Conformational flexibility models for the receptor in structure based drug design.
The problem of incorporating receptor flexibility in routine in silico screening of databases of small chemical compounds for the purposes of structure based drug design is still an unsolved problem. The main reason behind this difficulty is the large number of degrees of freedom that have to be considered to represent receptor flexibility. In this paper we review protein flexibility models that have been developed to limit the number of additional search parameters. These models can be roughly divided into five different categories. These are a) use of soft receptors which relax energetic penalties due to steric clashes, b) selection of a few critical degrees of freedom in the receptor binding site, c) use of multiple receptor structures either individually or by combining them using an averaging scheme, d) use of modified molecular simulation methods, and e) use of collective degrees of freedom as a new basis of representation for protein flexibility. All these flexible receptor models strive to balance an improvement in the accuracy of the binding predictions with an increase in computational cost. In addition, other challenges such as the development of accurate solvation models and scoring functions make the receptor flexibility problem even harder.
Teodoro
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Department of Computer Science and Department of Bioengineering, Rice University, 6100 Main St, MS 132, P.O. Box 1892, Houston, TX 77251-1892, USA. kavraki@rice.edu
Kavraki
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D015195:Drug Design; D008956:Models, Chemical; D011487:Protein Conformation; D011956:Receptors, Cell Surface / Q000737:chemistry*; D013329:Structure-Activity Relationship
D011956:Receptors, Cell Surface