World Index of BioMolecular Visualization Resources
Biochemical Structure Tutorials
Titles
Subjects
Authors:
Detailed
Compact
HOME
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Bergmann, Rolf
(www.biologie.uni-hamburg.de
)
- Highlights of biochemistry: molecular structures made visible.
Description
(English or German)
(Cross-indexing terms:
antibiotics; chloramphenicol acetyl transferase; concanavalin a; integration host factor; luciferase; lysozyme; nitrite reductase; proteasome; ribulose-1,5-bisphosphate carboxylase; rubisco; tobacco mosaic virus; TATA box binding protein; diphtheria toxin; hemolysin; cholera toxin; colicin; transport; porin; diffusion; ion channel; diabetes; jasmonic acid; hyperforin; Saint John's wort; sildenafil; fosmidomycin; malaria; toxoplasmosis; herbicide; IPA; Alzheimer's; bacterial photosynthesis; light harvesting complex; photosynthetic reaction center; Johanniskraut; glutamate receptor; actinomycin; archaeal rhodopsins; hydroxylamine oxidoreductase)
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Biochemistry and Molecular Biology, American Society of
(www.biomoleculesalive.org
)
- BioMoleculesAlive.Org
Description
(Cross-indexing terms:
ASBMB; curriculum resources for biochemistry)
-
-
Boon, Elizabeth
(www.clunet.edu
)
- Catalase (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
oxidoreductase; hydrogen peroxide)
-
-
Bragin, Victoria (Vicki)
(www.paccd.cc.ca.us
)
- Web-Based Chemical Investigations
Description
(Cross-indexing terms:
organic chemistry; Valence-Shell Electron-Pair Repulsion Theory (VSEPR); cycloalkanes; isomerism, constitutional; stereoisomerism; lesson plans)
- Introduction to Protein Structure, Part I
Description
(Cross-indexing terms:
structure, protein, primary, secondary; polypeptide; sidechain; peptide bond; alpha-helix; ribbon; beta pleats; primary structure; secondary structure; tertiary structure; quaternary structure; hemoglobin; myoglobin)
- The 20 common amino acids
Description
(Cross-indexing terms:
amino acids and properties)
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Bruist, Michael
(tonga.usip.edu
)
- B-Form Deoxyribonucleic Acid (DNA)
Description
(Cross-indexing terms:
deoxyribonucleic acid,
DNA,
major groove,
minor groove)
- DNA Polymerase I from Thermus aquaticus
Description
(Cross-indexing terms:
DNA polymerase; primer; template; polymerization mechanism; exonuclease; DNA substrate; DNA polymerase tutorial; SN1 reaction; lesson plan)
- The Zinc Finger: A Protein Domain that Binds Specific DNA Sequences
Description
(Cross-indexing terms:
DNA binding protein; zinc finger; zif268; protein secondary structure; lesson plans)
- Exploring Glyceraldehyde-3-phosphate dehydrogenase
Description
(Cross-indexing terms:
glyceraldehyde-3-phosphate dehydrogenase; NAD+ binding; glyceraldehyde-phosphate binding; quaternary structure)
- Magnesium Adenosine Triphosphate (MgATP) Binding to an Enzyme
Description
(Cross-indexing terms:
dethiobiotin synthetase; Mg-ATP binding; substrate binding; hydrogen bonding; hydrophobic interactions; salt-briges)
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Cachau, Raul E.
(www.umass.edu
)
- Thermal motion of alpha helix
Description
(Cross-indexing terms:
XYZ format animation; animation with XYZ files)
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-
Caras, James
(www.harcourtcollege.com
)
- Garrett and Grisham Interactive Biochemistry Structure Tutorials
Description
(Cross-indexing terms:
nucleic acids; albumin, serum; myoglobin; MHC class I; secondary structure)
-
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Carney, Jessica
(www.clunet.edu
)
- MutH (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
mismatch repair; DNA repair; DNA methylation; MutH; MutS; MutL; endonuclease MutH; restiction enzyme, homolog MutH)
-
-
Carroll, Carla
(www.clunet.edu
)
- Nitrogen Regulatory Protein C (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
transcription factor; nitrogen metabolism; phosphorylation, protein; NtrC)
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Chem406 Class, Fall 1999, U Wisc-Eau Claire
(www.chem.uwec.edu
)
- Student Webpapers: The Structure-Function Relationships for the Enzymes in the Glycolytic and Lactate Fermentation Pathways.
