Mine the numerous Internet resources available to biochemists: Plugins Structures General Literature Medicine History Resources Fun Stuff By Chapter 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Molecular Graphics Home		Web Links This collection of Web Links was recognized as the"Best of Biochemistry" by Science Magazine, May 2000. Plugins: A number of the functionalities of this site depend upon the use of plugins for the web browser. Both the Shockwave Flash player (for animations) and the Chime program (for manipulation of molecules in three dimensions) provide the immersive experience that helps bring biochemistry to life. You can learn more about these programs by clicking on the following links. The Chime Support site http://www.mdli.com./support/chime/default.html Biochemical tutorials in Chime http://www.umass.edu/microbio/rasmol/tutbymol.htm#grisham A collection of Chime images http://info.bio.cmu.edu/Courses/BiochemMols/SelExMain.htm Flash: After you have installed Flash you may enjoy going here. http://www.shockwave.com/bin/shockwave/main/frame_set.jsp Some additional viewer links are: The Rasmol Home Page: Molecular visualization freeware. http://www.umass.edu/microbio/rasmol/ WebLab Viewer: Molecular simulation software. http://www.msi.com:80/weblab/ FoldIt: A freeware molecular modeling program for the Mac. http://www-timc.imag.fr/Jean-Claude.Jesior/ Cn3D: A helper application to view 3D structures from the Entrez retrieval service. http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.html Chemical Structures: Drugs Galore – in virtual reality http://www.chem.ox.ac.uk/mom/default.html The Klotho biochemical compound database http://www.ibc.wustl.edu/klotho/ Chemical structures and formulas from NIH http://ntp-db.niehs.nih.gov/Main_Pages/pub-Structures.html A collection of molecular models in PDB format http://www.sci.ouc.bc.ca/chem/molecule/molecule.html General Web Links: Links to Biochemical Literature Scientific American: Complete articles and more http://www.sciam.com/index.html J. Biol. Chem.: Home page of the Journal of Biological Chemistry http://www.jbc.org/ Nature Magazine: Home page of an important series of biochemistry journals http://www.nature.com/ Science Online: The weekly journal of the American Association for the Advancement of Science http://www.sciencemag.org/ Biochemical Journals listing: An extensive database of links to biochemical journals http://www.public.iastate.edu/~pedro/rt_journals.html A New Mode of Publishing Scientific papers http://www.scientificworld.com An online journal of undergraduate research http://www.jyi.org Medical Biochemistry Virus Surveillance http://www.nationalatlas.gov/virusmap.html BioMedNet: An Internet community for biological and medical researchers http://www.biomednet.com/ Medical Biochemistry: A link to the resources of the University of Kansas Medical Center http://www.kumc.edu/biochemistry/bioc800/start.html More medical biochemistry: From the Terre Haute Center for Medical Education http://web.indstate.edu:80/thcme/mwking/ Medical Biochemistry Review: From the Temple University School of Medicine http://www.temple.edu/medbiochem/medical_review.html NetBiochem: An extensive collection of topics in medical biochemistry http://www-medlib.med.utah.edu/NetBiochem/NetWelco.htm Communicable Disease Surveillance and Response: From the World Health Organization http://www.who.int/emc/index.html OMIM (Online Mendelian Inheritance in Man): Human genes and genetic