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Brazilian Journal of Medical and Biological Research

Print version ISSN 0100-879XOn-line version ISSN 1414-431X

Braz J Med Biol Res vol. 30 no. 3 Ribeirão Preto Mar. 1997

https://doi.org/10.1590/S0100-879X1997000300001 

Braz J Med Biol Res, March 1997, Volume 30(3) 283-288 (Concepts and Comments)

Useful Web sites for researchers studying proteins

C.L. Mafra1,2 , S.O. Paula2 , L.S. Ozaki1 and J.H. Patarroyo2

1Departamento de Bioquímica e Biotecnologia, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, 90050-170 Porto Alegre, RS, Brasil
2Núcleo de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Departamento de Veterinária, Universidade Federal de Viçosa, 36571-000 Viçosa, MG, Brasil

Text
References
Correspondence and Footnotes


Key words: protein analysis, WWW, resource


Introduction

The development of high performance computers both at hardware and software levels associated with the exponential growth of the Internet has opened new sources of information in all areas of knowledge (1). For biologists, the World Wide Web (WWW) today offers alternative information sources which are much easier to reach and unthinkable only a few years ago (2,3). In this Web, it is possible, for instance, to access libraries and databases, to engage in courses and discussion groups, and to use programs online (4), far beyond the electronic mail (e-mail), file transference protocol (ftp) and document retrieval system of the old days. Presently, technologies are explosively being developed that will enable direct visual contact world wide, both personal and in conference, and online discussion of files and data. Programs already exist whose better performance still depends on the development of the Internet itself.

In the present minireview we list the many Uniform Resource Locators (URLs) organized in different areas such as Immunology, Chemistry, Biochemistry, Molecular Biology and Crystallography, all of common interest to researchers dealing with protein-related subjects. Similar lists were compiled for cell and tissue culture (5), human genetics (6), molecular biology (7), thermocycling (8) and biotechnology companies (9).

We organized the Web pages by subjects related to protein research (Table 1), tools for online protein analysis (Table 2), organizations with useful references (Table 3), pages with announcements of meetings and related courses (Table 4), scientific journals (Table 5), and some biotechnology companies commonly consulted by the community (Table 6).

As the Web continually expands, this directory does not intend by any means to be complete. We hope, however, that it will be helpful as a starting point to look for and find useful protein-related information in the Web.


Table 1 - Protein-related sites.

 

URL

Biochemistry

 

Links to bioinformatics center-related servers

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/sites.html

Related protein structure links

http://www.yorvic.york.ac.uk/computing/links.html

Web resources for protein scientists

http://www.prosci.uci.edu/ProSciDocs/WWWResources.html

WWW Virtual library: Biochemistry and molecular biology

http://golgi.harvard.edu/biopages/biochem.html

WWW Virtual library: Biomolecules

http://golgi.harvard.edu/sequences.html

Biotechnology

 

BioTech Science resources

http://biotech.chem.indiana.edu/pages/scitools.html

Pedro's biomolecular research tools

http://www.public.iastate.edu/~pedro/research_tools.html

Useful links from Darst lab

http://darst-sgi2.rockefeller.edu/

WWW Virtual library: Biotechnology

http://www.cato.com/interweb/cato/biotech/

Chemistry

 

Chemistry databases and data collections

http://www.rpi.edu/dept/chem/cheminfo/chemres/chemres_03.html

Chemistry Today - Jobs, news and meetings

http://chemistry.mond.org/

Internet chemistry index

http://www.chemie.fu-berlin.de/chemistry/index/

Internet chemistry resources

http://www.rpi.edu/dept/chem/cheminfo/chemres.html

Latinamerican Web of chemistry

http://latina.chem.cinvestav.mx/

Molecular simulation on the Web

http://ganter.chemie.uni-dortmund.de/comp_chem.html

Silicon Grafics - Chemistry and biological sciences

http://www.sgi.com/ChemBio/

WWW Chemistry resources, jobs and academic and commercial sites

http://www-chem.harvard.edu/webchemistry/webchem.html

WWW Computational chemistry resources

http://www.chem.swin.edu.au/chem_ref.html

Immunology

 

