生物学领域的一些重要的英文网站

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生物学领域的一些重要的英文网站


Discussion Groups

BIOSCI Newgroup Network (http://www.bio.net ) ：BIOSCI Newsgroup Network is a set of electronic communication forums composed of Usenet newsgroup and parallel e-mail lists. This network was developed to allow worldwide communication between biological scientists over a variety of computer networks.

BioMOO (http://bioinformatics.weizmann.ac.il/BioMOO ) ：BioMOO is a virtual meeting place for biologists. The main physical part of BioMOO is located at the Bioinformatics Unit of the Weizmann Institute of Science, Israel. It is a place to come meet colleagues in Biology studies and related fields and brainstorm, to hold colloquia and conferences, to explore the serious side of this new medium.



MOLECULAR BIOLOGY

Cell & Molecular Biology Online (http://www.cellbio.com)：The goal of this site is to serve as a general resource for the biology community with an emphasis on information for cell and molecular biologists.

Pedro's BioMolecular Research Tools (http://www.public.iastate.edu/~pedro/research_tools.html)：A collection of WWW Links to information and services useful to molecular biologists.

The CMS molecular biology resource (http://www.sdsc.edu/ResTools/cmshp.html )：This website is a compendium of electronic and Internet-accessible tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry and Biomolecular Modeling.



BIOINFORMATICS RESOURCES

Computational Biology on Bioinformatics References at UCSC (http://www.cse.ucsc.edu/~karplus/compbio_pages.html )：A very thorough list of tools for computational biologists, some with a bit of brief annotation.


Human Genetic Resources

Genlink (http://www.genlink.wustl.edu )：GenLink is a multimedia database resource for human genetics that is currently under development. GenLink will provide linkage mapping information and software tools that will facilitate the integration of physical and genetic linkage data to produce unified maps of the human genome.

Human Molecular Genetics Group (http://www.path.cam.ac.uk )：The home page for the Human Molecular Genetics Group, led by Dr. Nabeel Affara, contains a host of information regarding the human Y chromosome. An anonymous FTP site is available to their data.

National Center for Genome Resources (http://www.ncgr.org/ncrg/HGP.html )：The NationalCenter for Genome Resources. is one of four international centers providing central organization and analysis of genetic information flowing in from all parts of the globe, including the Human Genome Project, the effort to map and sequence humans' complete genetic structure. NCGR is a non-profit organization serving scientists and society through a range of programs, all guided by three principles: to provide quality resources, to serve as a nexus for decision makers, and to inform and educate.

Nucleic acid Sequence Database

GenBank (http://www.ncbi.nlm.nih.gov )：Genbank provides easy search interfaces and simply presented, but information-loaded returns. It is good for identifying genes based on sequence or finding relationships with other organisms. Note: Molecular biologists don’t miss the Coffee Break ( http://www.ncbi.nlm.nih.gov/Coffeebreak /Archive/about.html ) section to see how bioinformatics tools are used as a part of the research process.

EMBL (http://www.ch.embnet.org )：EMBL provides data for those not trying to identify genes. It archives the in vivo sequences of nucleic acids for lots of organisms so comparisons can be made easily. This database is mirrored by Genbank.

dbEST (http://www.ncbi.nlm.nih.gov/dbEST )：dbEST is a subdivision of GenBank specific for queries on expressed sequence tags (\"single pass cDNA sequences\").

DDBJ (http://www.genome.ad.jp)：DDBJ essentially covers the information found on GenBank and EMBL. Searching on DDBJ, though, can be confusing since interfaces are not as straightforward. One attribute of this site is that it offers a Japanese version.

GSDB:Genome Sequence Databases (http://www.ncgr.org/gsdb/gsdb.html)：The Genome Sequence DataBase (GSDB) is dedicated to supporting scientific research and development by creating, maintaining and distributing a complete, timely, accurate and useful collection of DNA sequences and related information. As an on-line, client-server, relational database, GSDB operates as part of the DOE federated information infrastructure and focuses on meeting the needs of the major genome sequencing laboratories.




Nucleic Acid Structure Resources - Codon Usage Tables

Nucleic Acid Structure Resources

- RNA Secondary Structures (http://pundit.icmb.utexas.edu).

This site provides information on secondary structures of rRNAs and group I introns. This site also contains some great links to other ribosomal and structural sites.

- Image LIbrary of Biological Macromolecules (gopher://gopher.imb-jena.de/11/ftp/images).

This gopher-based site contains hundreds of images of molecules and complexes along with the reference information. Images are well-categorized although entering the with a specific goal would be helpful.

Codon Usage Tables

- IndianaUniversity's Gopher-Based Codon List (gopher://ftp.bio.indiana.edu/11/IUBIO.Software+data/molbio/codon).

IndianaUniversity's codon tables summarizes amino acid information for over 50 organisms.

- Codon Lists at Harvard (ftp://weeds.mgh.harvard.edu/pub/codon).

More comprehensive than IndianaUniversity's codon lists, Harvard's codon lists includes more organisms and more information. For the novice or uninitiated, though, it can be quite intimidating.

Protein Sequence Databases

CATH (http://www.biochem.ucl.ac.uk/bsm/cath/index.html)：The CATH database, maintained at University College London, provides a hierarchical domain classification of protein structures in the Brookhaven protein databank. The site's glossary - like BioTech a \"work in progress\" - may prove helpful for those new to the language of protein classification. On the other hand, if you are new to protein classifications then CATH may be too arcane for you.

Genobase (http://spector.dcrt.nih.gov)：Incorporating the information on EMBL, GenBank, Swiss-Prot and others, Genobase is a comprehensive molecular biology database covering nucleic acid, proteins, structure, etc.