disorders http://www.ncbi.nlm.nih.gov/Omim/ PubMed: The National Library of Science search service for Medline http://www.ncbi.nlm.nih.gov/PubMed/ Public Health and Hepatitis C http://www.cmc.sandia.gov/HEP_C Essays on the History of Biochemistry Profile of Oswald Avery http://www.profiles.nlm.nih.gov/CC/ An interview with James Watson http://www.accessexcellence.org/AB/CC/watson.html An interview with Francis Crick http://www.accessexcellence.org/AE/AEC/CC/crick.html Women in Science http://www.sdsc.edu/ScienceWomen/ Barbara McClintock Memorial http://www.nobel.se/medicine/laureates/1983/ Online Books, Quizzes, and General Biochemistry Resources Essays on the process of scientific discovery http://biocrs.biomed.brown.edu/Books/Essays/Essays.html Molecular Epidemiology: Health and the Human Genome Project http://www.pitt.edu/~super1/lecture/lec0131/001.htm An introduction to X-Ray Crystallography http://www-structure.llnl.gov/Xray/101index.html Multi-talented Database Searcher http://searchlight.cdlib.org/cgi-bin/searchlight Science Comes Alive Series: Images of biomolecules from the San Diego Supercomputer Center http://www.sdsc.edu/ScienceAlive/sciencealive.html Molecular biology links from Harvard University http://mcb.harvard.edu/BioLinks.html Discovery Channel Online http://www.discovery.com/online.html Biology Links: Internet resources in biology from the U.S. Geological Survey http://info.er.usgs.gov/network/science/biology/index.html Beyond Bio-101: A report from the Howard Hughes Medical Institute on undergraduate biology education http://www.hhmi.org/BeyondBio101/ Yahoo Science: Links, animations, databases, and more http://dir.yahoo.com/Science/Chemistry/Biochemistry/ World Lecture Hall: A collection of biochemistry resources from a number of U.S. universities http://www.utexas.edu/world/lecture/bch/ Virology on the World Wide Web http://www.tulane.edu/~dmsander/garryfavweb.html BioChemLinks: A large resource collection for biology and chemistry education http://biochemlinks.com/bclinks/bclinks.cfm Molecular Biology Protocols: From the Northwest Fisheries Sciences Center http://research.nwfsc.noaa.gov/protocols.html Biology Hypertextbook: A Web approach to cell and molecular biology from MIT http://esg-www.mit.edu:8001/esgbio/7001main.html Access Excellence: An extensive resource site for bioscience teachers and students http://www.accessexcellence.org/index.html The Biology Project http://www.biology.arizona.edu/default.html Molecular Biology Swiss-Quiz: An interactive site for answering questions from a database http://www.expasy.ch/swiss-quiz/ On-Line Biology Book: A full-featured text in general biology http://gened.emc.maricopa.edu/bio/bio181/BIOBK/BioBookTOC.html Biomolecular Self-Assembly: A major report on this area from the U.S. National Academy of Sciences http://www.nas.edu/bpa/reports/bmm/bmm.html#MembraneProteins Bioinformatics http://www.sciencemag.org/feature/data/biodiversity2000.shl How it is done in Molecular Biology - Protocols for almost everything http://www.protocol-online.net/ Gene/Protein Database Links http://www.expasy.ch/alinks.html Fun Stuff Olfaction – the smell of things http://www.leffingwell.com Virtual Dissection http://www.le.ac.uk/pathology/teach/VA Gel Science http://www.solgel.com/ Fun Science Links http://www.amasci.com Microbe Library http://www.microbelibrary.org/ An interactive listing of Undergraduate Research Projects http://www.firstmarket.com/fitzroy/ Weird Virology