16th National and 4th International Conference of Biology , 2010-09-14

Title : ( Coupling molecular dynamics and docking simulations to identification ligand binding sites )

S. Ebadi , Mohammad Reza Housaindokht , M. R. Bozorgmehr ,

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Abstract

Investigation about Ligand binding characteristics is an important issue to study in biology and medicine sciences. Interactions and the ability of proteins binding into different ligands particularly have a potential role in achieving many of the systems and biological processes. Evaluation of structure and energy of molecular components is the key factor to understanding these processes and can create effective and beneficial relationship between structure and function of biomolecular systems. In this work, molecular dynamics simulation along with docking was used to identification of ligand binding sites. Carbonic Anhydrase enzyme- sodium dodecyl sulfate (SDS) complex was used as a case study. In molecular dynamics method, the collisions of ligand with every residue of the enzyme are evaluated and the average numbers of collisions with each residue is identified, then a measure of the affinity of a residue is defined by values.These calculated parameters with values that are greater than one were considered in docking simulation. Prediction of site in docking approach is done by using of free binding energy, scoring functions and relevant algorithms. All the possible binding sites and the special ones are recognized and finally evaluated in accordance with the residues and Docking results. The most preferred binding site predicted in this study is SER195, ASN23, LEU196, ALA22, LEU201, PRO20, ILE21 residues.

کلمات کلیدی

, simulation, molecular dynamics, docking, ligand binding
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@inproceedings{paperid:1017248,
author = {Housaindokht, Mohammad Reza},
title = {Coupling molecular dynamics and docking simulations to identification ligand binding sites},
booktitle = {16th National and 4th International Conference of Biology},
year = {2010},
location = {مشهد, IRAN},
keywords = {simulation; molecular dynamics; docking; ligand binding site},
}

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%0 Conference Proceedings
%T Coupling molecular dynamics and docking simulations to identification ligand binding sites
%A Housaindokht, Mohammad Reza
%J 16th National and 4th International Conference of Biology
%D 2010

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