[gmx-users] Re:rather theoretical question

Alexander yakovenko_a at ukr.net
Fri Jul 4 16:11:01 CEST 2003

Hi Dmitry,
My experience based on dynamic study of kinase-inhibitor complexes, so
it will be some differences with native substrates and other
proteins. The main problem is to find correct energy minima, when
structures are dynamic. The MD very often reproduces domains moving,
but they not very sensitive to ligand structure, much more for its
presence :(, especially in long MD experiments.
Similar to X-ray structures I had found only with 20-25%
methanol-water mixes (with GROMOS96FF). If you sure that you apo- structure correct, you
can make constrains and so on as say Vojtech Spiwok, but I recommend
you to use molecular docking with energy minimization and visual
checking of obtained complexes.

Best regards,

Alexander Yakovenko
Institute of Molecular Biology & Genetic of NAS of Ukraine
acad.Zabolotnogo str. 150
E-mail: yakovenko_a at ukr.net

>Dear Alexander Yakovenko, thank you very much for your answer, I just wanted
>know how much are the chances that MD can  right fit ligand from one X-ray
>protein-ligand conformation to another, theoretical derived from first apo
>structure ( not with MD) conformation, where ligand state is not known. So
>as I understood, it is likely not possible to obtain  with good probability
>wanted structure. Once more  thank you very much.
>D. Egorov.

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