| |
Jump to [Chapter 6] [Chapter 7] [Chapter 8] [Appendix 3]
The following Web Links relate specifically to material in Chapters 6-8 and Appendix 3 of your textbook. There are no links for Chapters 1 through 5.
CHAPTER 6
The Institute for Genomic Research
www.tigr.org
Founded in 1992, The Institute for Genomic Research (TIGR) is a not-for-profit research institute whose primary research interests are in structural, functional and comparative analysis of genomes and gene products from a wide variety of organisms including viruses, eubacteria (both pathogens and non-pathogens), archaea (the so-called third domain of life), and eukaryotes (plants, animals, fungi and protists such as the malarial parasite.)
A partial list of the many prokaryotic genomes that have been sequenced to date:
A partial list of eukaryotic genome sequencing projects:
- Saccharomyces cerevisiae (yeast)
genome-www.stanford.edu/Saccharomyces
SGDTM is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
- Caenorhabditis elegans
www.sanger.ac.uk/Projects/C_elegans/
The C. elegans sequencing project is a collaboration between the Sanger Institute, Hinxton, Cambridge and the Genome Sequencing Center at the Washington University School of Medicine, St. Louis.
- Drosophila melanogaster (fruit flies)
flybase.bio.indiana.edu
FlyBase is a database of genetic and molecular data for Drosophila. FlyBase includes data on all species from the family Drosophilidae; the primary species represented is Drosophila melanogaster.
- Danio rerio (zebrafish)
zfin.org/
Database of information for zebrafish researchers funded by the W. M. Keck Foundation, the National Science Foundation and the National Institutes of Health.
- Homo sapiens (humans)
www.ncbi.nlm.nih.gov/genome/guide/human/
Human genome resources from the National Center for Biotechnology Information in Bethesda, Maryland.
Codon Usage Database
UniGene
www.ncbi.nlm.nih.gov/UniGene/ddd.cgi?ORG=Hs
UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters.
Entrez
www.ncbi.nlm.nih.gov/Entrez/
Entrez is a retrieval system for searching several linked databases.
[top]
CHAPTER 7
Protonation of a Caroxylate Group
www.science.ubc.ca/~chem/tutorials/pH/section19/content.html
Tutorial developed at the University of British Columbia in Vancouver.
Folding@Home
foldingathome.stanford.edu
A distributed computing project at Stanford University which studies protein folding, misfolding, aggregation, and related diseases.
The Levinthal Paradox
brian.ch.cam.ac.uk/~mark/levinthal/levinthal.html
Levinthal's Paradox, or the fact that many naturally-occurring proteins fold reliably and quickly to their native state despite the astronomical number of possible configurations, is reproduced verbatim.
PredictProtein
cubic.bioc.columbia.edu/predictprotein/
PredictProtein is a service for sequence analysis, and structure prediction from the Columbia University Bioinformatics Center.
Genamics
genamics.com/expression/strucpred.htm
Genamics Expression is an application, developed by a firm in New Zealand, for DNA and protein sequence analysis.
Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide
[top]
CHAPTER 8
Enzyme Nomenclature
www.chem.qmw.ac.uk/iubmb/enzyme/
Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and classification of Enzyme-Catalysed Reactions.
SCOP
wehih.wehi.edu.au/scop/
Searchable database of the Structural Classification of Proteins from The Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia.
CATH Protein Structure Classification
www.biochem.ucl.ac.uk/bsm/cath_new/index.html
CATH is a novel hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H).
FSSP
www.hgmp.mrc.ac.uk/Databases/fssp-help.html
The Fold classification based on Structure-Structure alignment of Proteins database is a repository for secondary structure assignment data.
The Protein Data Bank
www.rcsb.org/pdb/
Comprehensive worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
AutoDock
www.scripps.edu/pub/olson-web/doc/autodock/
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
FTDock
www.bmm.icnet.uk/docking/ftdock.html
Fourier Transform Dock performs rigid-body docking on two biomolecules in order to predict their correct binding geometry.
FLEXX
cartan.gmd.de/flexx/
FlexX is a computer program for predicting protein-ligand interactions. For a protein with known three-dimensional structure and a small ligand molecule, FlexX predicts the geometry of the protein-ligand complex and estimates the binding affinity.
The Protein Data Bank
www.rcsb.org/pdb/
Comprehensive worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
The Protein Information Resource
pir.georgetown.edu
The Protein Information Resource (PIR) is a division of the National Biomedical Research Foundation (NBRF) which is affiliated with Georgetown University Medical Center.
ExPASy Server
www.expasy.ch
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures.
RasWin
www.bernstein-plus-sons.com/software/rasmol/
RasWin is a molecular graphics visualisation tool Based on RasMol 2.6 by Roger Sayle.
The Swiss PDB Viewer
www.expasy.ch/spdbv
Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time.
Visual Molecular Dynamics
www.ks.uiuc.edu/Research/vmd/
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
SPOCK
quorum.tamu.edu/spock/
Spock is a full-featured molecular graphics program developed by Jon A. Christopher while in the lab of Thomas O. Baldwin of the Department of Biochemistry and Biophysics at Texas A&M University.
Protein Explorer
The Protein Explorer can make visual exploration of protein structure much more accessible to novices, occasional users, or nonspecialists, as well as making it much more convenient than RasMol, even for experts.
DINO
www.bioz.unibas.ch/~xray/dino
DINO is a realtime 3D visualization program for structural biology data.
Molecular Graphics
www.rcsb.org/pdb/software-list.html#Graphics
List of software available for the creation of molecular graphics compiled on the Protein Data Bank Web site.
Prediction of Protein Sorting Signals and Localization Sites in Amino Acid Sequences
psort.nibb.ac.jp
PSORT is a Japanese program for the prediction of protein localization sites in cells.
SignalP
www.cbs.dtu.dk/services/SignalP
The SignalP World Wide Web server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
Prediction Algorithm for Proteasomal Cleavages
www.paproc.de
PAProC is a prediction tool for cleavages by human and yeast 20S proteasomes, based on experimental cleavage data developed at the University of Tübingen, Germany.
CBS
www.cbs.dtu.dk
The Center for Biological Sequence Analysis at the Technical University of Denmark.
ExPASy tools page
www.expasy.ch/tools
Protein identification and characterization tools from the ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB).
There are no links for Appendices 1 and 2.
[top]
APPENDIX 3
The Protein Data Bank
www.rcsb.org/pdb/
Comprehensive worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
|
