User:Karsten Theis/Sandbox 3

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==Your Heading Here (maybe something like 'Structure')==
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== Proteopedia annotated bibliography ==
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<StructureSection load='2y04' size='340' side='right' caption='Caption for this structure' scene=''>
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This is a default text for your page '''Karsten Theis/Sandbox 3'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
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You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
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== Function ==
 
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== Disease ==
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https://www.learntechlib.org/p/35558/
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Rule, G., Bajzek, D. & Kessler, A. (2010). Molecular Visualization in STEM Education: Leveraging Jmol in an Integrated Assessment Platform. In J. Sanchez & K. Zhang (Eds.), Proceedings of E-Learn 2010--World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education (pp. 304-309). Orlando, Florida, USA: Association for the Advancement of Computing in Education (AACE). Retrieved February 20, 2021 from https://www.learntechlib.org/primary/p/35558/.
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== Relevance ==
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Unfolding Proteins
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<scene name='60/609966/Subutamol/1'>TextToBeDisplayed</scene>
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Maura C. Flannery
 +
The American Biology Teacher (2012) 74 (4): 278–281.
 +
https://doi.org/10.1525/abt.2012.74.4.13
 +
https://online.ucpress.edu/abt/article/74/4/278/18418/Unfolding-Proteins
-
<scene name='60/609966/Subutamol/2'>TextToBeDisplayed</scene>
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Rice ’n Beans or Ricin Beans?
 +
A Deadly Swap
 +
Author(s)
 +
Ann T.S. Taylor
 +
https://sciencecases.lib.buffalo.edu/cs/files/ricin.pdf
 +
https://sciencecases.lib.buffalo.edu/collection/detail.html?case_id=847&id=847
-
<scene name='60/609966/Subutamol/3'>TextToBeDisplayed</scene>
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Free Access
 +
Educational Uses of Molecular Visualization: A Survey of the Community
 +
Paul A Craig Lea V. Michel Robert C. Bateman
 +
First published: 01 April 2011 https://doi.org/10.1096/fasebj.25.1_supplement.575.1
 +
https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.25.1_supplement.575.1
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<jmol>
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Biochemistry/Molecular Biology
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<jmolLink>
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Free Access
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<script> slab on; depth 40; var a = [90,80,70,60,55,54,53,52,51]; for(var i IN a) {slab @i; delay 0.4;}
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Undergraduate SMART Teams: Exposing Students to the Process of Science through Physical Modeling
-
</script>
+
Tim Herman Margaret Franzen Shannon Colton Marvin O'Neal
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<text>Fade surface to invisible</text>
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First published: 01 April 2010 https://doi.org/10.1096/fasebj.24.1_supplement.16.1
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</jmolLink>
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https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.24.1_supplement.16.1
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</jmol> (basic)
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-
== Structural highlights ==
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Multimedia in Biochemistry and Molecular Biology Education
 +
Free Access
 +
Teaching structure: Student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course
 +
Sheila S. Jaswal Patricia B. O'Hara Patrick L. Williamson Amy L. Springer
 +
First published: 10 September 2013 https://doi.org/10.1002/bmb.20718
 +
https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20718
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
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Improving the Student Experience of Learning and Teaching in Second Year Biochemistry: Assessment to Foster a Creative Application of Biochemical Concepts
 +
Jessica Vanderlelie
 +
International Journal of Innovation in Science and Mathematics Education, 21(4), 46-57, 2013https://openjournals.library.sydney.edu.au/index.php/CAL/article/view/7299
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</StructureSection>
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Known Structure, Unknown Function: An Inquiry-based Undergraduate Biochemistry Laboratory Course
-
== References ==
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July 2015Biochemistry and Molecular Biology Education 43(4)
-
<references/>
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DOI: 10.1002/bmb.20873
 +
https://www.researchgate.net/profile/Linda-Columbus/publication/280092379_Gray_BAMBED_2015_SI/links/55a81b8d08ae815a04213253/Gray-BAMBED-2015-SI.pdf
 +
 
 +
Biochemistry/Molecular Biology
 +
Free Access
 +
Physical models designed to demonstrate the folding pathway of FiP35 WW domain as predicted by molecular dynamics (MD) simulations using Anton, an MD dedicated supercomputer: 2011 Pingry School S.M.A.R.T. Team Project
 +
Andrew Benton Alfano Abba E Leffler Willy Wriggers Tim Herman Alex Epifano Jack Hickey Will LaCosta Sydney Li Henry Meiring Daniell Temares … See all authors
 +
First published: 01 April 2011 https://doi.org/10.1096/fasebj.25.1_supplement.909.1
 +
https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.25.1_supplement.909.1
 +
 