Swiss Prot (http://expasy.hcuge.ch/sprot/sprot-top.html)：Ideal for initial searches for protein information, Swiss Prot generates search returns that are straightforward and very informative. The database is organized by EMBL accession numbers but is searchable by description, identification, author, date, and more.

PIR (http://www-nbrf.georgetown.edu/pir)：The Protein Information Resource - A collection of other databases, PIR compiles protein information based on what is known about each protein. As such, this could be a very useful tool for anyone seeking data on obscure proteins. Conversely, it could overwhelm those looking for information on well-studied proteins with too much information.

GenQuest (http://www.bis.med.jhmi.edu/Dan/gq/gq.form_rm.html)：This server allows for quick comparisons between unknown sequences and those found within the Genome Sequence Database, Swiss Prot, Prosite and PDB.

ExPASy Molecular Biology Server(http://expasy.hcuge.ch/tools.html)：Aside from the sequence identification provided by most databases, the ExPASy site provides a number of tools for protein analysis including peptide mass calculations, amino acid matching between sequences, nucleic acid sequence translation to protein, and much more. There are also tools to aid in structure projections and visualization.

PRODOM (http://protein.toulouse.inra.fr/prodom.html)：Based on the homologous domains from Swiss Prot, this database provides information on the domain arrangement of proteins and consensus sequences.

Blocks (http://www.blocks.fhcrc.org)：This is a database that searches for sequence homology based on blocks, \"multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins.\" These blocks are determined by cross-referencing several databases for highly conserved sequence regions.

Kabat Database (http://immuno.bme.nwu.edu)：Ssearch the Kabat database of sequences of proteins of immunological interest. This site is updated frequently.

SBASE (http://base.icgeb.trieste.it/sbase)：A protein domain sequence databse, SBASE is cross-referenced with most of the other major sequence databases. This database, therefore, can provide the same information as others, but the interface is not as user-friendly.

Protein Structure Resources

Chemical MIME Connection (http://biotech.chem.indiana.edu/mime)：All the molecules and chemical structure images off the Web can be quite confusing without a little understanding of some of the image formats and viewing software. Marilynn Dunker's site briefly explains the different types of computer images one might find and provides links to other sites where

SCOP - Structural Classification of Proteins -(http://www.pdb.bnl.gov/scop)：As its name implies, SCOP classifies all proteins for which science has structural information in order to examine the relationships between proteins. The result is a database with a wealth of structural information on folding patterns, sequence, phylogeny and more.

NRL-3D (http://www.bis.med.jhmi.edu/Dan/fields/nrl3d.form.html)：Not only does NRL 3D provide protein sequence and structural information, it also serves as a link between the Protein Data Bank and certain structural manipulation software which cannot interpret the information from PDB. Although very informative, searching can be a little tricky, and reading the instructions is very highly recommended.

Image Library of Biological Macromolecules (gopher://gopher.imb-jena.de/11/ftp/images)：This gopher-based site contains hundreds of images of molecules and complexes along with the reference information. Images are well-categorized although entering with a specific goal would be helpful

Protein Motions Database (http://bioinfo.mbb.yale.edu/MolMovDB)：This database provides information on the movements of proteins.

Amino Acids - Enzyme Databases - Electrophoresis Databases

Amino Acids

Amino Acid Properties (http://prowl.rockefeller.edu/aainfo/contents.htm)：This site contains a grotesquely large amount of information about amino acids including structure, pKa, geometry, solubility, images, etc.

Enzyme Databases

EC Enzyme -(http://www.bis.med.jhmi.edu/Dan/protteins/ed-enzyme.html)：This database was designed to provide information on enzymes as they were discovered and characterized. Recently, though, the server has been finicky in responding and may not provide much if any information at all.

REBASE: The Restriction Enzyme Database (http://www.neb.com/rebase/rebase.search.html) REBASE is a comprehensive database with everything one would want to know about an enzyme. User-friendly, it provides references and other resources in addition to the expected sequence, function and structural information.



Electrophoresis Databases

SWISS-2D: Two-Dimensional Polyacrylamide Gel Electrophoresis Database (http://expasy.hcuge. ch/ch2d/ch2d-top.html)：Swiss-2D references proteins to 2D PAGE maps. This provides a source for comparisons of proteins relative to others by size, shape, etc.

Quest (http://siva.cshl.org/index.html)：This center focuses on the design and analysis of protein databases. As such, this site provides links to other similar resources. Protein information at this site is derived from 2D PAGE gels.



MISCELLANEOUS

The Visible Human Project (http://www.nlm.nih.gov/research/visible )：The Visible Human Project is an outgrowth of the National Library of Medicine's 1986 Long-Range Plan. It is creating complete, anatomically detailed, three-dimensional representations of the male and female human body. The current phase of the project is collecting transverse CT, MRI and cryosection images of representative male and female cadavers at one millimeter intervals.

Oncology Online ( http://ontnet.com )：Oncology Online is an educational program which provides access to medical literature and serves as a communication vehicle among clinicians in the fields of oncology and hematology.

Technical Tips Online (http://tto.trends.com )：Technical Tips Online from Elsevier Trends Journals publishes peer-reviewed Technical Tips, Core Protocols, and Application Notes.

The Jackson Laboratory (http://www.jax.org )：The Jackson Laboratory is an independent non-profit mammalian research laboratory and a world leader in the genetics revolution.

Cold Spring Harbor Laboratory (http://www.cshl.org )：ColdSpringHarbor Laboratory is a research and educational institution. The Laboratory has research program focusing on cancer, neurobiology and plant genetics and a broad educational mission.



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