Induced-fit effect

Birch L, Murray CW, Hartshorn MJ, et al. Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase. J Comput Aided Mol Des 2002 16 855 569. 

Sotriffer CA (2011) Accounting for induced-fit effects in docking what is possible and what is not Curr Top Med Chem 11(2) 179-191... 

The Sensitivity of the Results of Molecular Docking to Induced Fit Effects Application to Thrombin, Thermolysin and Neuraminidase. 

Figure 4.4 Comparison of a ligand-free (2hnp) with a complexed (lbzj) structure of PTP-1B reveals a pronounced induced-fit effect.

KaUblad P, Dean PM. Efficient conformational sampling of local side-chain flexibility. J. Molec. Biol. 2003 326 1651-1665. Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J. Med. Chem. 2006 49 534-553. 

A further requirement for a successfully positioned fragment is that it does not overlap with the protein. However, small overlaps of up to 0.5 A are tolerated, in order to account for induced fit effects. 

Kufareva, I. and Abagyan, R. (2008) Strategies to overcome the induced fit effects in molecular docking. In Hansmann, U. H. E., Meinke, J. H., Mohanty, S., Nadler, W., and Zimmermann, O. (eds.) From Computational Biophysics to Systems Biology (CBSB08). H John von Neumann Institute for Computing (NIC), Jiilich, pp. 1-6. 

C. W. Murray, C. A. Baxter, and A. D. Frenkel. The sensitivity of the results of molecular docking to induced fit effects Application to thrombin, thermolysin and neuraminidase. Journal of Computer-Aided Molecular Design, 13 547-562, 1999. 

Sherman, W Day T, Jacobson, M.P., Friesner, R.A., and Farid, R. (2006) Novel procedure for modeling ligand/receptor induced fit effects. Journal of Medicinal Chemistry, 49 (2), 534—553. 

Side-Chain Conformation Induced Fit Effects of Ligands... 

In brief, with this mechanism the carboxylate group of Glu-270 acts as a general base to deliver nucleophilic water to the carbonyl. In the presence of methanol the first step would simply reverse. Consequently, only a second deprotonation could drive the reaction in the forward direction, and this proton transfer might well involve the hydroxyl group of Tyr-248 as a bridge between the OH and the N of the amide bond to be cleaved. This proposal has the advantage of giving a justification for the induced-fit effect mentioned earlier in this section. 

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