Biochemistry Online: An Approach Based on Chemical Logic
Jmol Files
12/18/2015
6/10/14 With a
few exceptions (which are bit difficult to convert), all of the Jmol files below
(except those designated as external which are out of my control) are updated to
Jmol 14 and JSMol. JSmol does not require the Java plugin and hence can be
viewed in any browser and on any device. Rotation and upload speeds are
slowed however when JSmol is used.
Updated Jmol14 (Java) | JSMol (HTML5)
The following information about the safe use of Java with Jmol comes from Proteopedia.
Jmol require Java. Jmol can be used, in any web page containing it, to report the version of Java currently installed: Click on Jmol, then on About Jmol. There are several free websites that report your java version, such as Java Tester. Java.Com also reports the java version on Windows: click on Do I Have Java?. Java has historically had flaws enabling criminals/vandals to commit identity theft and to compromise computers. Simply visiting a malicious website with a java-enabled web browser can compromise your computer.
How can you minimize your risk? Whenever an update for Java is available, install it. To confirm that you have the latest Java, visit java.com, click on the link "Do I have Java?" and then on the button "Verify Java". Do not visit unfamiliar websites. Especially do not click on unknown links or attachments in emails that you receive from sketchy senders. Also be careful when clicking links in google searches. Disable java in the web browser that you use for general-purpose browsing, email, google searches, etc. Here are instructions for disabling java in a particular browser. Use a different browser for resources that require Java. Windows users: Due to a limitation in Internet Explorer, you should use Internet Explorer for java. Use a different browser such as Firefox or Chrome for general web browsing, and disable java in that browser. Disabling java in Firefox is not really necessary. The browser will simply wait to start it until you request it to do so, which is safe to do for Jmol sites. These recommendations were made by Michael Horowitz in his Defensive Computing Blog in his January 2013 post How to be as safe as possible with Java.
The list below contains modeling tutorial files that are available from Biochemistry Online: An Approach Based on Chemical Logic. Some are links to outside files, but the majority have been created specifically for this course, some by students.
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Chapter 1: Lipid Structure |
| Updated di-18:0 PC Jmol14 (Java) | JSMol (HTML5) |
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Updated Triacylglyceride Jmol14 (Java) | JSMol (HTML5) |
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Updated Human serum albumin complex with 18:0 Jmol14 (Java) | JSMol (HTML5) |
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Chapter 2: Protein Structure |
 Amino Acids |
| Updated RhoA - a cytoplasmic protein - The complexity of protein analysis Jmol14 (Java) | JSMol (HTML5) |
| Updated An isolated helix from an Antifreeze Protein Jmol14 (Java) | JSMol (HTML5) |
| Updated Twisted beta sheet from Arabinose Binding Protein Jmol14 (Java) | JSMol (HTML5) |
| Beta barrel from triose phosphate isomerase |
| Updated Reverse Turn: Trypsin Inhibitor Jmol14 (Java) | JSMol (HTML5) |
| Updated A protein with a buried nonpolar amino acid Jmol14 (Java) | JSMol (HTML5) |
| Updated helix-loop-helix of the lambda Repressor Jmol14 (Java) | JSMol (HTML5) |
| Updated helix-loop-helix (EF hand) from calmodulin Jmol14 (Java) | JSMol (HTML5) |
| Updated beta-hairpin from bovine pancreatic trypsin inhibitor Jmol14 (Java) | JSMol (HTML5) |
| Updated beta-helix-beta motif from triose phosphate isomerase Jmol14 (Java) | JSMol (HTML5) |
| Updated cytochrome B562 Jmol14 (Java) | JSMol (HTML5) |