Description
(Cross-indexing terms:
glycolysis; gluconeogenesis; lactate fermentation; Classroom use of Chime; lesson plan)
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Cox, Ricky
(campus.murraystate.edu
)
- Noncovalent Interactions in Proteins
Description
(Cross-indexing terms:
noncovalent interactions in proteins; ligand-protein complexes; pi-orbital interactions; cation-pi interactions; aromatic sidechains: face-to-face, side-to-face, face-to-cation; salt bridges)
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Craig, Paul
(bioeditor.sdsc.edu
)
- Zinc Binuclear Clusters
Description
(Cross-indexing terms:
transcription activator; zinc finger; BioEditor)
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Dallakyan, Sargis
(mgltools.scripps.edu
)
- Molecular Electrostatics with PMV
Description
(Cross-indexing terms:
Molecular Electrostatics; Poisson Boltzmann; APBS)
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Decatur, Wayne
(www-unix.oit.umass.edu
)
- Large Ribosomal Subunit Tour for Specialists
Description
(Cross-indexing terms:
ribosome, large subunit for specialists; RNA, ribosomal; rRNA; translation; ribozyme)
- Ribosome Tour
Description
(Cross-indexing terms:
RNA, ribosomal; translation; peptide bond synthesis; tRNA; mRNA; 30S ribosomal subunit; 70S Ribosome architecture; 50S ribosomal subunit)
- Large Ribosomal Subunit Tour
Description
(Cross-indexing terms:
ribosome, large subunit; translation; ribozyme; rRNA; peptide bond synthesis; RNA, ribosomal; 50S ribosomal subunit)
- RNA Silencing Suppression by a Plant Viral Protein: Structural Basis
Description
(Cross-indexing terms:
RNA; p19; plant; viruses; sirna; rna silencing; rna interference; RNAi; carnation italian ringspot virus; tombusviruses; ring spot virus; suppressor; mirna; tomato bushy stunt virus)
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Douglass, Ben
(www.clunet.edu
)
- HhaI DNA Methyltransferase (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
DNA methylation; methyltransferases; DNA binding; DNA modification)
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Driscoll, Timothy
(www.worthpublishers.com
)
- Protein Architecture at Biochemistry in 3D
Description
(Cross-indexing terms:
amino acids; peptide bond; secondary structure; tertiary structure; supersecondary motifs; domains, protein; quaternary structure; Lehninger's Principles of Biochemistry)
- Lac Repressor: Biochemistry in 3D
Description
(Cross-indexing terms:
transcription; lac repressor; lacR; transcriptional regulation; gene regulation in bacteria)
- GFP (Green Fluorescent Protein)
Description
(Cross-indexing terms:
GFP; Aequoria victoria; beta barrel; fluorescence; chromophore; green fluorescent protein)
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Engen, John R
(www.embl-heidelberg.de
)
- Explore the c-Src tyrosine kinase
Description
(Cross-indexing terms:
tyrosine kinase; kinase, tyrosine; src-family)
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Flammer, Kristin
(www.clunet.edu
)
- Porin Proteins (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
OMPF; Maltoporin; LamB Porin; Porins; lambda receptor)
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Fries, David
(www.clunet.edu
)
- DNA Polymerase Beta (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
polB; polymerase, DNA)
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Garrett, R. H.
(www.harcourtcollege.com
)
- Garrett & Grisham Interactive Biochemistry
Description
(Cross-indexing terms:
albumin; secondary structure; myoglobin; major histocompatibility class I; nucleic acids)
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Gasser, Charles
(www.mcb.ucdavis.edu
)
- Molecules and Structures Homepage
Description
(Cross-indexing terms:
amino acid; disulfide bond; nucleosome; TATA-binding protein; transcription factor; Glucocorticoid receptor; GCN4; Engrailed; Gal4; Lambda Repressor; TFIIIA; MAD; MyoD; Zif; NFAT; Fos; Jun; NFKappaB; Serum Response Factor (SRF); MADS box; SP1)
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Gibson, Andrew
(www.bi.umist.ac.uk
)
- Protein/DNA interactions
Description
(Cross-indexing terms:
434 repressor; trp repressor; Met J repressor; zinc fingers; leucine zippers; EcoRI)
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Gille, Christoph
(www.charite.de
)
- Structural Alignment Program for Proteins
Description
(Cross-indexing terms:
alignment; protein superposition; pymol; jmol; rasmol; vmd; mutations; residue annotation; java; multiple structure alignment)
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Glaser, Fabian
(consurf.tau.ac.il
)
- ConSurf Server for the Identification of Functional Regions in Proteins by Surface Mapping of Phylogenetic Information
Description
(Cross-indexing terms:
mutation; evolution; conservation; multiple sequence alignment coloring of a protein; hypervariable residues)
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Glover III, Claiborne
(bmbiris.bmb.uga.edu
)
- Protein Kinase CKII
Description
(Cross-indexing terms:
casein kinase II; protein kinase; phosphorylation; kinase, protein)
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Goldman, Matthew
(www.clunet.edu
)
- HIV-1 Reverse Transcriptase (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
reverse transcriptase and non-nucleoside inhibitors thereof; retrovirus; azt)