http://www.tulane.edu/~dmsander/WeirdVirology.html Weird Science http://www.tulane.edu/~dmsander/WeirdScience.html Textbook Chapter Web Links: Chapter 1: Biochemistry and Organization of Cells Problem sets and tutorials in molecular biology http://www.biology.arizona.edu/cell_bio/cell_bio.html Chemistry Hypermedia Project http://www.chem.vt.edu/chem-ed/vt-chem-ed.html Chapter 2: Water: The Solvent for Biochemical Reactions Water ionization http://learn.chem.vt.edu/tutorials/acidbase/waterion.html More on Water Ionization http://www.sbu.ac.uk/water/ionis.html Acids and bases – a slide presentation http://www.public.asu.edu/~jpbirk/chpt15/sld027.htm Acids and bases problem set http://www.biology.arizona.edu/biochemistry/problem_sets/ph/ph.htm Clinical corrlates of pH levels http://www.biology.arizona.edu/biochemistry/problem_sets/medph/medph.html Chapter 3: Amino Acids and Peptides A variety of properties of amino acids http://prowl.rockefeller.edu/aainfo/contents.htm Amino acids and peptide bonds http://www.iacr.bbsrc.ac.uk/notebook/courses/guide/aa.htm Amino Acid Repository http://www.imb-jena.de/IMAGE_AA.html General Amino Acid Information http://www.eng.uci.edu/~hslee/aminoacid.html Online quizz on amino acids http://info.bio.cmu.edu/Courses/BiochemMols/PQuiz/PQInst.html Chime structures of all the amino acids http://www.clunet.edu/BioDev/omm/aa/aa.htm Colorful photos of amino acids http://micro.magnet.fsu.edu/micro/gallery/aminoacid/aminoacid.html Green Fluorescent Protein http://www.biochem.missouri.edu/~lesa/LIPIDS/membrane_lipid.html Chapter 4: The Three Dimensional Structure of Proteins Strategies for Protein Purification: a virtual lab http://www.tlsu.leeds.ac.uk/courses/bioc2060/proteinlab102/proteinlab.html Protein Similarities http://www.sdsc.edu/GatherScatter/GSsummer96/bourne.html Proteomics Server of the Swiss Institute of Bioinformatics http://www.expasy.ch Strategies for Protein Sequencing http://esg-www.mit.edu:8001/esgbio/lm/proteins/sequencing/strategies.html Protomap: classifications of protein sequences http://www.protomap.cs.huji.ac.il/ Rapid prototyping of molecular models http://www.npaci.edu/online/v3.8/z402.html A database of pairwise aligned 3D structures http://cl.sdsc.edu/ce/ache.pdf Morphology of protein-protein interfaces http://www.scripps.edu/pub/goodsell/interface/ Optimal path method for 3D structure similarities http://cl.sdsc.edu/ce.html Alpha helix and beta pleated sheets http://www.bio.cmu.edu/Courses/BiochemMols/BuildBlocks/ProtG.html Protein architechture http://www.bio.cmu.edu/Courses/BiochemMols/ProtG/ProtGMain.htm X-Ray crystallography http://www.imb-jena.de/www_sbx/manfred/teach/page1.html Circular dichroism http://osu.orst.edu/dept/biochem/varselec.html Green Fluorescent Protein Chime Tutorial http://www.biochem.mcw.edu/science_ed/Pages/gfp/exercise_1/chime/index.htm Evolution of chaperones http://www.uni-erlangen.de/pharmakologie/arbeit/fitforli.htm Large molecule problem set http://www.biology.arizona.edu/biochemistry/problem_sets/large_molecules/large_molecules_problems.html Hyperactive molecules http://www.ch.ic.ac.uk/chemical_mime.html Hyperactive molecules - Part 2 http://www.ch.ic.ac.uk/hm_second.html Studying protein molecules with CHIME http://cti.itc.Virginia.EDU/~cmg/Demo/molecule.html Cell movement http://yakko.bme.virginia.edu/cm/cell_mov.html Actin molecular dynamics http://yakko.bme.virginia.edu/cm/test.html Molecular motors book http://www.portlandpress.co.uk/books/isbn/1855781034.htm Kinesin