From emartz at microbio.umass.edu  Sat Aug 21 20:37:00 2021
From: emartz at microbio.umass.edu (Eric Martz)
Date: Sat, 21 Aug 2021 20:37:00 -0400
Subject: [Proteopedia] New FirstGlance simplified, plus electron density maps
Message-ID: <5714d3ed-c476-0cdc-fcbb-b1f87111889a@microbio.umass.edu>

FirstGlance in Jmol <http://firstglance.jmol.org> is linked to every PDB 
entry in Proteopedia. *Educators* please note that FirstGlance enables 
exploration of protein structure with remarkable ease of use. A *new 
version*, just released, starts out in a "less detailed" or *simplified 
mode* for beginners. See secondary structure, hydrophobic cores, 
distribution of charges, salt bridges, cation-pi interactions, disulfide 
bonds and 6 other kinds of protein crosslinks with a few clicks each. 
Links go to explanations and illustrations of each of these in 
Proteopedia.Org 
<https://proteopedia.org/w/About_Macromolecular_Structure>. See 
non-covalent interactions with ligands. Isolate any moiety or hide 
components with a few clicks. Find by short sequence motifs, sequence 
numbers, etc.

Any view can be saved with a few clicks either as a static image, or as 
an animation ready to drop into a presentation slide (see examples 
<http://tinyurl.com/movingmolecules>). Excellent for student reports 
(see lesson plans 
<https://proteopedia.org/w/User:Eric_Martz/Introduction_to_Structural_Bioinformatics>). 


FirstGlance displays amino acid sequences and provides instructions 
<https://proteopedia.org/wiki/fgij/seqalign.htm> for doing multiple 
sequence alignments and clear visualization with MSAReveal.Org 
<http://msareveal.org>.

Press "Show more details" if you're up for any of: electron density maps 
<https://proteopedia.org/w/Electron_density_maps> (new and super easy), 
alternate locations (easily animated 
<https://proteopedia.org/w/Alternate_locations>), occupancy values, 
crystal contacts or the unit cell. See FirstGlance-generated animations 
of electron density maps 
<https://docs.google.com/presentation/d/1t-hAL5AWeGmXJdanNNusIbiLN0_c53laQe7PJrjQRe8/edit#slide=id.gead9198f4d_0_60>.

Please feel free to reply with questions or suggestions.

-Eric Martz

P.S. If problems with the new version, hold down the Shift key while 
reloading the page to force the browser's cache to update.

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From emartz at microbio.umass.edu  Tue Aug 24 17:04:30 2021
From: emartz at microbio.umass.edu (Eric Martz)
Date: Tue, 24 Aug 2021 17:04:30 -0400
Subject: [Proteopedia] Dazzling movies of COVID spike protein opening
Message-ID: <f4a36452-7fec-f50e-052d-3e7a48ea1e02@microbio.umass.edu>

An article published this month offers gorgeous movies of SARS-CoV-2 
spike protein opening to expose its receptor binding domain. The movies 
are based on extensive molecular dynamics simulations. The authors 
conclude that spike protein surface glycosylations act as "gates" in the 
opening transition. These movies would be dramatic in the classroom.

https://proteopedia.org/w/SARS-CoV-2_spike_protein_priming_by_furin#Glycan_gate

-Eric