Molecular dynamics simulations with GPU: from protein dynamics to drug design

The exploration at the molecular level of the conformational changes of a protein can help to elucidate and explain its functionality. This knowledge is tremendously important for a successful drug design. Molecular Dynamics is a high-computing resource demanding technique largely used to explore the conformational space of molecular objects. Nowadays, the introduction of Graphics Processing Unit (GPU) as High Performance Computing tools allows to much larger conformational spaces compared to the traditional CPUs. We present two multidisciplinary kinase studies [1] where the use of molecular dynamics coupled to the speed of GPU permit the achievement of a fast and accurate convergency in the results. ClickMD [2], an integrated web-oriented platform for processing and analyzing the time dependent behaviour of a bio-molecular system in a molecular dynamic workflow, will also be presented. 1. A. Cristiani, G. Costa, G. Cozza, F. Meggio, L. Scapozza and S. Moro, “The Role of the N-Terminal Domain in the Regulation of the ‘Constitutively Active’ Conformation of Protein Kinase CK2α: New Insight from a Molecular Dynamics Investigation” ChemMedChem, 2011, 10.1002/cmdc.201100046. 2. A. Cristiani, N. Brisotto, F. Chatwin Cedrati, M. Floris, L.Scapozza, S. Moro, “ClickMD : an Intuitive Web-Oriented Molecular Dynamics Platform”, Future Medicinal Chemisty, 2011, accepted.

@InProceedings{Cri11,
  author       = {Cristiani, A.},
  title        = {Molecular dynamics simulations with GPU: from protein dynamics to drug design },
  booktitle    = {Collana Talks@CRS4},
  number       = {20110505},
  month        = {may},
  year         = {2011},
  note         = {contatti: matteo.floris@crs4.it},
  keywords     = {GPU, parallel computing, molecular dynamics, kinase, protein plasticity, interdisciplinarity},
  url          = {https://publications.crs4.it/pubdocs/2011/Cri11},
}