Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online

Biochemistry Online: An Approach Based on Chemical Logic

Jsmol Files


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. Jsmol molecular modeling tutorials based on Javascript and HTML5 work best in Firefox and Safari.  They work worst in Internet Explorer.

Optimal Browsers: from Eric Martz at

System Browser JSmol (No Java) Jmol Java applet
Windows Internet Explorer (notes) Unworkably slow Good
Edge (notes) Very Slow Not Supported
Chrome (notes) Slow Not Supported
Firefox (notes) Best! Good
Opera (notes) Slow Good
Maxthon (notes) Slow Good
Mac OS X Chrome (notes) Slow Not Supported
Firefox (notes) Best! Good*
Safari (notes) Best! Good
Opera (notes) Slow Not Working
Maxthon (notes) Best! Not Supported


Tables:  Under construction as of 4/16

Chapter 1:  Lipids
Jsmol: BC Online PDB Protopedia First Glance Others
Newman projections ethane ChemTube 3D
Newman projection butane       ChemTube 3D
With Movie
di-18:0 PC   Link Link  
triacylglyceride   Link Link  
Micelle    Link Link  
Nonhydrated Bilayer   Link Link  
Human serum albumin complex with 18:0 1E7I Link Link  


Chapter 2  Protein Structure
Jsmol: BC Online PDB Protopedia First Glance Others
Amino Acids       OMM- Cal Lutheran
RhoA - a cytoplasmic protein - The complexity of protein analysis        
An isolated helix from an Antifreeze Protein        
Twisted beta sheet from Arabinose Binding Protein        
Beta barrrel from triose phosphate isomerase        
Reverse Turn: Trypsin Inhibitor        
A protein with a buried nonpolar amino acid         
 helix-loop-helix of the lambda Repressor        
helix-loop-helix (EF hand) from calmodulin        
beta-hairpin from bovine pancreatic trypsin inhibitor         
beta-helix-beta motif from triose phosphate isomerase        
cytochrome B562        
triose phosphate isomerase        


Chapter 2:  Protein Structure

Beta barrel from triose phosphate isomerase
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)

Updated   Prion Protein, Mad Cow Disease, and Mutations    Jmol14 (Java) |  JSMol  (HTML5)


Chapter 3:  Carbohydrates

Updated   β-D-glucopyranose    Jmol14 (Java) |  JSMol  (HTML5)
D Glucose
Acetal Formation
Updated  Peptidoglycan glycosyl transferase    Jmol14 (Java) |  JSMol  (HTML5)
N-linked Glycoprotein
Updated  Oseltamivir: Neuramindase N1 complex    Jmol14 (Java) |  JSMol  (HTML5)
Updated  P-Selectin Lectin/EGF Domains (IG1Q)    Jmol14 (Java) |  JSMol  (HTML5)


Chapter 4:  DNA, Genomics, and Proteomics

DNA Tutorial


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)


Chapter 6:  Transport and Kinetics

Updated Lactose Permease Jmol14 (Java) |  JSMol  (HTML5)
Updated  Glycerol-3-Phosphate Transporter From E. Coli Jmol14 (Java) |  JSMol  (HTML5)
Updated  Aquaporin Monomer Jmol14 (Java) |  JSMol  (HTML5)
Updated  Maltoporin Transport Protein Jmol14 (Java) |  JSMol  (HTML5)


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)
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) 
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       Calluthan A B Z DNA Jsmol
Comparison of ds DNA and Not updated Fix


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) 
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) 


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


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Creative Commons License
Biochemistry Online by Henry Jakubowski is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.