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Bioinformatics Vol. 18 no. 7 2002
Pages 939-948
© 2002 Oxford University Press

Ligand-induced changes in the binding sites of proteins

Xavier Fradera 1, Xavier de la Cruz 2,3, Carlos H. T. P. Silva 2, Jose Luis Gelpí 2, F.J. Luque 1,* and Modesto Orozco 2,*

1 Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain
2 Departament de Bioquímica i Biología Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
3 Institut Catala de Recerca i Estudis Avançats (ICREA), Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain

Received on June 20, 2001 ; revised on October 1, 2001 ; accepted on October 4, 2001

Classical molecular interaction potentials, in conjunction with other theoretical techniques, are used to analyze the dependence of the binding sites of representative proteins on the bound ligand. It is found that the ligand bound introduces in general small structural perturbations at the binding site of the protein. However, such small structural changes can lead to important alterations in the recognition pattern of the protein. The impact of these findings in docking procedures is discussed.

Contact: modesto{at}luz.bq.ub.es; javier{at}far1.far.ub.es

* To whom correspondence should be addressed.


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