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Gopalan, Vivek
(surya.bic.nus.edu.sg
)
- XdomView: A Chime-based Graphical Tool for Protein Domain and Exon Position Visualization
Description
(Cross-indexing terms:
domain; CATH; SCOP; DALI; FSSP; MMDB; NCBI; ExInt; BLAST; intron; NUS; Singapore; protein; PDB; structural domain; gene; gene evolution; intron evolution; strucuture; 3DEE; exon; intron)
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Gorga, Frank
(webhost.bridgew.edu
)
- Introduction to Protein Structure
Description
(Cross-indexing terms:
protein structure; peptide structure; amino acid chemistry; primary structure; secondary structure; tertiary structure; quarternary structure; alpha helix; beta sheet)
- Ras Oncogene Product
Description
(Cross-indexing terms:
oncogene product, ras; conformational changes in ras oncogene product; G protein, low molecular weight; p21; guanine nucleotide binding protein)
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Hansson, Orjan
(www.bcbp.gu.se
)
- Biomolecular Structures
Description
(Cross-indexing terms:
amino acids; peptides; basic biochemistry for undergrads; protein structure; nucleotides; DNA; RNA; lesson plan)
- Redox Proteins
Description
(Cross-indexing terms:
cytochromes; iron-sulfur proteins; copper proteins; lesson plan)
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Harrison, Karl (editor)
(www.chem.ox.ac.uk
)
- Molecule of the Month/Oxford University
-
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Heerssen, Heather
(www.clunet.edu
)
- RecA Protein (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
DNA recombination; SOS response; LexA protease; DNA, single stranded; DNA; Holliday Junction; DNA recombination)
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Herraez, Angel
(biomodel.uah.es
)
- Biomodel - in English
Description
(Cross-indexing terms:
amino acids; peptides; proteins; alpha-helix; beta-sheet; hemoglobin; DNA; RNA; bilayer, lipid; lipid bilayer; gramicidin channel; water; Jmol)
- DNA Structure (with Jmol)
Description
(Cross-indexing terms:
GC base pair; AT base pair; hydrogen bonding, Watson-Crick; Watson-Crick base pairing and hydrogen bonding; double helix, DNA; Jmol)
- Lipid Bilayers and the Gramicidin Channel (Jmol version)
Description
(Cross-indexing terms:
gramicidin channel in lipid bilayer; cholesterol; phosphatidyl choline; bilayer, lipid; phospholipid bilayers; Jmol)
- 3D Periodic Table of Radii (using Jmol)
Description
(Cross-indexing terms:
periodic table of the elements; elements, periodic table of; atomic radii; trends, periodic, in atomic and ionic sizes; van der Waals; Jmol)
- Water Simulation - using Jmol
Description
(Cross-indexing terms:
theoretical simulation of water; simulation, theoretical, water; lesson plan; Jmol)
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Honegger, Annemarie
(www.biochem.unizh.ch
)
- AHo's Amazing Atlas of Antibody Structure
Description
(Cross-indexing terms:
antibody; antibodies; multiple sequence alignment; sequence variability; homology modelling; immunoglobulin; domains; color-coded multiple sequence alignment)
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Howard, Vince
(www.kent.wednet.edu
)
- Hemoglobin-S Polymerization Binding Site
Description
(Cross-indexing terms:
hemoglobin; sickle cell anemia, point mutation; high school audience)
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Jakubowski, Henry
(employees.csbsju.edu
)
- Chime and Jmol Files
Description
(Cross-indexing terms:
student work; chime; jmol)
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Kahn, Kalju
(www.chem.ucsb.edu
)
- Macromolecular Visualization Laboratory Exercise
Description
(Cross-indexing terms:
DNA; transfer RNA; HIV protease; tRNA synthetase; rhinovirus; lesson plan; SYBYL; RasMol; SGI workstations)
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-
Klevickis, Cindy
(www.isat.jmu.edu
)
- Molecular Visualization Resources for Project VISM
Description
(Cross-indexing terms:
Bowen's Reaction Series; small molecules; micromolecules; lesson plans; K-12 education)
- Course Home Page for "Computer Applications in Biotechnology"
Description
(Cross-indexing terms:
NMR; amino acids; animated gifs; spermine; nucleotides; student-authored tutorials)
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Krieger, Elmar
(www.yasara.org
)
- Accessible, molecular and Van der Waals surfaces explained
Description
(Cross-indexing terms:
surfaces; solvent accessible surface; molecular surface; van der Waals surface; YASARA)
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Kysela, David
(www.clunet.edu
)
- DNA Topoisomerase I (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
topoisomerase, type I; DNA supercoiling; DNA unwinding)
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Lawson, Cathy
(rutchem.rutgers.edu
)
- The E. coli trp Repressor Chime Movie
Description
(Cross-indexing terms:
trp repressor; trpR; repressor; trp operator; operator; DNA binding protein; ligand activation; tryptophan)
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Mana, Miyeko
(www.clunet.edu
)
- HIV-1 Protease (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
viral protease; retroviral protease; protease, HIV-1)
-
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Marcey, David
