Proteopedia:What's New
What's New in Proteopedia?
This page lists new pages, substantially updated pages, and new capabilities within Proteopedia. In contrast, Proteopedia:News lists external news such as adoptions, blogs, press, meetings, seminars and workshops about Proteopedia.
A major purpose of this page is to make it easier for users to find out about new user-created pages with substantial content. Only user-created pages that have substantial content (at least one paragraph of user-added text with three or more green links), and that are reasonably complete should be listed below. Pages that are started, but not yet completed, should not be listed until they are reasonably complete. Automatically seeded new pages, titled with PDB codes, are not listed here[1]. Minor updates to existing pages should not be listed.
Please add new items at the top. If a linked page is not new, but has been updated with substantial new content, please say so. Each page's history tab (at the top) shows when it was created and the date of each update.
The left arrow symbol (<-) signifies a page that redirects to another page.
October, 2009October, 2009
This month's list is incomplete:
March, 2009March, 2009
This month's list is incomplete:
- Mechanosensitive channels: opening and closing includes morphs of the ion-conducting channel opening and closing.
- High school teachers' resources
- Richards, Frederic M. (1925-2009) including a photo of "Fred's Folly".
February, 2009February, 2009
This month's list is incomplete:
- Ion channels is an attempt to cover a family of proteins and list their available PDB structures.
January, 2009January, 2009
This month's list is incomplete:
December, 2008December, 2008
- Conservation, Evolutionary now includes instructions on how to show a ConSurf result as a scene in Proteopedia, complete with the standard ConSurf color key.
- Resolution now includes a movie illustrating the relation between the atomic model and the electron density map while resolution ranges from 0.5 to 5.0 Ångstroms.
November, 2008November, 2008
- RNA silencing: suppression by viruses. Concerns the research awarded the 2006 Nobel Prize in Physiology or Medicine. Linked are new pages on specific RNA silencing proteins: Plant viral protein p19 and Tomato aspermy virus protein 2b.
- Transcription Termination Factor Rho.
- Mechanosensitive ion channel of large conductance, with open, intermediate, and closed conformations, 2oar.
- Crucial role of electrostatic features in halotolerance of carbonic anhydrase, 1y7w.
- Hydrogen in macromolecular models
- Molecular modeling and visualization software, whick links to new pages on PyMOL, Jmol, RasMol, and Chime.
October, 2008October, 2008
- Lac repressor structure, including a morph of the DNA-binding domain bending the operator DNA.
- Poly(A) Polymerase, 2q66: A new section complementing this month's article in Molecule of the Month.
- Structure Gallery Generator generates galleries of thumbnail molecular images, linked to Proteopedia, for external websites or within Proteopedia pages.
- Acetylcholinesterase in complex with anti-Alzheimer's drug candidates: Crystal packing mediates enantioselective ligand recognition, 1zgb.
- Thermal stability analysis of alcohol dehydrogenase: 2oui, 2nvb.
- Confirmation of a heterodimer predicted by computational genomic analysis (neither chain could be crystallized alone): 2g38.
- Complex Of S. griseus Proteinase B And Polypeptide Chymotrypsin Inhibitor-1 From Russet Burbank Potato Tubers, 4sgb.
- Structures Saving the Most Lives is a new list added to the Highest impact structures page originally created in February, 2008.
- Hydrogen bonds
- Nobel Prizes for 3D Molecular Structure
- Morphs: Although this page was created in March, 2008, most of its content was added this month.
- Proteopedia: Email list
- What's New in Proteopedia? (this page).
- Several pages about visualization software: FirstGlance in Jmol, Swiss-PDBViewer = DeepView, and Protein Explorer.
September, 2008September, 2008
- Anticancer Prodrug CPT-11 complexed with Torpedo californica Acetylcholinesterase 1u65
- Avian Influenza Neuraminidase, Tamiflu and Relenza
- Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis.
- TEM1-β-Lactamase/ β-Lactamase Inhibitor Protein (BLIP), 2b5r and 1s0w.
- Acid-beta-glucosidase covalently bound to conduritol B epoxide, 1y7v.
- Ribonuclease A, 1rta has a new section complementing this month's article in Molecule of the Month.
- DRuMS, standard color schemes for macromolecules, and color key templates for use in Proteopedia.