Antibody resources

http://www-chem.ucsd.edu/Faculty/goodman/antibody.html/abpage.html

Antibody structure and sequence information

http://www.biochem.ucl.ac.uk/~martin/antibodies.html

Links to cytokine-related sites

http://www.lmb.uni-muenchen.de/groups/ibelgaufts/links.html

Kabat database - Sequences of proteins of immunological interest

http://immuno.bme.nwu.edu/

WWW Virtual library: Immunology

http://golgi.harvard.edu/biopages/immuno.html

Molecular Biology

 

Biologists's control panel

http://gc.bcm.tmc.edu:8088/bio/bio_home.html

DNA vaccine Web

http://www.genweb.com/Dnavax/dnavax.html

Compilation of resources in Internet for the molecular biologist

http://www.ifrn.bbsrc.ac.uk/gm/lab/docs/iftmb.html

Molecular biology information servers

http://research.nwfsc.noaa.gov/bioinformatics.html

Molecular biology protocols

http://grimwade.biochem.unimelb.edu.au/sigtrans.htm

http://research.nwfsc.noaa.gov/protocols.html

Molecular biology related WWW sites

http://www.oxmol.co.uk/oth_link.html

Molecular biology servers, databases and Web sites

http://pdb.pdb.bnl.gov/mole.html

The Biocatalog in molecular biology and genetics

http://www.ebi.ac.uk/biocat/


Table 2 - Analysis and search online.

Institution

Service

Mnemonic

URL

BMERC

Protein sequence analysis

 

http://bmerc-www.bu.edu/protein-seq/

BCM

Protein secondary structure prediction

 

http://dot.imgen.bcm.tmc.edu:9331/pssprediction/pssp.html

Center for Molecular Modeling - NIH

Protein database and analyzed sequences

 

http://cmm.info.nih.gov/modeling/net_services.html

CBS

O-glycosylation sites in mammalian proteins

NetOglyc

http://www.cbs.dtu.dk/netOglyc/cbsnetOglyc.html

 

Signal peptide cleavage sites in amino acid sequences

Signalp

http://www.cbs.dtu.dk/signalp/cbssignalp.html

CNRS

Assistance with the analysis of domain arrangement in proteins

ProDom

http://protein.toulouse.inra.fr/prodom/form.html

CNUSC

Immunogenetic database

IMGT

http://imgt.cnusc.fr:8104

Cohen Group

Protein secondary structure prediction

NNPREDICT

http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html

CSBS

Structural classification of proteins

SCOP

http://scop.mrc-lmb.cam.ac.uk/scop/

EBI

Protein database search

BLITZ

http://www.ebi.ac.uk/searches/blitz_input.html

 

Nucleotide to protein translation

The Protein Machine

http://www.ebi.ac.uk/contrib/tommaso/translate.html

EMBL

Protein secondary structure prediction from a single sequence or from a set of sequences

PREDATOR

http://www.embl-heidelberg.de/argos/predator/predator_form.html

 

Search for multiple sequence alignments, prediction of secondary structure, solvent accessibility, transmembrane helices, topology for transmembrane protein, fold recognition by prediction-based threading, evaluation of secondary structure prediction accuracy

PredictProtein

http://www.embl-heidelberg.de/predictprotein/predictprotein.html

 

Search for structural similarity

PROPSEARCH

http://www.embl-heidelberg.de/prs.html

 

Database of secondary structure assignments

DSSP

http://www.embl-heidelberg.de:80/srs/srsc?-info+DSSP

 

Secondary structure prediction of proteins

SSPRED

http://www.embl-heidelberg.de/sspred/sspred_info.html

 

Transmembrane segments prediction

TMAP

http://www.embl-heidelberg.de/tmap/tmap_sin.html

ExPASy

Theoretical pI and MW for a protein sequence

pI/MW

http://expasy.hcuge.ch/ch2d/pi_tool.html

 

Enzyme nomenclature database

 

http://expasy.hcuge.ch/sprot/enzyme.html

 

Physical and chemical parameters of protein sequences

ProtParam

http://expasy.hcuge.ch/sprot/protparam.html

 

Compute and represent the profile produced by any amino acid sequence (hydrophobicity, polarity, MW, secondary structure prediction, etc.)