| Updated met-myoglobin Jmol14 (Java) | JSMol (HTML5) |
| Updated triose phosphate isomerase Jmol14 (Java) | JSMol (HTML5) |
| Updated hexokinase Jmol14 (Java) | JSMol (HTML5) |
| Updated superoxide dismutase Jmol14 (Java) | JSMol (HTML5) |
| Updated human IgG1 antibody Jmol14 (Java) | JSMol (HTML5) |
| Updated retinol binding protein Jmol14 (Java) | JSMol (HTML5) |
| Updated RNase A Jmol14 (Java) | JSMol (HTML5) |
| Updated Apolactalbumin (w/o Ca2+)/Hololactalbumin Jmol14 (Java) | JSMol (HTML5) |
| Updated Engrailed homeodomain - denatured and native state Jmol14 (Java) | JSMol (HTML5) |
| Updated GroEL/ES Jmol14 (Java) | JSMol (HTML5) |
| Updated Cyclophilin Jmol14 (Java) | JSMol (HTML5) |
| Updated SecYEB Protein Translocase Jmol14 (Java) | JSMol (HTML5) |
| Updated Top7 - A designed 93 amino acid protein with a novel fold Jmol14 (Java) | JSMol (HTML5) |
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Updated Prion Protein, Mad Cow Disease, and Mutations Jmol14 (Java) | JSMol (HTML5) |
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Chapter 3: Carbohydrates |
| Updated β-D-glucopyranose Jmol14 (Java) | JSMol (HTML5) |
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D
Glucose |
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Acetal Formation |
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Glycogen |
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Amylose |
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Amylopectin |
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cellulose |
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Heparin |
| Updated Peptidoglycan glycosyl transferase Jmol14 (Java) | JSMol (HTML5) |
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N-linked Glycoprotein |
| Updated Oseltamivir: Neuramindase N1 complex Jmol14 (Java) | JSMol (HTML5) |
| Updated P-Selectin Lectin/EGF Domains (IG1Q) Jmol14 (Java) | JSMol (HTML5) |
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Chapter 4: DNA, Genomics, and Proteomics |
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DNA Tutorial |
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Chapter 5: Binding |
| Updated Avidin:Biotin Complex (1AVD) Jmol14 (Java) | JSMol (HTML5) |
| Updated Cu(I) Form Of E. Coli Cuer, A Copper Efflux Regulator Jmol14 (Java) | JSMol (HTML5) |
| Updated deoxy-heme and carbon monoxide-heme Jmol14 (Java) | JSMol (HTML5) |
| Updated Met-Myoglobin Jmol14 (Java) | JSMol (HTML5) |
| Updated Symmetry in Protein Oligomers (beta version with lots of work left to do) Jmol14 (Java) | JSMol (HTML5) (button no show) |
| Unliganded gp120 core (HIV viral protein) FIX |
| Updated Parainfluenza Virus 5F Protein Jmol14 (Java) | JSMol (HTML5) |
| Updated Simple DNA Tutorial Jmol14 (Java) | JSMol (HTML5) |
| Updated TATA Box Binding Protein Jmol14 (Java) | JSMol (HTML5) |
| Updated RNA Polymerase II/DNA/RNA complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Auxin Receptor Jmol14 (Java) | JSMol (HTML5) Auxin Receptor |
| Updated Lambda Repressor: DNA complex | Jmol14 (Java) | JSMol (HTML5) |
| Updated Zif268:DNA Complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Leucine Zipper Jmol14 (Java) | JSMol (HTML5) |
| Updated Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA Jmol14 (Java) | JSMol (HTML5) |
| Updated Nucleosome Jmol14 (Java) | JSMol (HTML5) |
| dsRNA (still figuring out to convert to JSMol) |
| Updated Dicer Jmol14 (Java) | JSMol (HTML5) Dicer |
| Updated TLR3:dsRNA complex Jmol14 (Java) | JSMol (HTML5) Needs updating |
| Updated Nf-Kb(P50)2 Complexed To A High- Affinity RNA Aptamer Jmol14 (Java) | JSMol (HTML5) |
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Chapter 6: Transport and Kinetics |
| Updated Lactose Permease Jmol14 (Java) | JSMol (HTML5) |
| Updated Glycerol-3-Phosphate Transporter From E. Coli Jmol14 (Java) | JSMol (HTML5) |
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Valinomycin |