 +
https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20805
 +
 
 +
https://www.sciencedirect.com/science/article/abs/pii/S0968000410000629
 +
 
 +
https://www.sciencedirect.com/science/article/abs/pii/S0022283618309884
 +
 
 +
https://pdfs.semanticscholar.org/6624/1c4f956bb26873386cda0a2e56bebec8be45.pdf
 +
 
 +
https://pubs.acs.org/doi/abs/10.1021/ed101022g
 +
 
 +
https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20693
 +
 
 +
https://books.google.co.uk/books?hl=en&lr=&id=aQW6BQAAQBAJ&oi=fnd&pg=PR7&dq=proteopedia&ots=wUUkVg-lq0&sig=VMNqV-Gn_RLqUpdGsbBysVeGuck#v=onepage&q=proteopedia&f=false
 +
 
 +
https://www.learntechlib.org/p/48575/
 +
 
 +
https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20769
 +
 
 +
https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20436
 +
 
 +
https://link.springer.com/chapter/10.1007/978-3-319-03919-0_42
 +
 
 +
https://academic.oup.com/bioinformatics/article/26/17/2210/198818?login=true
 +
 
 +
https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa003/5735620?login=true
 +
 
 +
Journal home page for Journal of Molecular Biology
 +
Review
 +
Molecular Illustration in Research and Education: Past, Present, and Future☆
 +
David S.Goodsell Jodie Jenkinson
 +
https://www.sciencedirect.com/science/article/abs/pii/S0022283618303693
 +
 
 +
https://arxiv.org/abs/1806.08332
 +
 
 +
https://www.lifescied.org/doi/full/10.1187/cbe.13-12-0247
 +
 
 +
https://pubs.acs.org/doi/abs/10.1021/bk-2019-1337.ch002
 +
 
 +
 
 +
 
 +
== More general citations ==
 +
 
 +
Most of these contain interactive 3D complements (I3DC)
 +
 
 +
Biochemistry and Molecular Biology
 +
Student Design of a Proteopedia Page to Reinforce Foundational Biochemistry Concepts and Molecular Visualization Skills
 +
Bonnie L. Hall
 +
First published: 18 April 2020 https://doi.org/10.1096/fasebj.2020.34.s1.06861
 +
https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.2020.34.s1.06861
 +
 
 +
Editorial
 +
Free Access
 +
Proteopedia and other exciting news
 +
Judith G. Voet Donald Voet
 +
First published: 13 September 2010 https://doi.org/10.1002/bmb.20445 Citations: 1
 +
PDFPDF
 +
https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20445
 +
 
 +
https://febs.onlinelibrary.wiley.com/doi/full/10.1111/febs.14316
 +
 
 +
https://www.nature.com/articles/nrm2512
 +
 
 +
https://repositorium.sdum.uminho.pt/bitstream/1822/28581/1/herraez%20a_bmbed_2013%20posp.pdf
 +
 
 +
https://scripts.iucr.org/cgi-bin/paper?S0108767309099279
 +
 
 +
https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.24.1_supplement.908.1
 +
 
 +
http://bichez.pedf.cuni.cz/archiv/article/92
 +
 
 +
https://www.tandfonline.com/doi/full/10.1080/21553769.2012.689262
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.713782
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.718526
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.759885
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.745168
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.736773
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.758056
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.712459
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.726191
 +
 
 +
Teaching foundational topics and scientific skills in biochemistry within the conceptual framework of HIV protease
 +
R. Jeremy Johnson
 +
First published: 20 March 2014 https://doi.org/10.1002/bmb.20793
 +
https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20793
 +
 
 +
https://scripts.iucr.org/cgi-bin/paper?rr5151
 +
 
 +
https://www.sciencedirect.com/science/article/abs/pii/S0009279719304570
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.736774
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.732340
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.712477
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.726532
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.737295
 +
 
 +
https://accessiblemeds.org/sites/default/files/2019-11/Sarah_Yim_GRxBiosims2019.pdf
 +
Slide uses image from insulin page
 +
 
 +
https://dspace.mit.edu/handle/1721.1/121878
 +
 
 +
https://www.tandfonline.com/doi/full/10.1080/07391102.2012.762722
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.721496
 +
 