ProtScale

http://expasy.hcuge.ch/cgi-bin/protscale.pl

 

Automated knowledge-based protein modeling server

Swiss-Model

http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html

FU Berlin

Amino acid structure

 

http://www.chemie.fu-berlin.de/chemistry/bio/aminoacids.html

IBCP

Sequence analysis, secondary structure prediction and pattern search in protein database

 

http://www.ibcp.fr/mailserver.html

ISREC

Statistical Analysis of Protein Sequence

SAPS

http://ulrec3.unil.ch/software/SAPS_form.html

 

Prediction of transmembrane regions and orientation

TMpred

http://ulrec3.unil.ch/software/TMPRED_form.html

Johns Hopkins University Bioinformatics Web Server

Searching for software and data for biology and general, available on the Internet

 

http://www.gdb.org/Dan/softsearch/softsearch.html

MRC/HGMP

Protein sequence databases menu - A collection of protein sequence databases, motifs and protein families and some information on 3D structures

 

http://www.hgmp.mrc.ac.uk/Public/protein-seq-db.html

NCBI

GenBank database

 

http://www2.ncbi.nlm.nih.gov/genbank/query_form.html

NIH

Three-dimensional drug structure databank

 

http://cmm.info.nih.gov/modeling/drugbank.html

NIBB

Analysis and prediction of protein sorting signals coded in amino acid sequence

PSORT

http://psort.nibb.ac.jp/

SBDS

Secondary structure prediction

GOR

http://molbiol.soton.ac.uk/compute/GOR.html

Skirball Institute of Biomolecular Medicine

Amino acid images

 

ftp://128.122.10.5/pub/pmsa/images

 

Amino acid properties

 

http://128.122.10.5/aainfo/contents.htm

University of North Carolina at Chapel Hill

Biosequence analysis

BioSCAN

http://genome.cs.unc.edu/online.html


Table 3 - Reference organizations.

Organization

Abbreviation

URL

American Association for the Advancement of Science

AAAS

http://www.aaas.org/

American Chemical Society

ACS

http://www.acs.org/

American Type Culture Collection

ATCC

http://www.atcc.org/atcc.html

Argos Group

 

http://www.embl-heidelberg.de/ExternalInfo/argos/argos-group.html

Baylor College of Medicine

BCM

http://www.bcm.tmc.edu/

BioMolecular Engineering Research Center

BMERC

http://bmerc-www.bu.edu/bmerc-main.html

Birkbeck College - Department of Crystallography

 

/www.cryst.bbk.ac.uk/

Brookhaven National Laboratory

BNL

http://www.bnl.gov/

Cambridge School of Biological Sciences

CSBS

http://www.bio.cam.ac.uk/

Cambridge University Chemical Laboratory

 

http://www.ch.cam.ac.uk/

Center for Biological Sequence Analyses

CBS

http://www.cbs.dtu.dk/

Centre de Recherche en Biochimie Macromoleculaire

 

http://xerxes.crbm.cnrs-mop.fr/

Centre National de la Recherche Scientifique

CNRS

http://www.cnrs.fr/

Centre National Universitaire Sud de Calcul

CNUSC

http://www.cnusc.fr/

Cohen Group

 

