Visualizing and identifying conformational ensembles in molecular dynamics trajectories

Using a conformational distance measure based on the changes in intramolecular atom distances, the authors show that a planar map can help visualize molecular dynamics trajectories efficiently such that conformational ensembles appear as well-separated point sets. The cluster analysis can then be used to automatically identify conformations.

[1]  X. Daura,et al.  Folding–unfolding thermodynamics of a β‐heptapeptide from equilibrium simulations , 1999, Proteins.

[2]  R L Somorjai,et al.  Fuzzy cluster analysis of molecular dynamics trajectories , 1992, Proteins.

[3]  A. Hoffman,et al.  Lower bounds for the partitioning of graphs , 1973 .

[4]  H. Berendsen,et al.  Essential dynamics of proteins , 1993, Proteins.

[5]  Hybrid Monte Carlo with adaptive temperature in mixed‐canonical ensemble: Efficient conformational analysis of RNA , 1998 .

[6]  C. Brooks,et al.  Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV. , 1993, Biochemistry.

[7]  Alan M. Frieze,et al.  Clustering in large graphs and matrices , 1999, SODA '99.

[8]  Wilhelm Huisinga,et al.  From simulation data to conformational ensembles: Structure and dynamics‐based methods , 1999 .

[9]  Bruce Hendrickson,et al.  An Improved Spectral Graph Partitioning Algorithm for Mapping Parallel Computations , 1995, SIAM J. Sci. Comput..

[10]  Wolfram Saenger,et al.  INITIAL STATE OF AN ENZYMATIC REACTION. THEORETICAL PREDICTION OF COMPLEX FORMATION IN THE ACTIVE SITE OF RNASE T1 , 1995 .

[11]  M. Fiedler.  A property of eigenvectors of nonnegative symmetric matrices and its application to graph theory , 1975 .

[12]  H. Berendsen,et al.  Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme , 1998, Proteins.

[13]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.