Changes between Version 7 and Version 8 of SiteVisit

Timestamp:

Aug 24, 2011, 4:50:43 PM (15 years ago)

Author:

goddard

Comment:

--

SiteVisit

@@ -19 +19 @@
 
  ==== Biological Systems ====
+
+ Alpha Crystallin
+ * [http://plato.cgl.ucsf.edu/chimera/data/3dem-june2011/fitdemo_long.html Alpha Crystallin] - Already prepared multifaceted demo including BLAST, homology modeling, crystal unit cell, EM fitting, and SAXS, for Gordon conf but cut due to time limits.  Connected to heart disease, cataracts and amyloid aggregation diseases.
+ * Clathrin cage tomography from Yifan Cheng.  Similar to alpha crystallin cages.  Could demo Segger segmentation and proposed tomogram filtering.
+
+ HIV Capsid
  * [http://www.cgl.ucsf.edu/chimera/data/hiv-core-june2011/hivcore.html HIV Capsid] - Illustrates composite model building of HIV conical core particle.  Capsid protein interfaces highly conserved drug target (June 2011 PNAS [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136285/?tool=pubmed paper])
- * [http://www.cgl.ucsf.edu/chimera/animations/hivrna/hivrna.mov HIV RNA] - Secondary structure of full HIV RNA, I made 3-d model and animation with Chimera script. Nature 2009 [http://www.ncbi.nlm.nih.gov/pubmed/19661910 paper]).
+ * [http://plato.cgl.ucsf.edu/chimera/data/tutorials/eman2011 Rous sarcoma virus] - Retrovirus with very similar capsid to HIV.  Did EM fitting and comparison to HIV at EMAN 2011 workshop.
+ * [http://www.cgl.ucsf.edu/chimera/animations/hivrna/hivrna.mov HIV RNA] - Secondary structure of full HIV RNA, I made 3-d model and animation with Chimera script. Nature 2009 [http://www.ncbi.nlm.nih.gov/pubmed/19661910 paper]).  Might add nucleocapsid protein tightly packed on RNA, and collapse RNA into capsid.
  * [http://www.cgl.ucsf.edu/home/goddard/temp/dengue2.mov Dengue virus] - Maturation of dengue virus involves major rearchitecting of capsid.  Chimera animation shows hypothetical model from Michael Rossmann lab.
+
+ Others
  * [http://www.cgl.ucsf.edu/Research/auer/gut-sep2010/ Termite gut] - Segmentation tool demo.
  * [http://en.wikipedia.org/wiki/Myofibrils Muscle filaments], myosin / actin / tropomyosin.  Another good "composite" model example.  Haven't done much with this system yet though.  Recent Roger Craig / Raul Padron [http://www.ncbi.nlm.nih.gov/pubmed/21705660 paper], PNAS July 2011