(www.clunet.edu
)
- Online Macromolecular Museum
Description
(Cross-indexing terms:
Amino Acid Structures; Protein Structure and Chemical Bonds; DNA Structure; Protein Secondary Structure; Extracellular Matrix Components; Fibronectin; HhaI DNA Methylase; Methylase, DNA; Hin Recombinase; Recombinase; HIV-1 Integrase; HIV-1 Protease; RecA (E. coli); Topoisomerase I; polymerases, DNA; DNA polymerases; HIV Reverse Transcriptase; Reverse Transcriptase, HIV; Phage T7 DNA Replication Complex; Eukaryotic DNA Polymerase Beta; Proliferating cell nuclear antigen (PCNA); Antibody Recognition of Antigen; Immunoglobulin Structure; Viral Antigens; E. coli Porins: OMPF and Maltoporin (LamB); Porins; Catalase; Spliceosomal Protein-RNA Interactions, U1A; Signal Recognition Particle Core (E. coli); Protein Tyrosine Phosphatase; Nitrogen Regulatory Protein; MutS DNA Mismatch Repair Protein; BamHI endonuclease; Tryptophan Repressor; cro repressor; lambda repressor)
- Chemical Bonds and Protein Structure (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
chymotrypsin; hydrogen bonds; ionic bonds; salt bridges; hydrophobic bonds; noncovalent bonds; Van der Waals forces)
- DNA Polymerase III-Beta Subunit (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
DNA polymerase; Sliding DNA clamp; processivity subunit)
- U1A Spliceosomal Protein (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
RNA splicing; Splicesomal Protein; snRNP)
- Signal Recognition Particle Core (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
signal recognition; protein targeting; SRP)
- Antibody Recognition of Antigen (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
hypervariable regions, immunoglobulin; immunoglogulin binding; complementarity-determining regions; CDRs)
- Immunoglobulin Structure (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
antibody structure; immunoglobulin fold)
- Cro Repressor of Temperate Bacteriophages (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
bacteriophage cro; bacteriophage repressor; operator DNA; transcription regulation; genetic switch)
- Erythropoietin - EPO Receptor Complex (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
EPO; Erythropoietin; receptor binding; cytokine)
- DNA Conformers (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
DNA Structure; A-DNA; B-DNA; Z-DNA)
- DNA Structure (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
B-DNA; DNA structure; major groove; minor groove; nucleotide; phosphodiester linkage; antiparallel strands)
-
-
Martz, Eric
(www.umass.edu
)
- DNA Structure
Description
(English, German, Portuguese, Spanish)
(Cross-indexing terms:
GC base pair; AT base pair; hydrogen bonding, Watson-Crick; Watson-Crick base pairing and hydrogen bonding; double helix, DNA)
- Hemoglobin
- Antibody
Description
(Cross-indexing terms:
immunoglobulin and Ig domains; IgG; epitope structure, lysozyme bound to antibody; disulfide bonds in immunoglobulin; complementarity-determining regions in antibody; glycosylation of antibody, N-linked; lesson plan, antibody)
- Major Histocompatibility Complex
Description
(Cross-indexing terms:
MHC classes I and II; virus peptides, binding to MHC; epitopes, T-cell; H-2 (mouse MHC); HLA (human MHC); lesson plan, MHC)
- Amino Acid Quizzer
Description
(Cross-indexing terms:
quizzer, amino acid; lesson plan, amino acid quizzer)
- Protein Explorer for Novices
Description
(Cross-indexing terms:
RasMol-like exploration; Chime made easy to use; QuickViews and FirstView; Explorer, Protein; Sequence, clickable, mapping to structure; Seq3D)
- Protein Explorer, Advanced
Description
(Cross-indexing terms:
Advanced Protein Explorer; Noncovalent Bond Finder; Multiple protein sequence alignment coloring; MSA3D; Contact surfaces; NMR ensembles played as movie)
- PDB Lite
Description
(Cross-indexing terms:
Searching for molecules; Molecules, finding)
- Morpher, Protein
Description
(Cross-indexing terms:
recoverin, morph; conformational changes, morphs; EF-hand, morph; calmodulin, morphs; influenza hemagglutinin, morph; integrin CD11b MIDAS domain, morph; cAMP kinase, morph; calcium binding to an EF-hand, morph)
- NonCovalent Bond Finder (NCBF)
Description
(Cross-indexing terms:
hydrogen bonds, finding; hydrophobic interactions, finding; van der Waals interactions, finding; salt bridges, finding)
- Lipid Bilayers and the Gramicidin Channel (Chime version)
Description
(Cross-indexing terms:
gramicidin channel in lipid bilayer; cholesterol; phosphatidyl choline; bilayer, lipid; phospholipid bilayers)
- How to Create New Chime Tutorials
Description
(Cross-indexing terms:
scripting methods in Chime; Chime methods and tools; authoring new Chime websites, methods; methods for constructing new Chime websites and scripts)
- Water Simulation
Description
(Cross-indexing terms:
theoretical simulation of water; simulation, theoretical, water; lesson plan; Chime)
- MolviZ.Org
- Lac repressor bending DNA operon
Description
(Cross-indexing terms:
bending of DNA; animations; Chime; lesson plan)
- Flagellar Hook, Bacterial -- A Molecular Universal Joint
Description
(Cross-indexing terms:
hook, flagellar; universal joint, molecular: flagellar hook)
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May, Paul (editor)
(www.bris.ac.uk
)
- Molecule of the Month/University of Bristol
Description