http://www.blocks.fhcrc.org/kinesin/ Molecular motors behaviour http://perso.curie.fr/Frank.Julicher/mmfitc/ Primer on Molecular Genetics; from the Dept. of Energy http://www.bis.med.jhmi.edu/Dan/DOE/intro.html Genetic Analysis Tools http://www.textco.com Muscle Structure http://ortho84-13.ucsd.edu/musintro/Jump.shtml Kinesin – with movies and links http://www.proweb.org/kinesin Chapter 5: The Behavior of Proteins: Enzymes Enzymes problem set http://www.biology.arizona.edu/biochemistry/problem_sets/energy_enzymes_catalysis/energy_enzymes_catalysis.html Enzyme kinetics book http://ir2lcb.cnrs-mrs.fr/~athel/fek.htm Model of enzyme kinetics http://dept.physics.upenn.edu/courses/gladney/mathphys/subsection4_1_6.html Lab tutorials for enzyme kinetics http://wunmr.wustl.edu/EduDev/LabTutorials/ Enzyme inhibition http://www.bio.mtu.edu/campbell/401lec13p1.html Hemoglobin http://www.bio.cmu.edu/Courses/BiochemMols/BuildBlocks/Hb.html Enzyme labs using Jello http://www.woodrow.org/teachers/bi/1991/enzymes.html Enzyme specificity http://tidepool.st.usm.edu/crswr/enzspecificity.html HIV and key enzymes http://www.sdsc.edu/GatherScatter/GSsummer96/larsen.html Lysozyme http://www.bio.cmu.edu/Courses/BiochemMols/BuildBlocks/lysozyme.html The Body - AIDS and Information Resource http://www.thebody.com/index.shtml Globin Genes http://globin.cse.psu.edu/ Enzymes http://www.ibis.sfu.ca/~rhlogan/enzymes.html More on enzymes http://pharmacy.drake.edu/faculty/L_henderson/Unit_2/Eoutline.html Biochemical Thermodynamics http://www.chem.qmw.ac.uk/iubmb/thermod/ Applying Thermodynamics to Biological Problems http://www.rensselaer.edu/dept/chem-eng/Biotech-Environ/THERMO/intro.html Oxidation/Reduction and Enzyme Catalysis http://www.rrz.uni-hamburg.de/biologie/b_online/e18/18.htm http://www.rrz.uni-hamburg.de/biologie/b_online/e18/18.htm Chapter 6: Lipids and Membranes PDB files of Lipids http://www.america-tomorrow.com/gmu/biochem/lipids.htm A Lipids Lecture Outline http://class.fst.ohio-state.edu/fst601/Lectures/LIPID.htm Lipids in 3D http://www.nyu.edu/pages/mathmol/library/lipids/ A Rasmol animation of membranes http://info.bio.cmu.edu/Courses/BiochemMols/BuildBlocks/Membrane.html Phospholipid Interaction in Sperm http://www.bioscience.org/1996/v1/d/martine1/htmls/103-117.htm Lipid bilayer membranes http://www.umass.edu/microbio/rasmol/bilayers.htm Membrane 3D model http://www.bio.cmu.edu/Courses/BiochemMols/BuildBlocks/Membrane.html Rasmol scripts for lipids and membranes http://www.umass.edu/microbio/rasmol/scrip_mz.htm#bil Phospholipids in cell membranes http://www.cbc.umn.edu/~mwd/cell_www/chapter2/membrane.htm Gap junctions http://www.sdsc.edu/journals/jmb/1998/perkins/ Ion Channel http://scv.bu.edu/SCV/vizgal/ion/ion.html Membrane transport mechnisms http://esg-www.mit.edu:8001/esgbio/cb/membranes/transport.html Membrane transport book http://www.oup-usa.org/docs/0195207734.html Membrane transport graphics http://www.wellesley.edu/Chemistry/chem227/lipids/transport.htm Lipid Bilayer in Motion http://pipeline.mhpcc.edu/research/ab96/ab19.html Rasmol and bilayers http://www.umass.edu/microbio/rasmol/bilayers.htm An essay on mitochondrial DNA http://biocrs.biomed.brown.edu/Books/Essays/MitochondrialDNA.html Algal Toxins http://www.redtide.whoi.edu/hab/default.html Shellfish Toxins http://grimwade.biochem.unimelb.edu.au/cone/index1.html Psychoactive drugs http://PDSP.cwru.edu/PDSP.asp How E.coli binds to Intestinal cells http://www.hhmi.org/news/finlay2.html Chapter 7: