Visual molecular dynamics

VMD (Visual Molecular Dynamics) MD-generated trajectories can be read. 

Humphrey, W., Dalke, A., Schulten, K. VMD-visual molecular dynamics. J. Molec. Graphics 1996, 14, 33-38. 

W. Humphrey, A. Dalke, and K. Schulten (1996) VMD Visual molecular dynamics. Journal of Molecular Craphics 14, pp. 33-38... 

Visual Molecular Dynamics Model (Humphrey et al., 1996) of BSA from Protein Data Bank ID 4F5S (Bujacz. 2012) determined at 2.47 A resolution by X-ray diffraction. 

Visual Molecular Dynamics. Download VMD from http //www.ks.uluc.edu/Research/vmd/. 

Fig. 4 Native and hybrid protein folds after energy minimization with AMBER." All proteins drawn in the same colour have the same amino acid sequence. The four native folds are displayed along the diagonal. The first row has the conformations for protein IQLX (cyan), the second row has the conformations for IIOS (red), the third row has the conformations for lAAP (yellow) and the fourth row has the conformations for IIGD (green). Along each column, the non-native conformations are obtained by imposing the backbone fold, or part of the backbone fold, of the native structure in that column on to the backbone of the other proteins. Below each conformation is the value of its potential energy in kcal/mol. This figure was adapted from and made with the help of the software package Visual Molecular Dynamics (VMD). ...

Humphrey W, Dalke A and Schulten K. VMD- Visual Molecular Dynamics. J. Molecular Graphics 1996 14 33-38. 

The RCSB Protein Data Bank (www.pdb.org) is the repository of more than 57,000 three-dimensional structures that have been determined by X-ray crystallography (shown on the opening page of this chapter) or multidimensional NMR (Section 15.22). The structures are publicly available for download in a PDB format. The structures can be visualized and manipulated with free programs such as Visual Molecular Dynamics (http //www.ks.uiuc.edu/Research/ vmd/) or Chimera (http //www.cgl.ucsf.edu/chimera). 

Fig. 3 Scheme representing the non-solvent contact area (NSCA). This area intends to represent by which amount each residue is buried in the protein surface. All surface areas are evaluated by the sasa measure command present in the visual molecular dynamics (VMD) software... 

In recent years a very versatile, user friendly, and robust code evolved from the early Visual Molecular Dynamics (VMD) software, created by K. Schulten s group at UIUC in the US (Humphrey et al. 1996). There are thousands of users of this package. An example of VMD visualization of the gradual stretching of modular adhesive protein contactin is presented in O Fig. 31-3. Preparation of a similar picture is not difficult if one uses a VMD guide (Hsin et al. 2008). 

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