(Cross-indexing terms:
Cisplatin; Thalidomide; Histrionicotoxin; Chlorophyll; Melatonin; cis-g-Irone; Frankincense; Boswellic Acid; DNA; Tamoxifen; Tetrodotoxin; Psilocybin; Mescaline; Anatoxin; Salbutamol; Zyban; Bupropion; Nitrous oxide; Adrenaline; Staurosporine; Ptaquiloside; Sarin, cubane; LSD; Polythiophene; Ferritin; Saxitoxin; Water; Formaldehyde; Finasteride; Mustard Gas; Proline; MCM-41; Ozone; Sulfanilamide; Adenosine Triphosphate; ATP; ChemSymphony)
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Mazur, Eric
(www.clunet.edu
)
- Viral Antigens (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
HIV gp120; influenza hemagglutinin; flu virus; hemagglutinin, influenza)
-
-
McClure, Will
(www.bio.cmu.edu
)
- Estrogen Receptor Structures & Function
Description
(Cross-indexing terms:
nuclear hormone receptor; transcription activation)
- 70S Ribosome Architecture
Description
(Cross-indexing terms:
30S ribosomal subunit; 50s ribosomal subunit; protein synthesis; ribosome structure and translation; translation (animation) and ribosome structure; animation of translation in the ribosome)
-
-
McClure, William
(www.bio.cmu.edu
)
- Molecules for Modern/Cell Biology
Description
(Cross-indexing terms:
Elements; H2O cluster; Functional Groups; Enantiomers of glyceraldehyde; Fats: Glycerol & Fatty Acids; Phospholipid; Membranes; Bacteriorhodopsin: A membrane-spanning protein; Cholesterol; Sucrose -> Fructose & Glucose; Amino Acids & Peptides; a-Helix & b-Sheet in a Small Protein; Lysozyme & substrate; Hemoglobin; Nucleotides: A, C, G, T, & U; DNA & RNA; ATP; NAD+; CAP (cAMP binding protein) & DNA; cAMP)
- Side-by-Side Amino Acid Viewer
Description
(Cross-indexing terms:
amino acids, all 20; Met-enkephalin; oxytocin; peptides and peptide bond)
- Protein Structures List
Description
(Cross-indexing terms:
Rubredoxin (1caa.pdb), a small protein consisting mostly of b-meanders; Prealbumin (1eta.pdb), (a.k.a. transerythrin), an antiparallel b-barrel; Triose Phosphate Isomerase (1ypi.pdb), a parallel b-barrel with alternating bab motifs; Collagen (1a89.pdb), a theoretical model of the triple helix; a-lactalbumin (1b90.pdb), a human plasma transport protein; Myoglobin (oxy) (1mbo.pdb), a monomeric O2 carrier; Hemoglobin (oxy) (1hho.pdb), the red blood cell O2 carrier; Hemoglobin(deoxy) (1b86.pdb), with bound 2,3-bisphosphoglycerate (BPG); Tropomyosin (2tma.pdb), a fibrous coiled-coil protein; Rop Protein Dimer (1rop.pdb), a globular coiled-coil protein; Immunoglobulin G (Igg.pdb), an all-b antibody protein; Concanavalin A (2cna.pdb), an antiparallel b-barrel; Pyruvate Kinase (1pkn.pdb), a multi-domain protein with three discrete b-structures; Lactate Dehydrogenase (1ldm.pdb), a two-domain protein with a nucleotide-binding motif; Silk Protein (2slk.pdb), a theoretical model of the fibrous b-sheet protein; Bacteriorhodopsin (Br.pdb), a light-driven proton pump; K+-Channel (1bl8.pdb), an ion-selective pore; Maltoporin (2mpr.pdb), a trimeric sugar transporter in bacteria; Hemolysin (7ahl.pdb), a heptameric channel-forming toxin; Photosynthetic Reaction Center (1qov.pdb), the bacterial electron pumping complex)
- Protein G Structure Tutorial
Description
(Cross-indexing terms:
Protein G (1pgb.pdb), crystal structure; Protein G (2gb1.pdb), NMR structure)
- Signal Recognition Particle
Description
(Cross-indexing terms:
SRP, the E. coli signal recognition particle, (1dul.pdb); E. coli Ffh protein: the protein subunit without RNA (2ffh.pdb); Domain IV RNA Structure (1cq5.pdb).)
- Bacteriorhodopsin
Description
(Cross-indexing terms:
bacteriorhodopsin (1brx.pdb))
- Overviews of DNA & RNA Structure
Description
(Cross-indexing terms:
DNA (1bna.pdb); RNA (RNA.pdb))
- Images of Glycolysis Intermediates
- Structures for Molecular Biology
Description
(Cross-indexing terms:
B-Form DNA helix; A-Form RNA helix; cAMP Receptor Protein (CRP); Yeast GAL4 Protein; Human hnRNP A1; snRNP U1A; EF-Tu, tRNAPhe, and GTP; Zif268 zinc finger; EcoRI Res. Endonuclease; HhaI Res. Methylase; Nucleosome)
- Amino Acid Identification Quiz
Description
(Cross-indexing terms:
lesson plan; quiz; amino acids)
- Nucleotide Identification Quiz
Description
(Cross-indexing terms:
lesson plan; quiz; nucleotides)
- Images of TCA Cycle Intermediates
Description
(Cross-indexing terms:
Tricarboxylic acid cycle; Citric acid cycle; Kreb's cycle)
- tRNA Tour
- Molecular Models for Biochemistry at CMU
Description
(Cross-indexing terms:
lesson plan; tutorials on molecular structures; quizzes using Chime displays and GIF images; links to other sites with graphics displays related to biochemistry)
- Chime 2 Tutorial
- Membrane Channel & Pump Structures
Description
(Cross-indexing terms:
KcsA K+ Channel (1k4c.pdb); MthK K+ Channel (1lnq.pdb); KvAP, a Voltage-Gated K+ Channel (1orq.pdb, 1ors.pdb); KirBac1.1 K+ Channel (1p7b.pdb); EcClC Chloride Channel (1ots.pdb, 1otu.pdb); E. coli Glycerol Channel (1fx8.pdb, 1ldi.pdb); AQP1 Aquaporin Channel (1j4n.pdb); MscS, Mechanosensitve Small Conductance Channel (1mxm.pdb); MscL, Mechanosensitve Large Conductance Channel (1msl.pdb); Ionophores: Gramicidin & Valinomycin; SERCA1 Ca2+ Pump (1eul.pdb, 1iwo.pdb); Bacteriorhodopsin (1c3w.pdb, 1dze.pdb))
- Amino Acid Structure Quiz
Description
(Cross-indexing terms:
quiz, amino acid structure; lesson plan)
-
-
McCool, Gabriel J.