http://www.cmpharm.ucsf.edu/cohen/

European Bioinformatics Institute

EBI

http://www.ebi.ac.uk/ebi_home.html

European Collection of Animal Cell Cultures

ECACC

http://www.gdb.org/annex/ecacc/HTML/ecacc1.html

European Molecular Biology Laboratory

EMBL

http://www.embl-heidelberg.de/

European Molecular Biology Network

EMBnet

http://beta.embnet.unibas.ch/embnet/info.html

Expasy - Molecular Biology Server

ExPASy

http://expasy.hcuge.ch/

Free University Berlin - Department of Chemistry

FU Berlin

http://www.chemie.fu-berlin.de/index_e.html

Food and Drug Administration

FDA

http://www.fda.gov/

Harvard Biological Laboratories - Genome Research

 

http://golgi.harvard.edu/

Institute of Biology and Chemistry of Proteins

IBCP

http://www.ibcp.fr/

Medical Research Council

MRC

http://www.mrc.ac.uk/MRC/

National Academy of Sciences

NAS

http://www.nas.edu/

National Center for Biotechnology Information

NCBI

http://www.ncbi.nlm.nih.gov/

National Institute for Basic Biology

NIBB

http://www.nibb.ac.jp/

National Institutes of Health

NIH

http://www.nih.gov/

National Science Foundation

NSF

http://www.nsf.gov/

Northwest Fisheries Science Center

NWFSC

http://research.nwfsc.noaa.gov/

Oxford Molecular Group

 

http://www.oxmol.co.uk/

Protein Data Bank

PDB

http://www.pdb.bnl.gov/

Shouthampton Bioinformatics Data Server

 

http://molbiol.soton.ac.uk/sbds.html

Skirball Institute of Biomolecular Medicine

 

http://www.med.nyu.edu/Skirball/HomePage.html

Swiss Institute for Experimental Cancer Research

ISREC

http://www-isrec.unil.ch/isrec.htm

Weizmann Institute

 

http://www.weizmann.ac.il/


Table 4 - Meetings, courses and workshops on protein and related areas.

Announcer

Comments

URL

American Chemistry Society Meetings

A list of meetings in chemistry by geographical areas in USA

http://www.acs.org/meetings/welcome.htm

Bioinformatics Courses

A list of bioinformatics courses in USA, UK and Europe

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/courses.html

Bioinformatics Practical

A pratical guide on protein sequence and structure analysis on line

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/jj

Cato Research's List of Meetings

A list of meetings in biotechnology and pharmaceutical development around the world

http://www.catosource.com/fyi

Calendar of Events - Center for Molecular Modeling/NIH

Events in chemistry, biology and related subjects

http://cmm.info.nih.gov/modeling/events.html

Chemical Conferences

Conferences on the various disciplines of chemistry

http://hackberry.chem.niu.edu:70/0/ConferenceListings/SpecialistMeetings/index.html http://ccl.osc.edu/ccl/crc.html

Educational Courses on the Web

Courses on the WWW

http://lenti.med.umn.edu/~mwd/courses.html

Meetings, Courses and Workshops in Bioscience and Medicine

A list of scientific events

http://www.informatik.uni-rostock.de/HUM-MOLGEN/anno/meetings.html

Structure-based Drug Design

A short course on structural drug design

http://www.cryst.bbk.ac.uk/SBDD/course.html

The Principles of Protein Structure Using the Internet

Internet course on protein structure

http://www.cryst.bbk.ac.uk/PPS/index.html


Table 5 - Publishers and scientific journals.

Publisher or Journal

URL

Academic Press Journals

http://www.apnet.com/www/journal/journals.htm

American Chemistry Society Publications

http://pubs.acs.org/

Biochemistry and Molecular Biology Journals

http://www.princeton.edu/~beasley/journals.html

Blackwell Science

http://www.blacksci.co.uk/

Cambridge University Press

http://www.cup.cam.ac.uk/

Cell

http://www.cell.com/

Cold Spring Harbor Laboratory Press

http://www.cshl.org/admin/press.html

CRC Press, Inc.