 +
https://www.sciencedirect.com/science/article/abs/pii/S0167779917303074
 +
 
 +
https://www.sciencedirect.com/science/article/abs/pii/S0009279719304508
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.732343
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.721495
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.755134
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.726529
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.712460
 +
 
 +
https://www.researchgate.net/profile/Kelley_Swanberg/publication/279515655_Enhanced_baseline_locomotor_response_to_cocaine_without_alteration_in_drug-specific_conditioned_place_preference_or_behavioral_sensitization_in_adult_male_C57Bl6_mice_subjected_to_left_parietal_contro/links/559439c708ae793d13797ffa/Enhanced-baseline-locomotor-response-to-cocaine-without-alteration-in-drug-specific-conditioned-place-preference-or-behavioral-sensitization-in-adult-male-C57Bl-6-mice-subjected-to-left-parietal-contr.pdf
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.763216
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.721497
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.712458
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.680034
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.680030
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.726530
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.721498
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.745378
 +
 
 +
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0025246
 +
 
 +
https://link.springer.com/content/pdf/10.1007/s00775-015-1319-6.pdf
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.719111
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.680028
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.713780
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.762752
 +
 
 +
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.713781
 +
 
 +
https://books.google.co.uk/books?hl=en&lr=&id=yV61DwAAQBAJ&oi=fnd&pg=PP1&dq=proteopedia&ots=dOYoMOMeX6&sig=cEn0ICj6eDWxai4l1sl5m2xv5Io
 +
 
 +
https://pubs.acs.org/doi/abs/10.1021/acs.jchemed.8b00426
 +
 
 +
https://pubs.acs.org/doi/abs/10.1021/bk-2011-1087.ch004

Current revision

Proteopedia annotated bibliography

https://www.learntechlib.org/p/35558/ Rule, G., Bajzek, D. & Kessler, A. (2010). Molecular Visualization in STEM Education: Leveraging Jmol in an Integrated Assessment Platform. In J. Sanchez & K. Zhang (Eds.), Proceedings of E-Learn 2010--World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education (pp. 304-309). Orlando, Florida, USA: Association for the Advancement of Computing in Education (AACE). Retrieved February 20, 2021 from https://www.learntechlib.org/primary/p/35558/.

Unfolding Proteins Maura C. Flannery The American Biology Teacher (2012) 74 (4): 278–281. https://doi.org/10.1525/abt.2012.74.4.13 https://online.ucpress.edu/abt/article/74/4/278/18418/Unfolding-Proteins

Rice ’n Beans or Ricin Beans? A Deadly Swap

Author(s) Ann T.S. Taylor https://sciencecases.lib.buffalo.edu/cs/files/ricin.pdf https://sciencecases.lib.buffalo.edu/collection/detail.html?case_id=847&id=847

Free Access Educational Uses of Molecular Visualization: A Survey of the Community Paul A Craig Lea V. Michel Robert C. Bateman First published: 01 April 2011 https://doi.org/10.1096/fasebj.25.1_supplement.575.1 https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.25.1_supplement.575.1

Biochemistry/Molecular Biology Free Access Undergraduate SMART Teams: Exposing Students to the Process of Science through Physical Modeling Tim Herman Margaret Franzen Shannon Colton Marvin O'Neal First published: 01 April 2010 https://doi.org/10.1096/fasebj.24.1_supplement.16.1 https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.24.1_supplement.16.1

Multimedia in Biochemistry and Molecular Biology Education Free Access Teaching structure: Student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course Sheila S. Jaswal Patricia B. O'Hara Patrick L. Williamson Amy L. Springer First published: 10 September 2013 https://doi.org/10.1002/bmb.20718 https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20718

Improving the Student Experience of Learning and Teaching in Second Year Biochemistry: Assessment to Foster a Creative Application of Biochemical Concepts Jessica Vanderlelie International Journal of Innovation in Science and Mathematics Education, 21(4), 46-57, 2013https://openjournals.library.sydney.edu.au/index.php/CAL/article/view/7299

Known Structure, Unknown Function: An Inquiry-based Undergraduate Biochemistry Laboratory Course July 2015Biochemistry and Molecular Biology Education 43(4) DOI: 10.1002/bmb.20873 https://www.researchgate.net/profile/Linda-Columbus/publication/280092379_Gray_BAMBED_2015_SI/links/55a81b8d08ae815a04213253/Gray-BAMBED-2015-SI.pdf

