Membrane protein structure quality in molecular dynamics simulation.

@article{citeulike:309034, abstract = {Our goal was to assess the relationship between membrane protein quality, output from protein quality checkers and output from molecular dynamics (MD) simulations. Membrane transport proteins are essential for a wide range of cellular processes. Structural features of integral membrane proteins are still under-explored due to experimental limitations in structure determination. Computational techniques can be used to exploit biochemical and medium resolution structural data, as well as sequence homology to known structures, and enable us to explore the structure-function relationships in several transmembrane proteins. The quality of the models produced is vitally important to obtain reliable predictions. An examination of the relationship between model stability in molecular dynamics (MD) simulations derived from RMSD (root mean squared deviation) and structure quality assessment from various protein quality checkers was undertaken. The results were compared to membrane protein structures, solved at various resolution, by either X-ray or electron diffraction techniques. The checking programs could predict the potential success of MD in making functional conclusions. MD stability was shown to be a good indicator for the quality of structures. The quality was also shown to be dependent on the resolution at which the structures were determined.}, address = {Laboratory of Molecular Biophysics, Department of Biochemistry, The University of Oxford, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK.}, author = {Law, Richard J J. and Capener, Charlotte and Baaden, Marc and Bond, Peter J J. and Campbell, Jeff and Patargias, George and Arinaminpathy, Yalini and Sansom, Mark S P S. }, citeulike-article-id = {309034}, doi = {http://dx.doi.org/10.1016/j.jmgm.2005.05.006}, issn = {1093-3263}, journal = {J Mol Graph Model}, keywords = {membrane, protein, review, simulations}, month = {August}, posted-at = {2005-08-31 17:46:10}, priority = {4}, title = {Membrane protein structure quality in molecular dynamics simulation.}, url = {http://dx.doi.org/10.1016/j.jmgm.2005.05.006}, year = {2005} }

TY - JOUR ID - citeulike:309034 L3 - citeulike-article-id:309034 N2 - Our goal was to assess the relationship between membrane protein quality, output from protein quality checkers and output from molecular dynamics (MD) simulations. Membrane transport proteins are essential for a wide range of cellular processes. Structural features of integral membrane proteins are still under-explored due to experimental limitations in structure determination. Computational techniques can be used to exploit biochemical and medium resolution structural data, as well as sequence homology to known structures, and enable us to explore the structure-function relationships in several transmembrane proteins. The quality of the models produced is vitally important to obtain reliable predictions. An examination of the relationship between model stability in molecular dynamics (MD) simulations derived from RMSD (root mean squared deviation) and structure quality assessment from various protein quality checkers was undertaken. The results were compared to membrane protein structures, solved at various resolution, by either X-ray or electron diffraction techniques. The checking programs could predict the potential success of MD in making functional conclusions. MD stability was shown to be a good indicator for the quality of structures. The quality was also shown to be dependent on the resolution at which the structures were determined. JF - J Mol Graph Model SN - 1093-3263 AD - Laboratory of Molecular Biophysics, Department of Biochemistry, The University of Oxford, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK. TI - Membrane protein structure quality in molecular dynamics simulation. KW - membrane KW - protein KW - review KW - simulations AU - Law, Richard J AU - Capener, Charlotte AU - Baaden, Marc AU - Bond, Peter J AU - Campbell, Jeff AU - Patargias, George AU - Arinaminpathy, Yalini AU - Sansom, Mark S P PY - 2005/08/12/ UR - http://dx.doi.org/10.1016/j.jmgm.2005.05.006 ER -