Search results

From Proteopedia

There is no page with the exact title "Karsten,_W.E". The search results for "Karsten,_W.E" are displayed below. You can create a page titled Karsten,_W.E (by clicking on the red link).

For more information about searching Proteopedia, see Help.

Showing below up to 20 results starting with #1.

Article title matches

1. User:Karsten Theis/Linear interpolation (911 bytes)
   1: ...conformation or position). Here, I am using residues 5 and 6 of 1BNA.
   6: five = {5}.xyz.all
   8: interp = six
   9: progress = 0.5
   10: ssergorp = 1 - progress
2. User:Karsten Theis/Rigid body interpolation (4,709 bytes)
   1: ...to perform supoerpositions and to create morph, see [[Jmol/Storymorph]].
   3: ... anchor (center of mass, given atom) is in the same location.
   5: ...ms in the same order, but with different coordinates.
   9: ...olation of coordinates in the atom sets sel1 and sel2
   10: ...t} sel1 First set of atoms, will be modified by the function
3. Image:Karsten-2024-03.png (0 bytes)
4. User:Karsten Theis/T7RNAP physical model explanation (3,838 bytes)
   1: ... of a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
   2: [[Image:1MSW butterfly.png|800px]]
   4: ...ve site at the palm. For an annotated image, see below.
   6: [[Image:1msw legend.png|800px]]
   8: ...on load='' size='340' side='right' caption='' scene='10/1081719/T7_rnap/2'>
5. User:Karsten Theis/Showcase (4,137 bytes)
   1: == Proteopedia and Biomolecular Visualization ==
   4: ...='350' side='right' caption='' scene='37/376372/Overall/3'>
   6: ...lycine/Emartz_ballandstick/1'>ball and stick</scene>
   7: ...scene name='78/786673/Gal_overal_view/1'>GAL</scene>
   8: === Access ===
6. User:Karsten Theis/Lactose (a sugar) (31 bytes)
   1: #REDIRECT [[Lactose (a sugar)]]
7. User:Karsten Theis/Sandbox 6 (1,166 bytes)
   1: https://www.frontiersin.org/articles/10.3389/fmicb.2020.02014/full
   2: Size comparison human cell and coronavirus
   4: Outline
   5: ...(Virus vs Bacterium), chronic diseases, other causes
   6: * Size of protein, virus, human cell
8. User:Karsten Theis (3,985 bytes)
   1: ...mical and Physical Sciences], Westfield State University
   4: ...ch Interests: Chemistry education, DNA repair, molecular motors, X-ray crystallography
   7: ...ademics/chemistry-degrees/faculty-staff/karsten-theis]
   12: ...impact structures]] (I added the bit about lysozyme in 2008)
   13: ...Feb 2010 version]], used for my job talk at Westfield that month)
9. User:Karsten Theis/Animation course (20,087 bytes)
   1: ...de='right' caption='' scene='52/520489/Ligand_pocket/2'>
   3: ==Animate a scene with Jmol==
   5: ===Load the scene and choose a look===
   6: ...</text></jmolLink></jmol> and try different representations and colors.
   8: 1. Choose a background:
10. User:Karsten Theis/DNA bulges (2,741 bytes)
    1: ...DNA, looped out nucleotides or a combination of the two.
    3: ==Evidence for structural distortions==
    4: ... footprinting-type experiments<ref>PMID:7543675</ref>.
    6: ...40' side='right' caption='' scene='10/1073371/Bulge5/1'>
    7: ==Bulges in 3D==
11. User:Karsten Theis/turns (22,503 bytes)
    1: ...peptide backbone, with a short distance between the first and fourth alpha carbon.
    3: ==Concepts you can explore here==
    5: ...ut sometimes overlapping with) alpha helices and beta strands
    6: ...ing a sharp turn, with a short distance between the first and last alpha carbon
    7: ...rface of globular proteins, often connecting helices and strands
12. User:Karsten Theis/Lactase (a protein) (33 bytes)
    1: #REDIRECT [[Lactase (a protein)]]
13. User:Karsten Theis/transition proposal (2,998 bytes)
    1: ...de='right' caption='UvrB in complex with ATP' scene='77/779435/Front/1'>
    2: ...ferent parts of a structure without losing their bearing.
    4: ==Proposal: smooth transition as default==
    6: ...re reloaded, show the new scene as fast as possible.
    8: ...oading a scene. This slows down browsing the figures.
14. Karsten Theis sandbox 1 (13,880 bytes)
    1: {{BAMBED
    2: |DATE=August 20, 2011
    4: |BAMBEDDOI=10.1002/bmb.20566
    7: ...l instructions for the development, survival and reproduction of organisms.
    8: ...ref name='gene'>http://www.genome.gov/25520880 </ref>
15. User:Karsten Theis/overall views (19,751 bytes)
    3: <gallery>
    4: Image:UvrB fold.JPG
    5: Image:UvrB charge.JPG
    6: Image:UvrB slab core.JPG
    7: Image:UvrB consurf.JPG
16. User:Karsten Theis/Trypsin (3,480 bytes)
    1: ...ate specificity, activation and degradation, and relationship to thrombin.
    3: ...he end of this brief session, students will be able to:
    5: ...nizing and binding positively charged residues like Arg and Lys.
    7: ...ng how differences in residue composition drive specificity.
    9: ...ds in the gut come from digestive enzymes themselves.
17. User:Karsten Theis/Textbook supplement (32 bytes)
    1: #REDIRECT [[Biochemistry in 3D]]
18. User:Karsten Theis/Sandbox 1 (2,192 bytes)
    1: <applet size='[450,338]' frame='true' align='right'
    2: scene='User:Karsten_Theis/Sandbox_1/Globe3/2'
    5: <ref>DOI:10.1002/open.201300012</ref>
    7: ...can rotate around its single bonds to get a different conformation:
    11: ...; rotate branch {C3}{C2} 2; set refreshing true; delay 0.05}}
19. User:Karsten Theis/Sandbox 3 (9,590 bytes)
    1: == Proteopedia annotated bibliography ==
    4: https://www.learntechlib.org/p/35558/
    5: ...etrieved February 20, 2021 from https://www.learntechlib.org/primary/p/35558/.
    7: Unfolding Proteins
    8: Maura C. Flannery
20. User:Karsten Theis/Lactose sugar (50 bytes)
    1: #REDIRECT [[User:Karsten Theis/Lactose (a sugar)]]