(www.umass.edu
)
- FtsZ, a prokaryotic cell-division protein and tubulin homologue.
Description
(Cross-indexing terms:
tubulin; Presentation in Protein Explorer (PIPE - prototype); GTP-binding protein FtsZ)
-
-
McGill, Gael
(molecularmovies.org
)
- Molecular Movies - A Portal to Cell and Molecular Animation
Description
(Cross-indexing terms:
dicer; RNA cleavage by dicer; selectins; spectrin; actin polymerization and depolymerization; tubulin polymerization and depolymerization; integrin activation and ICAM binding; kinesin mechanism; myosin mechanism; nucleosome assembly; chromatin packing and condensation; ATP synthesis and hydrolysis; transcription; translation; gp41-mediated membrane fusion; transcription; translation)
-
-
MDL Information Systems, Inc.
(www.mdli.com
)
- Chime: Great Sites
Description
(Cross-indexing terms:
organic chemistry sites; molecules, sources of, organic (PDB files); links to Chime sites)
-
-
Millard, Elizabeth
(www.clunet.edu
)
- Hin Recombinase (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
DNA recombination; DNA binding; chromosome rearrangement; recombinase; gene expression)
-
-
Morgan, Eleanor
(wbiomed.curtin.edu.au
)
- Carboxypeptidase A - Three Exercises with Chime
Description
(Cross-indexing terms:
Carboxypeptidase; protein structure; enzyme active site; carboxypeptidase A; carboxypeptidase enzyme; active site; quiz question interface)
-
-
Morris, Robert
(www.chem.utoronto.ca
)
- The Guided Tours of Metalloproteins
Description
(Cross-indexing terms:
Metal Ion Transport And Storage; transferrin; Ferritin; Aconitase; Oxygen Transport and Storage; myoglobin; hemerythrin; hemocyanin; Non-redox Enzymes; Carbonic Anhydrase; Carboxypeptidase A; Electron Carriers; Cytochrome C; Rubredoxin; 2Fe-2S Ferredoxin; 3Fe-4S and 4Fe-4S Ferredoxin; Copper Blue; Rieske Protein; Redox Enzymes; Methane Monooxygenase; Nitrogenase; Hydrogenase; Cu-Zn Superoxide Dismutase; Dimethylsulfoxide Reductase)
-
-
Motyka, Eric
(www.umass.edu
)
- Infrared spectra, animations of vibrational modes
Description
(Cross-indexing terms:
animations of vibrations, infrared spectra; XYZ files used for infrared vibrations; vibrational modes, infrared spectra, animated)
-
-
Nelson, David
(drnelson.utmem.edu
)
- Cytochrome P450 3D structures page
Description
(Cross-indexing terms:
Cytochrome P450; P450cam; CYP2C5; CYP101; oxygen binding pocket; WXXXR motif; EXXR motif; PKG motif; PERF motif; C-helix; I-helix; K-helix; thiolate ligand)
-
-
Newman, Jeff
(srv2.lycoming.edu
)
- The Lycoming College Macromolecular Modeling and Bioinformatics Page
Description
(Cross-indexing terms:
HIV protease; Ribosomal small subunit; Adenosine Kinase; Dystrophin; G-protein Beta and Gamma subunits; DNA glycosylase; Clathrin; Fibronectin; Myosin; Insulin receptor; Dihydrofolate reductase)
-
-
Niederhoffer, Eric
(www.siu.edu
)
- Chime Square
Description
(Cross-indexing terms:
metabolism; glycolysis; gluconeogenesis; electron transport chain; oxidative stress; oxidative phosphorylation; nitrogenase; photosynthesis; dioxygen carriers; citric acid cycle; metalloproteins; nucleic acids; DNA; DNA-binding; transcription factors; leucine zippers; zinc fingers; repressors; activators)
-
-
Nixon, John
(www.scicom.demon.co.uk
)
- Rubisco: a first look at the mechanism. An experiment in molecular visualisation.