Nucleotides and Nucleic Acids Nucleotides in 3D http://www.nyu.edu/pages/mathmol/library/dna/ Overview of Nucleotides http://www.ultranet.com/~jkimball/BiologyPages/N/Nucleotides.html Survey of Nucleotides http://www.accessexcellence.com/AB/GG/nucleotides1.html Histones and Chromatins http://www.cstone.net/~jrb7q/chrom.html An introduction to X-Ray Crystallography http://www-structure.llnl.gov/Xray/101index.html Nucleotides in 3D http://www.nyu.edu/pages/mathmol/library/dna/ More nucleotides in 3D http://info.bio.cmu.edu/Courses/BiochemMols/BuildBlocks/Nucs.html Nucleotide structures http://esg-www.mit.edu:8001/esgbio/lm/nucleicacids/nucleicacids.html Telomeres http://www.genlink.wustl.edu/teldb/tel.html A superb animated primer on DNA, genes and heredity http://vector.cshl.org/dnaftb/ Profile of Oswald Avery http://www.profiles.nlm.nih.gov/CC/ An interview with James Watson http://www.accessexcellence.org/AB/CC/watson.html An interview with Francis Crick http://www.accessexcellence.org/AE/AEC/CC/crick.html Ooops! Left and Right Handed DNA http://www.lecb.ncifcrf.gov/~toms/LeftHanded.DNA.html Chapter 8: Biosynthesis of Nucleic Acids Part A: Replication DNA replication http://esg-www.mit.edu:8001/esgbio/dogma/repl.html Eukaryotic chromosome structure http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/eukarychrom/eukaryo2.htm Site listing for DNA replication http://dir.niehs.nih.gov/dirlmg/repl.html RuvA and Holliday junctions http://www.sdsc.edu/journals/mbb/ Hershey-Chase experiment http://www.accessexcellence.org/AB/GG/hershey.html Nucleic acids problem set http://www.biology.arizona.edu/molecular_bio/problem_sets/nucleic_acids/nucleic_acids_1.html Animated genetics primer http://vector.cshl.org/ DNA repair genes http://www.cancergenetics.org/dnafix.htm The RNA World Website http://www.imb-jena.de/RNA.html DNA Replication http://www.csuchico.edu/~jbell/Biol207/replication.html DNA Replication Enzymes http://www.biochem.ucl.ac.uk/bsm/xtal/teach/repl/klenow.html Helicase http://chem-mgriep2.unl.edu/replic/Helicase.html Part B:Transcription CAP Structure http://www.bio.cmu.edu/Courses/BiochemMols/BuildBlocks/CAP.html Transcription overview http://esg-www.mit.edu:8001/esgbio/dogma/trx.html From DNA to RNA http://www.res.bbsrc.ac.uk/molbio/guide/trans.html Regulation of Transcription http://ruummc.med.uu.nl/Research/Txpn.htm Transcription http://www.botany.utexas.edu/facstaff/facpages/ksata/ecpf96/11b/page2.htm RNA and Spliceosomes http://www.neuro.wustl.edu/neuromuscular/pathol/spliceosome.htm Chapter 9: Protein Synthesis: Translation of the Genetic Message The genetic code - universal http://psyche.uthct.edu/shaun/SBlack/geneticd.html Invention of the genetic code http://www.amsci.org/amsci/issues/Comsci98/compsci9801.html The code for various organisms http://prowl.rockefeller.edu/aainfo/gencode.html Mitochondrial genetic code http://www.gen.emory.edu/MITOMAP/human_mito_code.html Discovery of the genetic code - Marshall Nirenberg http://www.calstatela.edu/faculty/nthomas/nirenber.htm DNA, RNA and protein synthesis http://photoscience.la.asu.edu/photosyn/courses/BIO_343/lecture/DNA-RNA.html Protein synthesis: a review http://gened.emc.maricopa.edu/Bio/BIO181/BIOBK/BioBookPROTSYn.html Protein degradation http://www.biochem.emory.edu/protdeg/home.html An Overview of Translation http://wsrv.clas.virginia.edu/~rjh9u/trtrpict.html Ribosomes – a collection of experimental data http://www.smi.stanford.edu/projects/helix/riboweb/kb-pub.html