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Recent advances in QSAR and their applications in predicting the activities of chemical molecules, peptides and proteins for drug design.

Abstract：

:This review is to summarize three new QSAR (quantitative structure-activity relationship) methods recently developed in our group and their applications for drug design. Based on more solid theoretical models and advanced mathematical techniques, the conventional QSAR technique has been recast in the following three aspects. (1) In the fragment-based two dimensional QSAR, or abbreviated as FB-QSAR, the molecular structures in a family of drug candidates are divided into several fragments according to the substitutes being investigated. The bioactivities of drug candidates are correlated with physicochemical properties of the molecular fragments through two sets of coefficients: one is for the physicochemical properties and the other for the molecular fragments. (2) In the multiple field three dimensional QSAR, or MF-3D-QSAR, more molecular potential fields are integrated into the comparative molecular field analysis (CoMFA) through two sets of coefficients: one is for the potential fields and the other for the Cartesian three dimensional grid points. (3) In the AABPP (amino acid-based peptide prediction), the bioactivities of peptides or proteins are correlated with the physicochemical properties of all or partial residues of the sequence through two sets of coefficients: one is for the physicochemical properties of amino acids and the other for the weight factors of the residues. Meanwhile, an iterative double least square (IDLS) technique is developed for solving the two sets of coefficients in a training dataset alternately and iteratively. Using the two sets of coefficients, one can predict the bioactivity of a query peptide, protein, or drug candidate. Compared with the old methods, the new QSAR approaches as summarized in this review possess machine learning ability, can remarkably enhance the prediction power, and provide more structural information. Meanwhile, the future challenge and possible development in this area have been briefly addressed as well.

journal_name

Curr Protein Pept Sci

journal_title

Current protein & peptide science

authors

Du QS,Huang RB,Chou KC

doi

10.2174/138920308784534005

subject

Has Abstract

pub_date

2008-06-01 00:00:00

pages

248-60

issue

eissn

1389-2037

issn

1875-5550

journal_volume

pub_type

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Recent advances in QSAR and their applications in predicting the activities of chemical molecules, peptides and proteins for drug design.