Page text matches

1. Image:DHFR 3dfr 1dls.pdb (175 bytes)
   2: ...s (human DHFR) with ligands NDP and MTX superimposed
   3: REMARK Karsten Theis 1/8/2022
   4: == Licensing ==
   5: {{self|cc-by-sa-3.0|GFDL}}
2. 1o0s (4,330 bytes)
   2: ...tal Structure of Ascaris suum Malic Enzyme Complexed with NADH==
   3: ...o0s]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
   5: ...://proteopedia.org/fgij/fg.htm?mol=1O0S FirstGlance]. <br>
   6: ..." id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
   7: ..., <scene name='pdbligand=TTN:TARTRONATE'>TTN</scene></td></tr>
3. Image:1a1v on 1d9z 1-411.pdb (335 bytes)
   2: ...containing a superposition of two crystal structures
   3: ...K MODEL 1 is 1D9Z, MODEL 2 is 1A1V (NS3 Helicase with ssDNA bound)
   4: REMARK 1A1V was superimposed on residues 1-411 or 1D9Z using Pymol's align command
   5: REMARK Karsten Theis, 3-31-2025
   7: == Licensing ==
4. User:Karsten Theis/Showcase (4,137 bytes)
   1: == Proteopedia and Biomolecular Visualization ==
   4: ...='350' side='right' caption='' scene='37/376372/Overall/3'>
   6: ...lycine/Emartz_ballandstick/1'>ball and stick</scene>
   7: ...scene name='78/786673/Gal_overal_view/1'>GAL</scene>
   8: === Access ===
5. Semaglutide (14,940 bytes)
   1: ... blue) [[4zgm]] (scroll down for interactive figures)]]
   3: ...across a wide range of diseases is currently studied.
   5: ==Discovery==
   7: ...e [[GLP-1]] hormone with modifications described below.
   14: ==Structure and binding to GLP-1R==
6. Proteopedia:Wishlist (29,517 bytes)
   1: ... try to implement the best and most appropriate ideas.
   3: ...sting feature, please do so at [[Proteopedia:Problems]].
   5: ...itext that is converted into your name and the date.
   7: ...Please insert your wish after items that seem higher in priority.
   9: ==Wishlist for Outside the [[SAT|Molecular Scene Authoring Tools (SAT)]]==
7. Synthetic nanomaterials from standardized protein blocks (12,946 bytes)
   1: ...kground-color: #ffffd0;" width="90%"><tr><td><center>
   2: <div style="font-size: 140%;">
   3: ...y. [[User:Eric Martz|Eric Martz]] 21:20, 23 December 2024 (UTC)
   5: </center></td></tr></table></center>-->
   6: ...on load='' size='340' side='right' caption='' scene='10/1068508/8v2d/2'>
8. Resolution (14,174 bytes)
   1: <table align="right" border="0" width="200"><tr><td>
   2: [[Image:Resolution-holton-5.0.png]]
   4: [[Image:Resolution-holton-3.5.png]]
   6: [[Image:Resolution-holton-2.5.png]]
   8: [[Image:Resolution-holton-1.4.png]]
9. DNA (14,157 bytes)
   1: {{BAMBED
   2: |DATE=August 20, 2011
   4: |BAMBEDDOI=10.1002/bmb.20566
   6: ...rag down in the viewer to see them) in orange as well.'>
   8: ...l instructions for the development, survival and reproduction of organisms.
10. Morphs (23,832 bytes)
    1: ...ressor#Specific Binding|Details]].</td></tr></table>
    2: ... an animation showing a transition between two molecular conformations.
    3: ==Examples of Morphs==
    5: ===Morphs in Proteopedia===
    7: * Coronavirus: [[SARS-CoV-2 spike protein fusion transformation]], a morph animation.
11. User:Karsten Theis (3,985 bytes)
    1: ...mical and Physical Sciences], Westfield State University
