![]() C.: Minimizing the object dimensions in circle and sphere packing problems (2008) Shen, Luming Chen, Zhen: A study of mechanical properties of pure and nitrogen-doped ultrananocrystalline diamond films under various loading conditions (2009).Kvamme, Bjørn Kuznetsova, Tatyana Uppstad, Daniel: Modelling excess surface energy in dry and wetted calcite systems (2009).Bonella, Sara Rocchia, Walter Amat, Pietro Nifosí, Riccardo Tozzini, Valentina: SDPhound, a mutual information-based method to investigate specificity-determining positions (2009).Hazout, Serge: Analyzing the sequence-structure relationship of a library of local structural prototypes (2009) Benros, Cristina de Brevern, Alexandre G.Tinsley Prudhomme, Serge: Adaptive multiscale modeling of polymeric materials with Arlequin coupling and goals algorithms (2009) Seth, Ajay Sherman, Michael Eastman, Peter Delp, Scott: Minimal formulation of joint motion for biomechanisms (2010).Malik, Adeel Firoz, Ahmad Jha, Vivekanand Ahmad, Shandar: PROCARB: a database of known and modelled carbohydrate-binding protein structures with sequence-based prediction tools (2010) ioport.Andrew: Browndye: A software package for Brownian dynamics (2010) Hoffgaard, Franziska Weil, Philipp Hamacher, Kay: Biophysconnector: connecting sequence information and biophysical models (2010) ioport.Hamacher, K.: Efficient perturbation analysis of elastic network models - application to acetylcholinesterase of T.In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
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