Integrative geometric-hashing approaches to binding site modeling and ligand-protein interaction prediction

Joanna Lipinski-Kruszka; Rahul Singh

doi:10.1007/978-3-540-76858-6_18

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Integrative geometric-hashing approaches to binding site modeling and ligand-protein interaction prediction

Conference proceeding

Peer reviewed

Integrative geometric-hashing approaches to binding site modeling and ligand-protein interaction prediction

Joanna Lipinski-Kruszka and Rahul Singh

ADVANCES IN VISUAL COMPUTING, PT I, Vol.4841(1), pp.179-188

Lecture Notes in Computer Science

01/01/2007

DOI: 10.1007/978-3-540-76858-6_18

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Abstract

The function of a protein is dependent on whether and how it can interact with various ligands. Therefore, an accurate prediction of protein-ligand interactions is paramount to understanding proteins' biological mechanisms and hence to the development of therapeutic agents. A ligand is most likely to bind in the largest pocket on the surface of the protein. Moreover, it requires that the pocket meets certain structural and geometric criteria that allow the ligand to "anchor" in place by forming stabilizing interactions with the protein. Based oil this logic, many geometry-based algorithms have been developed to predict protein-ligand interactions. Here we investigate a geometric-hashing based algorithm - to see how well it distinguishes proteins that do and do not bind a ligand, and propose enhancements that improve its robustness. We also introduce all alternative way of integrating geometric and biochemical propel-ties of Multiple binding mechanisms into a single representation.

Computer Science

Computer Science, Theory & Methods

Imaging Science & Photographic Technology

Science & Technology

Technology

Details

Title: Subtitle: Integrative geometric-hashing approaches to binding site modeling and ligand-protein interaction prediction
Creators: Joanna Lipinski-Kruszka - San Francisco State University
Rahul Singh - San Francisco State University
Contributors: G Bebis (Editor)
R Boyle (Editor)
B Parvin (Editor)
D Koracin (Editor)
N Paragios (Editor)
S M Tanveer (Editor)
T Ju (Editor)
Z Liu (Editor)
S Coquillart (Editor)
C CruzNeira (Editor)
T Muller (Editor)
T Malzbender (Editor)
Resource Type: Conference proceeding
Publication Details: ADVANCES IN VISUAL COMPUTING, PT I, Vol.4841(1), pp.179-188
Publisher: Springer Nature
Series: Lecture Notes in Computer Science
DOI: 10.1007/978-3-540-76858-6_18
ISSN: 0302-9743
eISSN: 1611-3349
Number of pages: 2
Language: English
Date published: 01/01/2007
Academic Unit: Computer Science
Record Identifier: 9984446543702771

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