- Glutamine Synthetase, which includes instructions on how to use the Jmol console for advanced scene authoring.
August, 2008August, 2008
- HIV-1 protease
- Pyruvate phosphate dikinase with a morph of the catalytic reaction and conformational changes.
- Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System with a morph of the catalytic reaction and conformational changes.
- Antizyme Inhibitor
- Selenocysteine Synthase, SelB Recognition is a new page complementing this month's article in Molecule of the Month.
- Teaching Strategies Using Proteopedia
- Protein structure lesson plan for BioSci 203
- Proteopedia: News
July, 2008July, 2008
- Biotin Protein Ligase
- YAGE, A Prophage Protein Belonging To The Dihydrodipicolinic Acid Synthase Family From E. Coli K12, 2v9d.
- Ramachandran Plots
- Flexibility of aromatic residues in acetylcholinesterase
- Horizontal gene transfer ssDNA binding protein from Agrobacterium tumefaciens VirE1/VirE2=3btp
- Proteopedia:Page of the Year Competition
- Student Projects
June 2008June 2008
- Computational design of a Kemp elimination catalyst 2rkx.
- Recoverin, a calcium-activated myristoyl switch
- G protein, ras oncogene: James_D_Watson/Proteins_Intro.
- Ribulose-1,5-bisphosphate carboxylase/oxygenase uses the Kinemage applet.
- Acid-beta-glucosidase
- Rop protein
- Institute of Clinical Biochemistry, Oslo, Norway.
- Research Groups <- Institutes
- Teaching Scenes, Tutorials, and Educators' Pages
About Macromolecular Structure
- About Macromolecular Structure <- About Protein Structure
- Amino Acids
- Asymmetric Unit
- Atomic coordinate file
- Biological Unit <- Quaternary structure
- Free R
- NMR Ensembles of Models
- PDB identification code
- Quality assessment for molecular models
- R value
- Resolution
- Temperature value <- Disorder, B value
- Unit cell
May 2008May 2008
- Acetylcholinesterase
- 2ace with an overview of the significance of this, the first acetylcholinesterase structure.
- Anti-Alzheimer's drug, Aricept, complexed with acetylcholinesterase 1eve.
- Tacrine Binding To Aromatic Residues In The Active-site Gorge Of Acetylcholinesterase, 1acj.
- Serum Paraoxonase-1 (PON1) via directed evolution 1v04.
- Human acid-beta-glucosidase, 1ogs.
- Photosystem II, an undergraduate project.
- Ozonolysis: cool animation of a chemical reaction!
April 2008April 2008
- Acetylcholinesterase inhibited by nerve agent soman 1som.
- Highest resolution acetylcholinesterase so far, 1ea5.
- Tetramerization domain of acetylcholinesterase 1vzj.
- Locations of mutations in oncogene phosphatidylinositol 3-kinase 2rd0, with many of the published figures made interactive in Jmol.
- Escherichia coli GlpG, an integral membrane protein rhomboid protease, unique in cleaving the transmembrane domains of other membrane proteins, 2ic8.
- Major Histocompatibility Complex Class I (no Jmol yet)
- Personal favorites
- Believe It or Not!
- Help:Protected Pages
March 2008March 2008
- Conformational flexibility in the peripheral site of Torpedo californica acetylecholinesterase revealed by the complex structure with a bifunctional inhibitor, 2cek.
- Proton Channels
- Proteopedia:Namespaces
- Proteopedia:About
- SGAP Streptomyces griseus Aminopeptidase (SGAP) (no Jmol)
February 2008February 2008
- Hemoglobin
- Highest impact structures of all time.
- Nucleosomes
- Scorpion alpha-toxin 1qlh.
- Peptide
- Proteopedia:Problems
- Personal favorites
January 2008January 2008
October-December 2007October-December 2007
- Serine Protease
- Nqo1 NADH quinone oxidoreductase (NQO1) in complex with its potent inhibitor dicoumarol.
- 1xjo S. griseus aminopeptidase.
- Glycine
- Bacterial Intein-Like Domains (BILs) (no Jmol, no green links)
- Hint auto-proteolytic protein-processing domains (no Jmol, no green links)
See AlsoSee Also
- Proteopedia:News
- Proteopedia: Email list
- Newest Pages appears to list only the current month, and mostly automatically seeded pages.
- Most Recent Changes
- Topic pages