Computer-aided homology modeling

For Trichoderma reesei the cellulases most thoroughly investigated with respect to their structural properties are CBH I and CBH II and to a lesser extent the two en-doglucanases (EG I and EG III) 11 (Table I). For most other cellulases structural characterizations are confined to the amino add sequence as deduced from the base sequence of the respective genes and to sequence related investigations such as hydro-phobic cluster analysis 10 or computer aided molecular modelling and homology... 

Koymans LMH, Vermeulen NPE, Baarslag A, Donne-Op den Kelder GM. A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building. J Comput-Aided Mol Des 1993 7 281-9. 

Park, H. and Lee, S. (2004) Homology modeling, force field design, and free energy simulation studies to optimize the activities of histone deacetylase inhibitors. Journal of Computer-Aided Molecular Design, 16, 375—388. 

Chambers JJ, Nichols DE. A homology-based model of the human 5-HT2A receptor derived from an in sihco activated G protein coupled receptor. J Comput Aided Mol Des 2002 16 511-520. 

Costanzi, S. (2008) On the applicability of GPCR homology models to computer-aided drug discovery a comparison between in sUico and crystal structures of the beta2-adrenergic receptor. Journal of Medicinal Chemistry, 51 (10), 2907-2914. 

Stockner, T., de Vries, S.J., Bonvin, A.M., Ecker, G.F. Chiba, P. (2009). Data-driven homology modelling of P-glycoprotein in the ATP-boxmd state indicates flexibility of the transmembrane domains. FEES /, Vol.276, No.4, pp. 964-72 Stouten, P.F.W. Brady, G.P. (2000). Fast prediction and visualization of protein binding pockets with PASS. Journal of Computer-Aided Molecular Design, Vol.l4, No.4, pp. 383-401... 

Computer-aided design of aminotransferases by homology modeling and rational design. 

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