Description
(Cross-indexing terms:
access to the active site; beta-elimination; carbon fixation; carbamate; carboxylase; coordination at metal site; enzyme kinetics; genetic engineering; hyperthermophilic archaeon; mage; most abundant enzyme; oxygenase; photosynthesis; role of water as reactant; real time animation; Rubisco; RuBP as substrate; Schreudr.kin; slowest enzyme; stereoelectronic control; structure and mechanism; thermophilic red alga; timing of active site closure.)
-
-
Nolan, Jim
(www.tulane.edu
)
- Nucleic Acid Structure Tutorials
Description
(Cross-indexing terms:
DNA, A, B, and Z forms; RNA; DNA-protein interactions; RNA protein interactions; catalytic RNA; ribozymes; homeodomain proteins; tRNA; nucleosome)
-
-
Oberholser, Karl
(www.messiah.edu
)
- Molecular Science Lab
Description
(Cross-indexing terms:
myohemerythrin; BPTI; trypsinogen-BPTI; myoglobin; cytochrome bc1; mitochondrial respiratory chain complexes; globular proteins; fibrous proteins; ligand binding)
-
-
Palaga, Tanapat
(www.umass.edu
)
- Retinoid X Receptor, Human
Description
(Cross-indexing terms:
nuclear hormone receptor; presentations in Protein Explorer)
-
-
Pijning, T
(www.xray.chem.rug.nl
)
- Interactive Quercetin 2,3-Dioxygenase Presentation
Description
(Cross-indexing terms:
dioxygenase; copper; glycosylation; cupin; quercetin)
-
-
Pillot, Paul
(www.ac-orleans-tours.fr
)
- MolUSc - Molecules pour un Usage Scholaire
Description
(French)
(Cross-indexing terms:
protein explorer, simplified; surfaces; sequence to structure; comparison of 2 molecules; French)
-
-
Pons, Gabriel
(www.ub.es
)
- Apoptosis: molecular visualizations on caspases, bcl-2 family and Nf-kappa B
Description
(Spanish, English)
(Cross-indexing terms:
programmed cell death; caspases; bcl-2; NF-kappa B; Ik-B; IAP)
- Proteínas: aspectos estructurales básicos
Description
(Spanish)
(Cross-indexing terms:
protein structure; aminoacid; peptide bond; secondary structure; tertiary structure; domain; helix; sheet; jmol)
-
-
Rausch, Martin
(www.osa.s.bw.schule.de
)
- Chemie und Internet am Gymnasium
Description
(German)
(Cross-indexing terms:
Alkohole, Kohlenhydrate, Carbonsaeuren, Aminosaeuren, Eiweisse)
-
-
Reichsman, Frieda
(www.worthpublishers.com
)
- G Proteins (Trimeric): Molecular On/Off Switches, at Biochemistry in 3D
Description
(Cross-indexing terms:
Lehninger's Principles of Biochemistry; G proteins; GTP/GDP binding site and induced conformational changes; conformational changes in G proteins)
- Oxygen Binding Proteins: Myoglobin and Hemoglobin
Description
(Cross-indexing terms:
myoglobin; hemoglobin; 2,3-bisphosphoglycerate (BPG); sickle cell anemia)
- DNA Structure
Description
(English, Italian)
(Cross-indexing terms:
nucleic acids; double helix; base pairs; deoxyribose)
- Protein Secondary Structure, versions 1.0, 2.0, 3.0
Description
(Cross-indexing terms:
alpha helix; beta sheet; Protein G; protein architecture; hydrogen bonds)
- Major Histocompatibility Complex
Description
(Cross-indexing terms:
MHC proteins; immune system, MHC)
- Restriction Enzymes: Eco RV
Description
(Cross-indexing terms:
cloning; endonuclease; recombinant DNA technology; genetic engineering)
- Hammerhead Ribozyme
Description
(Cross-indexing terms:
RNA; RNA enzyme; stem-loop; nucleophilic substitution; ribozyme)
- BioMolecular Explorer 3D: Resources for High School Biology
Description
(Cross-indexing terms:
antibody; collagen; DNA; hemoglobin; HIV; protease; protease inhibitor; HIV-protease inhibitor; AIDS; lactase; lac repressor; lipid bilayers; myosin; nucleosome; water; high school; high school biology; lesson plan; Chime)
-
-
Rojas, Nina Rosario L.
(www.chem.admu.edu.ph
)
- Protein Structure Analysis Using Internet Tools: A Tutorial Using Peroxidase
Description
(Cross-indexing terms:
peroxidase; horseradish peroxidase; databases on-line)
-
-
Rzepa, Henry (editor)
(www.ch.ic.ac.uk
)
- Molecules of the Month/Imperial College
-
-
Sabo, John
(bioweb.ncsa.uiuc.edu
)
- Sickle Cell Anemia: Understanding the Molecular Biology
Description
(Cross-indexing terms:
mRNA; introns; exons; DNA; base pairing; amino acids; transcription; translation; mutations; stop codons; reading frames; hemoglobin; disease)
-
-
Sanz, Jesus M.
