The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Export

@article{citeulike:211086, abstract = {The number of solved structures of macromolecules that have the same fold and thus exhibit some degree of conformational variability is rapidly increasing. It is consequently advantageous to develop a standardized terminology for describing this variability and automated systems for processing protein structures in different conformations. We have developed such a system as a 'front-end' server to our database of macromolecular motions. Our system attempts to describe a protein motion as a rigid-body rotation of a small 'core' relative to a larger one, using a set of hinges. The motion is placed in a standardized coordinate system so that all statistics between any two motions are directly comparable. We find that while this model can accommodate most protein motions, it cannot accommodate all; the degree to which a motion can be accommodated provides an aid in classifying it. Furthermore, we perform an adiabatic mapping (a restrained interpolation) between every two conformations. This gives some indication of the extent of the energetic barriers that need to be surmounted in the motion, and as a by-product results in a 'morph movie'. We make these movies available over the Web to aid in visualization. Many instances of conformational variability occur between proteins with somewhat different sequences. We can accommodate these differences in a rough fashion, generating an 'evolutionary morph'. Users have already submitted hundreds of examples of protein motions to our server, producing a comprehensive set of statistics. So far the statistics show that the median submitted motion has a rotation of approximately 10 degrees and a maximum Calpha displacement of 17 A. Almost all involve at least one large torsion angle change of >140 degrees. The server is accessible at http://bioinfo.mbb.yale. edu/MolMovDB}, address = {Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520, USA.}, author = {Krebs, W. G. and Gerstein, M.}, citeulike-article-id = {211086}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/10734184}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=10734184}, day = {15}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {database, framework}, month = {April}, number = {8}, pages = {1665--1675}, posted-at = {2008-04-17 07:22:49}, priority = {2}, title = {The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/10734184}, volume = {28}, year = {2000} }

TY - JOUR ID - citeulike:211086 L3 - citeulike-article-id:211086 N2 - The number of solved structures of macromolecules that have the same fold and thus exhibit some degree of conformational variability is rapidly increasing. It is consequently advantageous to develop a standardized terminology for describing this variability and automated systems for processing protein structures in different conformations. We have developed such a system as a 'front-end' server to our database of macromolecular motions. Our system attempts to describe a protein motion as a rigid-body rotation of a small 'core' relative to a larger one, using a set of hinges. The motion is placed in a standardized coordinate system so that all statistics between any two motions are directly comparable. We find that while this model can accommodate most protein motions, it cannot accommodate all; the degree to which a motion can be accommodated provides an aid in classifying it. Furthermore, we perform an adiabatic mapping (a restrained interpolation) between every two conformations. This gives some indication of the extent of the energetic barriers that need to be surmounted in the motion, and as a by-product results in a 'morph movie'. We make these movies available over the Web to aid in visualization. Many instances of conformational variability occur between proteins with somewhat different sequences. We can accommodate these differences in a rough fashion, generating an 'evolutionary morph'. Users have already submitted hundreds of examples of protein motions to our server, producing a comprehensive set of statistics. So far the statistics show that the median submitted motion has a rotation of approximately 10 degrees and a maximum Calpha displacement of 17 A. Almost all involve at least one large torsion angle change of >140 degrees. The server is accessible at http://bioinfo.mbb.yale. edu/MolMovDB IS - 8 JF - Nucleic Acids Res SN - 1362-4962 AD - Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520, USA. EP - 1675 TI - The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. VL - 28 SP - 1665 KW - database KW - framework AU - Krebs, WG AU - Gerstein, M PY - 2000/04/15/ UR - http://view.ncbi.nlm.nih.gov/pubmed/10734184 ER -