http://www.crcpress.com/

CW Henderson

http://www.homepage.holowww.com/

Elsevier Science

http://www.elsevier.nl:80/

Gene

http://www.elsevier.com:80/catalogue/SAH/185/05450/05450/506033/506033.html

John Wiley & Sons, Inc. Publishers

http://www.wiley.com/

Journal of Molecular Biology

http://www.hbuk.co.uk/jmb/

Macmillan Publishers

http://www.mcp.com/

Nature

http://www.america.nature.com/

New Scientist

http://www.newscientist.com/

On-line Journals for Immunologists

http://glamdring.ucsd.edu/others/aai/journals.html

Oxford University Press

http://www.oup.co.uk/

Proceedings of the National Academy of Sciences, USA

http://journals.at-home.com/PNAS/

Protein Science

http://www.prosci.uci.edu/

Science

http://www.sciencemag.org/

Springer-Verlag

http://www.springer.de/


Table 6 - Companies and suppliers.

Company

URL

Amersham Life Science

http://www.amersham.co.uk/life/

Amicon

http://www.amicon.com/

Beckman Instruments

http://www.beckman.com/

BDH

http://www.bucc.co.uk/vbp/bdn/index.html

Clontech

http://www.clontech.com/

Dako Corporation

http://www.dakousa.com/

Endogen, Inc.

http://www.endogen.com/

Eppendorf

http://www.eppendorf.com/

Fluka

http://www.sigma.sial.com/Fluka/

Glaxo Wellcome

http://www.glaxowellcome.co.uk/

Invitrogen

http://www.invitrogen.com/

Life Technologies, Inc.

http://www.lifetech.com/

Merck & Co., Inc.

http://www.merck.com/

Millipore

http://www.millipore.com/

New England Biolabs

http://www.neb.com/

Novagen

http://www.novagen.com/

Perstorp Corporation

http://www.perstop.se/Welcome.html

PerSeptive Biosystems

http://www.pbio.com/

Perkin-Elmer

http://www.perkin-elmer.com/

Pharmacia Biotech

http://www.biotech.pharmacia.se/

Poretics

http://www.semiweb.com/poretics/

Promega

http://www.promega.com/

R&D Systems

http://www.rndsystems.com/

Sandoz

http://www.sandoz.com/

Scienceware

http://www.bel-art.com/

Sigma-Aldrich Corporation

http://www.sigma.sial.com/

Takara Biomedicals

http://www.foodsci.purdue.edu/egc/trade/takara/tak0e.htm

Transduction Laboratories

http://translab.com/index.html

VWR Scientific Products

http://www.vwrsp.com/

WWW Chemicals - Chemical manufacturers and distributors

http://www.chem.com/

WWW Virtual Library: Biotechnology - Companies

http://www.cato.com/interweb/cato/biotech/bio-co.html


References

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2. Harper R (1995). World Wide Web resources for the biologist. Trends in Genetics, 11: 223-228.        [ Links ]

3. Jacobson D (1994). The World Wide Web for biologists. Protein Science, 3: 2159-2161.        [ Links ]

4. Appel RD, Bairoch A & Hochstrasser DF (1994). A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends in Biochemistry, 19: 258-260.        [ Links ]

5. Sikorski RS & Peters R (1996). Cell and tissue culture on the web. Nature Biotechnology, 14: 656.        [ Links ]

6. Franco GR & Pena SDJ (1996). A directory of world wide web sites for human genetics. Brazilian Journal of Genetics, 19: 371-374.        [ Links ]

7. Brenner SE (1995). World Wide Web and molecular biology. Science, 268: 622-623.        [ Links ]

8. Peters R & Sikorski R (1996). Thermocycling on the web: A user's guide. Nature Biotechnology, 14: 517.        [ Links ]

9. Goostein M (1996). Shopping for biotechnology products on the web: A user's guide. Nature Biotechnology, 14: 367.        [ Links ]

Correspondence and Footnotes

Address for correspondence: C.L. Mafra, Núcleo de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Departamento de Veterinária, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, 36571-000 Viçosa, MG, Brasil. E-mail: sctmafra@mail.ufv.br

Research supported by CAPES. C.L. Mafra is the recipient of a predoctoral fellowship from CAPES. Received November 27, 1996. Accepted January 13, 1997.

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