    4: ...ch Interests: Chemistry education, DNA repair, molecular motors, X-ray crystallography
    7: ...ademics/chemistry-degrees/faculty-staff/karsten-theis]
    12: ...impact structures]] (I added the bit about lysozyme in 2008)
    13: ...Feb 2010 version]], used for my job talk at Westfield that month)
12. Proteopedia:Team (2,499 bytes)
    1: ==The Proteopedia Team==
    2: ===Proteopedia Founders & Developers===
    3: <gallery perrow="3">
    4: ...ser:Jaime_Prilusky|Jaime Prilusky]]<br>'''Co-Founder'''
    5: ....png|[[User:Eran_Hodis|Eran Hodis]]<br>'''Co-Founder'''
13. Temperature value (12,946 bytes)
    1: ...acromolecular Crystallography] at ProXyChem.com</ref>.
    3: ... is a common way to visualize the uncertainty for each atom.
    5: ...all analyzed cryo-EM models"<ref>PMID: 28867613</ref>.
    8: ==Definition==
    9: ...rature value, B factor, B value'', or ''Debye-Waller factor'') is
14. Proteopedia:News (22,865 bytes)
    1: ...''' Proteopedia, please see [[Proteopedia:What's New]].
    3: ...ms at the Top of Each Section and Date Them, Please!==
    5: ...dings below ''Statistics'' are in alphabetical order.
    9: ... been viewed is displayed at the bottom of the page.
    13: .... [http://genomebiology.com/2008/9/8/R121 ''Genome Biology'' 9:R121, August 2008] or [http://dx.doi....
15. Electron density maps (12,314 bytes)
    1: ...//www.bioinformatics.org/molvis/edm/ Interactive Version]]]
    2: ...of the macromolecular structures available from the
    3: [[Protein Data Bank]] (PDB)
    4: were determined by
    5: ...ar model reveals regions of uncertainty in the model.
16. Ubiquitin Structure & Function (9,224 bytes)
    1: ...='right' caption='Human ubiquitin, [[1ubq]])' scene=''>
    3: ... degradation<ref name="mainpaper">PMID: 3041007</ref>
    7: ...uitin found in higher eukaryotes<ref name="mainpaper"/>.
    8: ...n structure: Arg74 in pink and Gly75 Gly76 in white.]]
    10: ... content below was inserted by the ConSurf template -->
17. Proteopedia:Scrapbook (5,944 bytes)
    1: ... about Proteopedia, its dissemination and development.
    3: ==Proteopedia People==
    4: ...ut upgrading the infrastructure of Proteopedia were:
    5: {| class="wikitable"
    6: |[[Image:Jaim-2024-03.png|150px]]
18. Thymidylate synthase (8,831 bytes)
    1: ...ame="Kholodar" >DOI:10.1021/acs.biochem.1c00063</ref>
    3: ... thymidine 5'-monophosphate(dTMP) + Dihydrofolate(H₂F)
    5: [[Image:TS Overview.jpg|1000px]]
    7: ... the substrates and products as a result of this reaction.
    9: ...structure. The TS ThyX are flavin-dependent enzymes.
19. Image:Turn 2mhr 67 70.pdb (267 bytes)
    2: REMARK Residues 67 through 70 from PDB 2mhr
    3: REMARK removed ATOM 1160 HG SER A 68 25.482 30.843 7.303 1.00 26.79 H
    4: ... because Jmol connects it to its hydrogen bond acceptor
    5: REMARK Karsten Theis 2_8_2025
    6: == Licensing ==
20. Jmol/Using the console (4,640 bytes)
    1: ...via a dedicated button under the Jmol window in the SAT.
    2: ...on load='' size='340' side='right' caption='' scene='86/865284/Myoglobin/1'>
    5: ...ipt></jmolButton></jmol><div id=JmolApplet0_console></div>
    7: show sequence
    9: This shows the residues that contain selected atoms

View (previous 20) (next 20) (20 | 50 | 100 | 250 | 500)