Chapter 10: Nucleic Acid Biotechnology Techniques Cloning: Dolly Company Used Woman’s DNA http://news.bbc.co.uk/hi/english/uk/scotland/newsid_816000/816791.stm Goat/Sheep Hybrid http://news.bbc.co.uk/hi/english/sci/tech/newsid_813000/813466.stm Pig Clone to Human Transplant http://news.bbc.co.uk/hi/english/sci/tech/newsid_677000/677637.stm The human genome and eugenics http://www.pbs.org/wnet/innovation/show1/html/2sb-eugenics.html Recombinant DNA technology problem set http://www.biology.arizona.edu/molecular_bio/problem_sets/Recombinant_DNA_Technology/recombinant_dna.html NIH Office of Recombinant DNA Activities http://www.nih.gov/od/oba/ Protocols for Recombinant DNA http://www.genome.ou.edu/protocol_book/protocol_index.html Historical events in recombinant DNA http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/debate/debate3.htm A bacterial genetics and recombinant DNA quizz http://biog-101-104.bio.cornell.edu/BioG101_104/tutorials/recomb_DNA.html Compilation of Genome Articles from Science Magazine http://www.sciencemag.org/feature/data/genomes/landmark.shl Restriction Enzyme Database http://rebase.neb.com/rebase/rebase.html E. coli Genome http://www.genetics.wisc.edu Human Genome http://www.nhgri.nih.gov/HGP Yeast Genome http://genome-www.stanford.edu/saccharomyces/sequence_done.html Chapter 11: The Importance of Energy Changes and Electron Transfer in Metabolism Biochemical electrochemistry http://www.compusmart.ab.ca/plambeck/che/p265/p06263.htm Stochiometry and kinetics http://www.ae.iastate.edu/Ae573_ast475/Bioenergetics_Notes.htm Metabolic Overview –with links to DNA Sequences http://wit.mcs.anl.gov/WIT2 Chapter 12: Carbohydrates Cellobiohydrolase animations http://www.csc.fi/lul/chem/movies/cbh1/cbh1_movies.html World-wide links to carbohydrates http://www.public.iastate.edu/~pedro/carbhyd/carbhyd.html Carbohydrate practice problems http://www.cem.msu.edu/~cem252/sp97/ch18/ch18practice.html Carbohydrates in PDB format http://www.molvent.com/download/sugars2.html Sugars in 3D http://www.nyu.edu/pages/mathmol/library/sugars/ Protein glycosylation http://www.uni-mainz.de/~frosc000/STRU2.html Chapter 13: Glycolysis Glycolysis in 3D http://www.gwu.edu/~mpb/glycolysis3d.htm Introduction to glycolysis http://www.jonmaber.demon.co.uk/glyintro/ Glycolysis and medical biochemistry http://web.indstate.edu/thcme/mwking/glycolysis.html Overview of glycolysis http://biotech.icmb.utexas.edu/glycolysis/glycohome.html Glycolysis and the Kreb's Cycle http://esg-www.mit.edu:8001/esgbio/glycolysis/dir.html Chapter 14: Storage Methods and Control in Carbohydrate Metabolism Glucoamylase http://www.public.iastate.edu/~pedro/glase/glase.html Pentose phosphate pathway in 3D http://www.gwu.edu/~mpb/pentphos3d.htm Glycogen synthesis and galactose pathway http://www.gwu.edu/~mpb/polysacc3d.htm Glucose-6-phosphate dehydrogenase deficiency http://rialto.com/g6pd/ Chapter 15: The Citric Acid Cycle The TCA cycle in 3D http://www.gwu.edu/~mpb/citric3d.htm Overview of the TCA cycle http://www.accessexcellence.org/AB/GG/citric_Cycle_a.html 2D and 3D representations of the TCA cycle http://www.gwu.edu/~mpb/citric.htm TCA cycle inputs, reactions and control http://www.chem.wsu.edu/Chem102/102-CitrAcCycOxPhos.html Graphics of the TCA cycle http://www.usm.maine.edu/~rhodes/GraphicsGallery/Views09/TCA.html Chapter 16: Electron Transport and Oxidative Phosphorylation Oxidation/Reduction linked to Oxidative Phosphorylation http://www.dentistry.leeds.ac.uk/biochem/thcme/oxphos.html