Abstract
The human genome and other genome sequencing projects have generated huge amounts of protein sequence information.Recently,a structural genomics project that aims to determine at least one representative three-dimensional structure from every protein family experimentally has been started.Homology modeling will play an essential role in structure based drug design such as in silico screening;because based on these representative structures the three-dimensional structures of the remaining proteins encoded in the various genomes can be predicted by homology modeling.The results of the last Critical Assessment of Techniques for Protein Structure Prediction (CASP5)demonstrated that the quality of homology modeling prediction has improved;reaching a level of reliability that biologists can now confidently use homology modeling.With improvements in modeling software and the growing number of known protein structures,homology modeling is becoming a more and more powerful and reliable tool.The present paper discusses the features and roles of homology modeling in structure based drug design, and describes the CHIMERA and FAMS modeling systems as examples.For a sample application,homology modeling of non-structural proteins of the severe acute respiratory syndrome (SARS)coronavirus is discussed. Many biological functions involve formation of protein-protein complexes;in which the protein molecules behave dynamically in the course of binding.Therefore,an understanding of protein-protein interaction will be very important for structure based drug design.To this end,normal mode analysis is useful.The present paper discusses the prediction of protein-protein interaction using normal mode analysis and examples of applications are given.
Keywords: protein structure prediction, homology modeling, structural genomics, structure based drug design, severe acute respiratory syndrome (sars), rna-dependent rna polymerase, normal mode analysis
Current Medicinal Chemistry
Title: Protein Structure Prediction in Structure Based Drug Design
Volume: 11 Issue: 5
Author(s): Mayuko Takeda-Shitaka, Daisuke Takaya, Chieko Chiba, Hirokazu Tanaka and Hideaki Umeyama
Affiliation:
Keywords: protein structure prediction, homology modeling, structural genomics, structure based drug design, severe acute respiratory syndrome (sars), rna-dependent rna polymerase, normal mode analysis
Abstract: The human genome and other genome sequencing projects have generated huge amounts of protein sequence information.Recently,a structural genomics project that aims to determine at least one representative three-dimensional structure from every protein family experimentally has been started.Homology modeling will play an essential role in structure based drug design such as in silico screening;because based on these representative structures the three-dimensional structures of the remaining proteins encoded in the various genomes can be predicted by homology modeling.The results of the last Critical Assessment of Techniques for Protein Structure Prediction (CASP5)demonstrated that the quality of homology modeling prediction has improved;reaching a level of reliability that biologists can now confidently use homology modeling.With improvements in modeling software and the growing number of known protein structures,homology modeling is becoming a more and more powerful and reliable tool.The present paper discusses the features and roles of homology modeling in structure based drug design, and describes the CHIMERA and FAMS modeling systems as examples.For a sample application,homology modeling of non-structural proteins of the severe acute respiratory syndrome (SARS)coronavirus is discussed. Many biological functions involve formation of protein-protein complexes;in which the protein molecules behave dynamically in the course of binding.Therefore,an understanding of protein-protein interaction will be very important for structure based drug design.To this end,normal mode analysis is useful.The present paper discusses the prediction of protein-protein interaction using normal mode analysis and examples of applications are given.
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Takeda-Shitaka Mayuko, Takaya Daisuke, Chiba Chieko, Tanaka Hirokazu and Umeyama Hideaki, Protein Structure Prediction in Structure Based Drug Design, Current Medicinal Chemistry 2004; 11 (5) . https://dx.doi.org/10.2174/0929867043455837
DOI https://dx.doi.org/10.2174/0929867043455837 |
Print ISSN 0929-8673 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-533X |
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