(cbmc.umh.es
)
- Estructura de Macromoleculas
Description
(Spanish)
(Cross-indexing terms:
General protein structure; General DNA structure)
-
-
Silva, Nathan
(www.clunet.edu
)
- BamHI Restriction Endonuclease (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
Type II restriction endonuclease; restriction enzymes; DNA-binding protein; DNA cleavage)
- Protein Tyrosine Phosphatase PTP1B (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
phosphorylation/dephosphorylation of proteins; tyrosine phosphatases)
-
-
Silva, Pedro
(www2.ufp.pt
)
- Animations on subjects of Structural and Metabolic Biochemistry
Description
(Cross-indexing terms:
alpha-helix; beta-sheet; oxyhemoglobin; deoxyhemoglobin; cytochrome c oxidase; succinate dehydrogenase; cytochrome bc1; respiratory chain complexers; electron transport chain)
-
-
Somple, Maggie
(www.clunet.edu
)
- HIV-1 Nef Protein (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
Nef; CD4 downregulation; SH3 domain interaction; retroviral Nef)
-
-
Sontum, Stephen
(alta1.middlebury.edu
)
- The Large Ribosomal Subunit: a structure/function tutorial
Description
(Cross-indexing terms:
protein synthesis; enzyme mechanism; translation; rRNA; tRNA; ribosome)
-
-
Stoffregen, Eric
(www.clunet.edu
)
- MutS DNA Repair Protein (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
mismatch repair; DNA repair; DNA methylation; DNA binding)
-
-
Students, Kenyon College
(www2.kenyon.edu
)
- Biomolecules at Kenyon College
Description
(English; CopG auf Deutch)
(Cross-indexing terms:
Tc3 transposase; NS3 protease; HIV-1 dimer; hemoglobin; CopG; Catabolite activator protein; tRNA synthetase; lac repressor; HIV reverse transcriptase)
-
-
Walsh, Matthew
(www.clunet.edu
)
- HIV-1 Integrase (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
DNA recombination; integrase; HIV-1; DNA binding)
-
-
Walters, D. Eric
(www.finchcms.edu
)
- Everything You Ever Wanted to Know about Sweeteners
Description
(Cross-indexing terms:
sweetener; acesulfame; aspartame; cyclamate; saccharin; sucralose)
- Structural Biochemistry of Blood Coagulation
Description
(Cross-indexing terms:
blood coagulation; tissue factor; factor II; factor III; factor VII; factor IX; factor XIII; von Willebrand factor; protein C; thrombin; hirudin; fibrin)
- The Rational Basis of Drug Design
Description
(Cross-indexing terms:
drug discovery; HIV; inhibitor, protease; protease inhibitor; HIV-protease inhibitor; saquinavir; indinavir; ritonavir; sildenafil; Viagra; structure-activity relationships)
-
-
Ward, Michael
(www.clunet.edu
)
- Fibronectin (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
extracellular matrix; integrin; RGD)
- DNA Polymerase of Bacteriophage T7 (at The Online Macromolecular Museum)
Description
(Cross-indexing terms:
Metal ion-induced catalysis)
-
-
Warren, L. Van
(www.wdv.com
)
- Isoprenoid Biosynthesis Pathway
Description
(Cross-indexing terms:
Acetyl-CoA; HMG-CoA; Mevalonate; pyrophosphate; Isopentenyl pyrophosphate; Geranyl pyrophosphate; Farnesyl pyrophosphate; Squalene; Lanosterol; Desmosterol; Cholesterol; Steroids)
- The Glycolytic Cycle
Description
(Cross-indexing terms:
glucose; hexokinase; ATP; ADP; phosphoglucoisomerase; phosphofructokinase; aldolase; glyceraldehyde-3-phosphate; phosphoglycerate kinase; 3-phosphoglycerate; phosphoglycerate mutase; 2-phosphoglycerate; enolase; 2-phosphoenolpyruvate; pyruvate kinase; pyruvate; lactate dehydrogenase; lactate)
-
-
Welte, Stefan
(www.welteweb.de
)
- SV40 capsid structure and assembly.
Description
(Cross-indexing terms:
Presentation in Protein Explorer (PIPE - prototype); VP1; virus capsid structure; icosahedral capsid structure)
-
-
Wherland, Scot
(www.wsu.edu
)
- 3D Periodic Table of Radii
Description
(Cross-indexing terms:
periodic table of the elements; elements, periodic table of; atomic radii; trends, periodic, in atomic and ionic sizes)
-
-
White, Brian
(intro.bio.umb.edu
)
- Hemoglobin I
Description
(Cross-indexing terms:
hemoglobin; side-chain interactions; conformational change)
- Hemoglobin II
Description
(Cross-indexing terms:
hemoglobin; sickle-cell anemia; mutant proteins)
- Alkaline phosphatase
Description
(Cross-indexing terms:
alkaline phosphatase; enzyme-substrate complex)
- Small Molecule Lab Exercise
Description
(Cross-indexing terms:
amino acid quizzer; lab exercise)
- DNA quizzer
Description
(Cross-indexing terms:
DNA sequence and quizzer; quizzer, DNA; lab exercise; lesson plan)
83 total first authors.
Visitor-Maintained Index
programming by Trevor D. Kramer.