Oxidative Phosphorylation – a detailed summary http://www.med.unibs.it/~marchesi/oxphos.html Oxidative phosphorylation overview http://www.bmb.leeds.ac.uk/illingworth/oxphos/Index.htm Enzymes and pathway of oxidative phosphorylation http://www.gwu.edu/~mpb/oxidativephos.htm Oxidative Phosphorylation http://www.gwu.edu/~mpb/oxidativephos.htm Chapter 17: Lipid Metabolism Activation and transport of fatty acids http://www.gwu.edu/~mpb/fa-activation3d.htm Beta oxidation of fatty acids http://www.gwu.edu/~mpb/betaox-odd3d.htm Polyunsaturated fatty acid oxidation http://www.gwu.edu/~mpb/polyunsaturated3d.htm Fatty acids tutorial http://www-medlib.med.utah.edu/NetBiochem/FattyAcids/index.html Mycobacterial lipids http://bioscience.org/1997/v2/d/barrow/d387-400.htm Cholesterol metabolism http://swnt240.swmed.edu/gradschool/webrib/goldstei.htm Eicosanoids http://www.oxfordbiomed.com/catalga4.htm Cox-2 Inhibitors http://www.thedrugmonitor.com/coxi.html Lipid Biosynthesis – a quick review http://www.biochem.usyd.edu.au/~gareth/BCHM2002/studgdes/Lipid_biosyn.htm E.coli Lipid A and Endotoxins http://ives.biochem.duke.edu/Raetz/Lipid%20A1.html Chapter 18: Photosynthesis Photosynthesis http://www.plbio.kvl.dk/plbio/photosyn.htm The Calvin Cycle http://esg-www.mit.edu:8001/esgbio/ps/dark.html Photosynthesis on Power Point http://www.sci.sdsu.edu/classes/biology/bio202/TFrey/Photosynthesis.html Photosynthesis components in 3D http://www.nyu.edu/pages/mathmol/library/photo/ Photosynthesis prroblem set http://www.biology.arizona.edu/biochemistry/problem_sets/photosynthesis_1/photosynthesis_1.html Photosynthsesis problem set2 http://www.biology.arizona.edu/biochemistry/problem_sets/photosynthesis_2/photosynthesis_2.html Chapter 19: The Metabolism of Nitrogen Urea cycle http://www.gwu.edu/~mpb/urea3d.htm Amino acid metabolism http://web.indstate.edu/thcme/mwking/amino-acid-metabolism.html Amino acids and functions http://microscopy.fsu.edu/aminoacids/ Amino acid disorders http://dem0nmac.mgh.harvard.edu/research/shih.html Nucleotide metabolism http://web.indstate.edu/thcme/mwking/nucleotide-metabolism.html Nucleotide enzymes http://www.mrc-lmb.cam.ac.uk/rlw/text/nucleotideenzymes.html Nucleotides and muscle metabolism http://www.bmb.leeds.ac.uk/illingworth/muscle/#nucleotides Purine and Pyrimidine Metabolism http://www.auhs.edu/netbiochem/pupyr/pp.htm Chapter 20: Metabolism in Perspective Metabolic pathways http://www.gwu.edu/~mpb/ Metabolism problem set http://www.biology.arizona.edu/biochemistry/problem_sets/metabolism/metabolism.html Fat and carbohydrate metabolism in liver http://www.bmb.leeds.ac.uk/illingworth/medics1/liver.htm#GPAT Inherited disorders of energy metabolism http://www.cwru.edu/med/CIDEM/cidem.htm Extracting energy from glucose http://muscle.ucsd.edu/musintro/glucose.shtml Inborn errors of metabolism http://web.indstate.edu/thcme/mwking/inborn.html Metabolism problem set http://www.biology.arizona.edu/biochemistry/problem_sets/metabolism/metabolism.html Nicotinic acetylcholine receptor http://www.sdsc.edu/GatherScatter/GSspring96/back_cover.html Protein kinase database http://cl.sdsc.edu/ce/align_db.html Protein kinases in disease http://www.sdsc.edu/Kinases/pkr/pk_medicine.html Protein kinase database http://www.sdsc.edu/kinases/pkr/pk_education.html#walk Apoptosis Resources http://vl.bwh.harvard.edu/apoptosis.shtml Ion Channels http://pb010.anes.ucla.edu/ Cellular Processes in Java http://www.nrcam.uchc.edu/ Everything you