UCSF Chimera

Figure 16 Interchain hydrogen bond network in collagen triple helix. The figure was generated using the UCSF Chimera package and coordinates from PDB structure 1QSU.

Figure 21 Structure of the collagen X NCI trimer (PDB accession number 1GR3). Ribbon representation of the NCI trimer viewed down the crystallographic three-fold axis Is given. Ca + Ions are represented as pink spheres. The figure was generated using the UCSF Chimera package.

Figure 23 The overall structure of the (GlyProPro)io foldon (PDB accession number 1 NAY). The symmetry axis and symmetry elements are shown by a line and symbolic representations, respectively. The backbones of different chains are shown in red, blue, and green. The figure was generated using the UCSF Chimera package. ...

Fig. 2 Membrane topography of the a-LTX pore. Cross-section of the a-LTX tetramer embedded in a membrane (as observed in liposomes) (Orlova et al. 2000) is shown alongside the cut-open voltage-dependent K+ channel (Kvl.2) (Long et al. 2005) and Ca2+ release channel (ryanodine receptor) (Serysheva et al. 2005). Fully hydrated cations and molecules known to permeate through the respective channels are shown next to each reconstruction (FITC, fluoresceine isothiocyanate NE, norepinephrine). The narrowest part of the a-LTX channel is 10 A. Molecular images were produced using the UCSF Chimera package (Pettersen et al. 2004).

Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera - a visualization system for exploratory research and analysis, vol 25. J Comput Chem... 

II. Product Summary UCSF Chimera is a 3-D molecular visualization program available free of charge for academic, government, non-profit, and personal use. For commercial use a license agreement must be obtained. The program can interact with the output of other computational programs and can be customized using Python. Similar terms are available for Dock. ZINC contains over 3.3 million compounds in ready-to-dock, 3D formats. 

Figure 1 Structural comparison of viral capsids and a heat shock protein assembly that are commonly used to build nanoscale materials. All structures are shown to scale except for Ml 3. The length of the TMV capsid has been truncated. The colors have been added to highlight the morphological units, and are not necessarily indicative of different protein sequences. All structural renderings were generated using UCSF Chimera.

Figure 5 Structures of closely and distantly related proteins. Protein images created with UCSF Chimera. ...

T. E. Ferrin,/. Comput. Chem., 25,1605 (2004). UCSF Chimera - A Visualization System for Exploratory Research and Analysis. Available http //www.cgl.ucsf.edu/chimera. 

Acknowledgments Molecular visualization was performed with the UCSF Chimera package developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311). 

UCSF Chimera package, http //www.cgl.ucsf.edu/chimera... 

Fig. 10. Stereoview of the 5 -d(GIGGATCICG)2-SJG-136 intrastrand adduct. DNA strands are colored blue, and SJG-136(4) is shown in atom colors. Watson-Grick base pairing has been maintained, and there is minimal distortion to the P-helical structure of the DNA backbone. Models were produced in the SYBYL modeling suite and images produced using UCSF Chimera. [ 1...

AGE binding site (grey). The figure was prepared using UCSF Chimera, alpha version 1.4... 

Figure 2 The surface of activated human N-ezrin is shown (PDB accession no 1NI2 The AGE binding site of ezrin (on the right) is distant from Tyrl45, the EGF receptor phosphorylation site (on the left). The figure was prepared using UCSF Chimera, alpha version 1.4...

Figure 1 Interactions in the active site of AAD. (a) Active site environment of the imine between Lysl 15 and acetoacetone (PDB code 3BH3 prepared with UCSF Chimera, http //www.cgl.iicsf.edu/ chimera/). The carbons of Lysl 15 and acetoacetone are highlighted in green the carbons forming the hydrophobic environment for Lysl 15 are highlighted in yellow. (b)The Westheimer proposal for the decreased of Lysl 15. The red arrows indicate electrostatic repulsion the blue arrows represent electrostatic attraction, (c) Structure-based proposal for the decreased pK of Lysl 15. The hydrophobic environment of Lysl 15 lowers its pK, and the proximity of Arg29 orients the carboxylate group in the plane of the imine with Lysl 15.

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