Biochemistry/Molecular Biology Free Access Physical models designed to demonstrate the folding pathway of FiP35 WW domain as predicted by molecular dynamics (MD) simulations using Anton, an MD dedicated supercomputer: 2011 Pingry School S.M.A.R.T. Team Project Andrew Benton Alfano Abba E Leffler Willy Wriggers Tim Herman Alex Epifano Jack Hickey Will LaCosta Sydney Li Henry Meiring Daniell Temares … See all authors First published: 01 April 2011 https://doi.org/10.1096/fasebj.25.1_supplement.909.1 https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.25.1_supplement.909.1

https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20805

https://www.sciencedirect.com/science/article/abs/pii/S0968000410000629

https://www.sciencedirect.com/science/article/abs/pii/S0022283618309884

https://pdfs.semanticscholar.org/6624/1c4f956bb26873386cda0a2e56bebec8be45.pdf

https://pubs.acs.org/doi/abs/10.1021/ed101022g

https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20693

https://books.google.co.uk/books?hl=en&lr=&id=aQW6BQAAQBAJ&oi=fnd&pg=PR7&dq=proteopedia&ots=wUUkVg-lq0&sig=VMNqV-Gn_RLqUpdGsbBysVeGuck#v=onepage&q=proteopedia&f=false

https://www.learntechlib.org/p/48575/

https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20769

https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20436

https://link.springer.com/chapter/10.1007/978-3-319-03919-0_42

https://academic.oup.com/bioinformatics/article/26/17/2210/198818?login=true

https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa003/5735620?login=true

Journal home page for Journal of Molecular Biology Review Molecular Illustration in Research and Education: Past, Present, and Future☆ David S.Goodsell Jodie Jenkinson https://www.sciencedirect.com/science/article/abs/pii/S0022283618303693

https://arxiv.org/abs/1806.08332

https://www.lifescied.org/doi/full/10.1187/cbe.13-12-0247

https://pubs.acs.org/doi/abs/10.1021/bk-2019-1337.ch002


More general citations

Most of these contain interactive 3D complements (I3DC)

Biochemistry and Molecular Biology Student Design of a Proteopedia Page to Reinforce Foundational Biochemistry Concepts and Molecular Visualization Skills Bonnie L. Hall First published: 18 April 2020 https://doi.org/10.1096/fasebj.2020.34.s1.06861 https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.2020.34.s1.06861

Editorial Free Access Proteopedia and other exciting news Judith G. Voet Donald Voet First published: 13 September 2010 https://doi.org/10.1002/bmb.20445 Citations: 1 PDFPDF https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20445

https://febs.onlinelibrary.wiley.com/doi/full/10.1111/febs.14316

https://www.nature.com/articles/nrm2512

https://repositorium.sdum.uminho.pt/bitstream/1822/28581/1/herraez%20a_bmbed_2013%20posp.pdf

https://scripts.iucr.org/cgi-bin/paper?S0108767309099279

https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fasebj.24.1_supplement.908.1

http://bichez.pedf.cuni.cz/archiv/article/92

https://www.tandfonline.com/doi/full/10.1080/21553769.2012.689262

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.713782

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.718526

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.759885

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.745168

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.736773

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.758056

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.712459

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.726191

Teaching foundational topics and scientific skills in biochemistry within the conceptual framework of HIV protease R. Jeremy Johnson First published: 20 March 2014 https://doi.org/10.1002/bmb.20793 https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20793

https://scripts.iucr.org/cgi-bin/paper?rr5151

https://www.sciencedirect.com/science/article/abs/pii/S0009279719304570

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.736774

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.732340

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.712477

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.726532

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.737295

https://accessiblemeds.org/sites/default/files/2019-11/Sarah_Yim_GRxBiosims2019.pdf Slide uses image from insulin page

https://dspace.mit.edu/handle/1721.1/121878

https://www.tandfonline.com/doi/full/10.1080/07391102.2012.762722

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.721496

https://www.sciencedirect.com/science/article/abs/pii/S0167779917303074

https://www.sciencedirect.com/science/article/abs/pii/S0009279719304508

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.732343

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.721495

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.755134

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.726529

https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.712460

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https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.763216

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https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.680034

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https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.713781

https://books.google.co.uk/books?hl=en&lr=&id=yV61DwAAQBAJ&oi=fnd&pg=PP1&dq=proteopedia&ots=dOYoMOMeX6&sig=cEn0ICj6eDWxai4l1sl5m2xv5Io

https://pubs.acs.org/doi/abs/10.1021/acs.jchemed.8b00426

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Karsten Theis

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