Biochemistry and Molecular Biology Program
Supported by
HHMI awards to Kenyon College
Molecules for Teaching
World Index of Molecular
Visualization Resources

Biomolecules at Kenyon: Chime Archive
See Jmol site (tutorials from 2005-present)

Alphabetized Index

Molecular Biology Tutorials

by students from BIOL 263: Molecular Biology and Genomics


C. elegans Tc3 Transposase HTH DNA-binding Motif
van Pouderoyen et al, 1997, Protein Data Bank
Updated  October 17, 2007
Please advise Joan Slonczewski of any corrections, and receive a free gift.


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For more recent Java-based tutorials (
Jmol) see current Biomolecules at Kenyon.
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These tutorials were created by students in collaboration with faculty at Kenyon. RasMol and Chime scripts were used to illustrate structural and chemical features of macromolecules; in some cases Jmol was used (preferred for future models).  The molecules and scripts are read by Chemscape Chime Files containing molecular information (*.pdb). The pdb files were downloaded from the Protein Data Bank of the Research Collaboratory for Structural Bioinformatics.   For each tutorial, the authors listed maintain copyright.

Chime Molecular Tutorials
Within each tutorial, click each link and cue button  , in the order in which they occur.

Index by molecule; by author

F-93: SSV1 DNA Binding Protein **Jmol**
Emilee Kaser '06 and Liz Narducci '05
Streptococcal Pyrogenic Exotoxin A1 **Jmol**
Joel Beckett '08 and Andy Boylan '08
Herpes Simplex Thymidine Kinase **Jmol**
Tim O'Neal '07 and Clayton Smith '07
Leptin-E100, the obese protein **Jmol**
Josephine Comas Bardot '08 and Ryan Ruffing '07
NF-kB p52 homodimer-DNA complex
Kyle Packer '08 and Josh Mitchell '08
Human Monoamine Oxidase B
Lara Cox '06 and Marissa Stearns '06
Human Cell Cycle Protein CksHs1
Karly Burke '06 Katelin Zaluski '06

C-reactive Protein
Jennifer Kao '07 and Melissa Martin '07
Hemagglutinin (HA) - Cell Binding Protein in Avian Influenza **Jmol**
Jack Cerchiara '06 and Brendan Holsberry '07
T4 Bacteriophage Cell-Puncturing Device **Jmol**
 Clint Priestley '03 and Matt Schefft '04
Pyrococcus furiosus Argonaute **Jmol**
Rebecca Schnitt '05 and Robert Northrup '05

Human Transcription Factor TBX3: T-Box Domain
Margaret Niehaus-Sauter '07

Tamoxifen, Diethylstilbesterol and Estrogen Receptor  **Jmol**
Sara Pecorak '04 and Tom Susman '04

Acetylcholinesterase with Inhibitor E2020
Mary E. Klecka '06 and Anne Harwood '06
HIV-1 reverse transcriptase **Jmol**
Oliver Benes '03, 

Rebecca Burke '03, Rebecca Palacios '03
Visual arrestin
Shana R. Scogin '07 and Jenna L. Rose '07
Diphtheria Toxin Protein
Paul Kaminsky '05 and Tim Rust '05
Erythropoietin **Jmol**
Diana Spahlinger '07 and Lisa King '07
Yersinia pestis Cytotoxin YopM
Daniel Goldberg '06 and Christopher Kerr '07

Glucocorticoid Receptor
Amy Aloe '06 and Marc Mergy '06

The core structure of gp41
Lauren Rand '06

fab192
Samantha L. Hudgins '05 & Amy Thurber '07
DJ-1 and Familial Parkinson's Disease
David Slochower '07 and Geetha Kannan '07
Prostaglandin H2 Synthase-1
Audrey Eisenberg '07 & Katie Wetzel '07
Human Endostatin Protein
Megan Marie Chambers '05
Dopamine Decarboxylase
Craig O'Neill '04 and John Paul Barringer '04
HIV Protease Complexed With A Tripeptide Inhibitor
Misty Kintzley '06 and Maggie Rosen '05
p53 protein-DNA complex
David Gold '04 and Dawn Sokolowski '04

Escherichia coli Serine Hydroxymethyltransferase
D. Michael Barnhart ‘04 and Dan Tate ‘06

The TGF-beta Receptor I
Cheyne Blair '03 and Nate Fergus '03
Nitrite Reductase
Uri Levine '03 and Ann E. Weinheimer '03
 Tumor Necrosis Factor Receptor, Factor 2
Andrew Koch '05 and Everett Hayes '05
Mutant Rat Trypsin
Andrew Worthington '03
RhoA: GTPase
Nell Burger '04 and Trey Smith '04
Myosin
Betsy Garratt '03 and Kate Holland '03
SRP9/14 Alu RNA Binding Heterodimer
Jon Keefe '03 and Kathy Lynd '04
Anthrax Protective Antigen and Lethal Factor *Jmol*
Ansley Scott '02 and Dawn Stancik '02
C. elegans Tc3 Transposase Protein.
Niki Watson '01 and Ashley Rowatt '03. Deutch
Phosphoglucose Isomerase
Briana Betz '03 and Lisa Maurer '04
HIV-1 Dimer Initiation Complex
Ann Palcisco '01 and Lauren Stancik '02. Deutch
Ebola Virus VP40 Matrix Protein
Neal Heilman '02 and Saber Khan '03
CopG Plasmid Regulator  Deutch.
John DePowell '02 and Timur Senguen '03
Influenza A Non-Structural Protein 1
Jeremy Lavine '04 and Tyler Perfect '03.
tRNA and seryl-tRNA synthetase
Michael Hapiak '99
Hepatitis C Virus NS3 Protease.   Deutch
 Catherine Beck '02 and Tanya Klimova '03
Catabolite Activator Protein in Escherichia coli **Jmol**
Marla Fiorelli '99
Hemoglobin
Lisa Natzke '98
Lac Repressor of Escherichia coli
Matt Glassman '99
Fibronectin
Michael Ward '99 and David Marcey
T7 DNA Polymerase 
Michael E. Ward '99 and David Marcey
Catalase
Elizabeth M. Boon '97, Aaron Downs '00, & David Marcey
HIV-I Reverse Transcriptase
Matthew Goldman'98
Porins of E. coli
Kristin Flammer '99, 
Aaron Downs '00, and David Marcey
HhaI DNA Methyltransferase
Ben Douglass '98, Aaron Downs'00 & David Marcey
Hin Recombinase
Elizabeth E. Millard '98, 

Aaron Downs '00, and David Marcey
Topoisomerase I
David Kysela and David Marcey