Computational tools for the analysis and visualization of multiple protein–ligand complexes
| Autor: | David G. Brown, James Edward John Mills, Christopher Phillips, Sean E. O’Brien, Gregg Morris |
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| Rok vydání: | 2005 |
| Předmět: |
Models
Molecular Proteomics Serine Proteinase Inhibitors Similarity (geometry) Protein Conformation Surface Properties Crystallography X-Ray Ligands Structure-Activity Relationship Protein structure X ray methods Materials Chemistry Cluster (physics) Cluster Analysis Computer Simulation Physical and Theoretical Chemistry Databases Protein Spectroscopy Chemistry Computational Biology Proteins Genomics Computer Graphics and Computer-Aided Design Combinatorial chemistry HIV Reverse Transcriptase Visualization Drug Design Factor Xa Metric (mathematics) Computer-Aided Design Reverse Transcriptase Inhibitors Biological system Software Factor Xa Inhibitors Protein ligand |
| Zdroj: | Journal of Molecular Graphics and Modelling. 24:186-194 |
| ISSN: | 1093-3263 |
| DOI: | 10.1016/j.jmgm.2005.08.003 |
| Popis: | Modern methods in genomics and high-throughput crystallography have ensured that we have access to a large and rapidly increasing, number of X-ray structures of protein-ligand complexes. A structure-based approach to drug design aims to exploit this information, but current methods are not suited to the examination of the large numbers of complexes available. We present computational tools that analyse and display multiple protein-ligand interactions and their properties in a simplified way. We illustrate how a novel binding-mode similarity metric is able to cluster 20 ligands complexed to HIV-1 reverse transcriptase into distinct groups. The properties of each cluster are then projected onto a group surface as a series of color gradients. Analysis of these surfaces reveals fundamental similarities and differences in the binding modes of these diverse compounds. In addition, the simplicity of the surface representations facilitates the transfer of information between the crystallographer, computational chemist and the chemist. We also show how two- and three-dimensional (2- and 3-D) similarities can be combined to provide enhanced understanding of 33 factor Xa inhibitor complexes. This methodology has enabled us to identify pharmaceutically relevant relationships between ligands and their binding modes that had previously been hidden in a wealth of data. |
| Databáze: | OpenAIRE |
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