, and their detailed physicochemical and structural characteriz ..."
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Prediction of protein-binding areas by smallworld residue networks and application to docking Carles Pons 1,2, Fabian Glaser 3 * and Juan Fernandez-Recio 1* Background: Protein-protein interactions are involved in most cellular processes, and their detailed physicochemical and structural
PatchSurfers: Two methods for local molecular property-based binding ligand prediction
"... a b s t r a c t Protein function prediction is an active area of research in computational biology. Function prediction can help biologists make hypotheses for characterization of genes and help interpret biological assays, and thus is a productive area for collaboration between experimental and co ..."
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is characterized by physicochemical properties such as shape, hydrophobicity, and electrostatic potentials. These properties on the surface are represented using three-dimensional Zernike descriptors (3DZD), which are based on a series expansion of a 3 dimensional function. Utilizing 3DZD for describing