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Gramicidin |
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Aquaporin |
| Updated Aquaporin Monomer Jmol14 (Java) | JSMol (HTML5) |
| Updated Maltoporin Transport Protein Jmol14 (Java) | JSMol (HTML5) |
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Chapter 7: Catalysis |
| Updated Immunoglobulin 48G7 Germline Fab Antibody Complexed With Hapten 5-(Para-Nitrophenyl Phosphonate)-Pentanoic Acid Jmol14 (Java) JSMol (HTML5) |
| Updated Carboxypeptidase A Jmol14 (Java) | JSMol (HTML5) |
| Updated Chymotrypsin:D-Leu-L-Phe-p-fluorobenzylamde complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Chymotrypin-Phenylethylboronate Inhibitor Complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Comparison of Chymotrypin and Subtilisin Jmol14 (Java) | JSMol (HTML5) |
| Updated E. Coli GlpG rhomboid intramembrane protease Jmol14 (Java) | JSMol (HTML5) |
| Updated Mammalian Proteasome - (1IRU) Jmol14 (Java) | JSMol (HTML5) |
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THIAMIN
DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE (1pyd)
(go to left hand Display Molecule, choose Jmol viewer). |
| Updated Glyceraldehyde-3-phosphate dehydrogenase (NAD) Jmol14 (Java) | JSMol (HTML5) |
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Tyrosine
Aminotransferase Jmol (from PDB) |
| Updated Self-splicing Group I intron with both exons Jmol14 (Java) | JSMol (HTML5) |
| Updated L1 Ligase Ribozyme Jmol14 (Java) | JSMol (HTML5) Not done; Fix |
| Puckering in ribose and deoxyribose Not updated Fix |
| Comparison of ds DNA forms Not updated Fix |
| Comparison of ds DNA and Not updated Fix |
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Chapter 8: Oxidative Phosphorylation |
| Updated Adenine DNA glycosylase:8-oxyG DNA complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Flavin dehydrogenase Jmol14 (Java) | JSMol (HTML5) |
| Updated Estrogen Receptor:Tamoxifen Complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Cytochrome P450cam Jmol14 (Java) | JSMol (HTML5) |
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Cyclooxygenase
I and II |
| Updated Cytochrome C Oxidase Jmol14 (Java) | JSMol (HTML5) |
| Updated ATP Jmol14 (Java) | JSMol (HTML5) | ADP Jmol14 (Java) | JSMol (HTML5) |
| Updated Glyceraldehyde-3-phosphate dehydrogenase (NAD) Jmol14 (Java) | JSMol (HTML5) |
| Updated Cytochrome C Oxidase Jmol14 (Java) | JSMol (HTML5) |
| Updated Succinate Dehydrogenase (Complex II) Jmol14 (Java) | JSMol (HTML5) |
| Updated Light Harvesting Complex from Spinach 1RWT Jmol14 (Java) | JSMol (HTML5) |
| Updated Detailed Photosystem II from S. elongatus Jmol14 (Java) | JSMol (HTML5) |
| Updated Photosystem I: A Photosynthetic Reaction Center and Core Antenna System From Cyanobacteria 1JBO Jmol14 (Java) | JSMol (HTML5) |
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Chapter 9: Energy and Signal Transduction |
| Updated Bacteriorhodopsin Crystallized From Bicelles Jmol14 (Java) | JSMol (HTML5) | LMW-PTP isoform A |
| Updated EmrE multidrug resistance transporter Jmol14 (Java) | JSMol (HTML5) |
| Updated Acetylcholine Receptor Pore Jmol14 (Java) | JSMol (HTML5) (1OED) |
| Potassium Channel Not updated; Needs work |
| Updated Mammalian Voltage-Dependent Shaker Family Potassium Channel Jmol14 (Java) | JSMol (HTML5) |
| Updated Chloride Channel Jmol14 (Java) | JSMol (HTML5) |
| NEW Low molecular weight protein tyrosine phsophatase Jmol14 (Java) | JSMol (HTML5) |
| Updated Gs-alpha/adenylate cyclase complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Beta andrenergic receptor Jmol14 (Java) | JSMol (HTML5) |
| Updated Beta andrenergic receptor:Gs Complex Jmol14 (Java) | JSMol (HTML5) |
| Updated Melancortin 4 Receptor Jmol14 (Java) | JSMol (HTML5) |
| Updated AMP-dependent Protein Kinase (AMPK) Jmol14 (Java) | JSMol (HTML5) |
General Sites
General Jmol Sites