want to know about cytokines http://www.copewithcytokines.de Asthma and Eosinophil Receptors http://www.pslgroup.com/dg/9b2e.htm Molecular Graphics One of the things that computers have been able to do in biochemistry and molecular biology, particularly in recent years with the availability of affordable, powerful desktop systems, is to allow for the visualization of biomolecules and their interactions in ways that truly enhance our appreciation and understanding of biological systems. An important part of these capabilities are the software programs and databases that suport these activities. We have provided below a listing of some tof the web links that researchers use in their everyday work. We hope that you will find these links both enjoyable and useful to explore. Molecular visualization tools and sites http://www.indiana.edu:80/~cheminfo/mvts.html RCSB: The home site for all PDB files http://www.rcsb.org/pdb/ A comprehensive database of molecular structures http://www.biomednet.com/db/msd A molecular graphics art show http://www.scripps.edu/pub/goodsell/mgs_art/mgs_art.html A more recent molecular graphics art show http://www.scripps.edu/pub/goodsell/mgs_art/mgs_art2/index.html The Protein Data Bank through Microsoft Windows http://www.sdsc.edu/pb/wpdb/wpdb.htm Software for biological data representation http://www.sdsc.edu/pb/Software.html Home page for a molecular graphics laboratory http://www.scripps.edu/pub/olson-web/ Hierarchical classification of proteins http://www.protomap.cs.huji.ac.il/ Biocomputing and molecular modeling http://www-bio.unizh.ch/ Computational molecular biology at NIH http://webasaurus.dcrt.nih.gov/molbio/ Online resources for molecular biology http://webasaurus.dcrt.nih.gov/molbio/servers.html A collection of biomolecular research tools http://www.public.iastate.edu/~pedro/research_tools.html Molecular models for biochemistry http://info.bio.cmu.edu/Courses/BiochemMols/BCMolecules.html Image library of biological macromolecules http://www.imb-jena.de/IMAGE.html The "Ribbons" software home page http://www.cmc.uab.edu/ribbons/ PovChem program for molecular graphics http://grserv.med.jhmi.edu/~paul/Manual.html The MolMol program for molecular visualization http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ Molecular biology database compendium http://www.tulane.edu/~dmsander/biotechniquessites.html Some biochemistry molecular models http://moby.ucdavis.edu/HRM/Biochemistry/molecules.htm A molecular library http://c4.cabrillo.cc.ca.us/projects/library/ Animated and still biochemistry graphics http://www-medlib.med.utah.edu/NetBiochem/graphlis.htm Online macromolecular museum http://www.clunet.edu/BioDev/omm/gallery.htm An art gallery of molecular models http://www2.kenyon.edu/depts/biology/eward/gallery/galleryintro.html Swiss PDB viewer http://expasy.expasy.ch/spdbv/ NIH Center for Molecular Modeling http://cmm.info.nih.gov/modeling/ VRML file creator for chemical structures http://www2.ccc.uni-erlangen.de/services/vrmlcreator/ Rendering techniques for molecular models http://scsg9.unige.ch/fln/eng/toc.html The Journal of Molecular Modeling http://link.springer.de/link/service/journals/00894/index.htm Using NMR for biomolecular structures http://www.ocms.ox.ac.uk/idc/structures/ Biomolecular structure and modeling in the United Kingdom http://www.biochem.ucl.ac.uk/bsm/ Copyright © 1999, Harcourt College Publishers, A Harcourt Higher Learning Company. 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