Online Biotechnology Resources PDF Print E-mail

Literature Databases

Pubmed
http://www.ncbi.nlm.nih.gov/sites/entrez/?db=pubmed

Biomednet
http://www.bmn.com

Science Direct
http://www.sciencedirect.com


Journals


Free Medical Journals List
http://www.freemedicaljournals.com

CiteSeer - Largest free full text index of science literature
http://www.citeseer.ist.psu.edu

Proceedings of the National Academy of Sciences (Free)
http://www.pnas.org

Journal of Biological Chemistry (Free)
http://www.jbc.org

Science (Free after one year of publication)
http://www.sciencemag.org

Nature  (Needs subscription)
http://www.nature.com


General Biology Links:

LBSN - The List of Bacterial Names both alphabetically and chronologically
http://www.bacterio.cict.fr

Microbiology Info - An information portal on microbiology
http://www.microbes.info

REBASE - A collection of information about restriction enzymes and related proteins
http://www.rebase.neb.com

American Type Culture Collection (ATCC) - The main repository of cell lines in the United States.
http://www.atcc.org

NCCC: The Cell Culture Center - The Cell Culture Center is a national resource facility established by the National Institutes of Health (NIH) to provide customized, large scale, cell culture services for basic research laboratories
http://www.nccc.com

TAB Cell Line Data Base - Extensive catalog of about 4916 human and animal cell lines available from European
http://www.biotech.ist.unige.it/cldb/indexes.html


Protocols and Research Tools

CMS Molecular Biology Resource
http://www.restools.sdsc.edu

Cell Biology Protocols
http://www.vlib.org/Science/Cell_Biology/methods.shtml

Molecular Biology Protocols
http://www.micro.nwfsc.noaa.gov/protocols/

Cell and Molecular Biology Online
http://www.cellbio.com/protocol.html

Molecular Biology Protocols- Oklahoma Medical Research Foundation
http://www.omrf.ouhsc.edu/~frank/toc.html

Protocol Online.org
http://www.protocol-online.org

Primer Design
http://www.genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi

Tavis PCR protocols
http://www.ifo.med.yale.edu/genetics/ward/tavi/PCR.html

Molecular Biology Protocols  Dermouth college
http://www.dartmouth.edu/~ambros/protocols.html

Bioprotocols
http://www.bioprotocol.com

Cell Biology Lab Manual - Collection of protocols
http://www.homepages.gac.edu/~cellab/index-1.html

Tissue culture methods - Site at University of South Wales
http://www.anatomy.med.unsw.edu.au/cbl/research/methods/culture.htm

Flow cytometry Flow cytometry WWW links list located at the Salk Institute CCMI, La Jolla, California.
http://www.pingu.salk.edu/flow/sitelink.html

Histology Protocols - At Nottingham University
http://www.nottingham.ac.uk/pathology/default.html


GENOMICS AND PROTEOMICS

NCBI Resources - complete resource catalogue of NCBI
http://www.ncbi.nlm.nih.gov

European Bioinformatics Institute -EBI home page
http://www.ebi.ac.uk

Genome web - Collection of useful genomics and proteomics links
http://www.hgmp.mrc.ac.uk/GenomeWeb/

BLAST (NCBI) - sequence alignment
http://www.ncbi.nlm.nih.gov/BLAST

SDSC Biology Work Bench - Single platform for several analyses at SanDiego Super computing centre
http://www.workbench.sdsc.edu

KEGG- Kyoto Encyclopedia of Genes and Genomes
http://www.genome.ad.jp

Genbank -  nucleotide database, sequence submissions
http://www.ncbi.nlm.nih.gov/GenBank/index.html

EMBL - nucleotide database
http://www.ebi.ac.uk/embl/

DDBJ - nucleotide database
http://www.ddbj.nic.ac.jp

Genome Annotations-ENSEMBL- automated annotation of whole genome
http://www.ensembl.org

GeneMark - gene predictions
http://www.opal.biology.gatech.edu/GeneMark

GenScan - gene predictions
http://www.genes.mit.edu/GENSCAN.html

VISTA - Comparative Genomics server at Lawrence Berkeley National Laboratory
http://www-gsd.lbl.gov/vista


Pipmaker - Comparative Genomics server at Pennsylvania State University, Bioinformatics Group
http://www.bio.cse.psu.edu/pipmaker

Pedro’s Biomolecular Research Tools - The most widely quoted collection of biology related web pages
http://www.gea.stanford.edu/luciano/bioservers.html

UCSC Genomics Best Links - Genomics Link at University of California Super computing centre
http://www.genome.ucsc.edu/bestlinks.html


Gene Expression Analysis

Microarray Bibliography - Papers on Microarray Data Analysis
http://www.nslij-genetics.org/microarray

The Chipping Forecast - is a collection of reviews on different aspects of microarray analysis
http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v21/n1s/index.html

SAGE - Serial Analysis of Gene Expression
http://www.sagenet.org

SAGE Map  - Is a SAGE data resource for the query and retrieval and analysis of SAGE data from any organism
http://www.ncbi.nlm.nih.gov/SAGE


Proteomics

Swissprot - protein database
http://www.us.expasy.org/sprot

Tools for proteomics -Collection of web tools for protein sequence and structure analyses at ExPASY.
http://www.us.expasy.org/tools

Biomolecular Interaction Database - full descriptions of interactions, molecular complexes and pathways.
http://www.bind.ca


Structure- Database and Prediction and Visualization
:

Protein Data bank - Database of solved protein structures
http://www.rcsb.org/pdb

Educational Resources at PDB
http://www.rcsb.org/pdb/education.html

Swissmod-Automated comparative protein modelling server
http://www.expasy.org/swissmod/SWISS-MODEL.html

DINAMO -Interactive sequence alignment/comparative model building tool.
http://www.bioweb.pasteur.fr/docs/dinamo

CPHmodels Server - Predict protein structure using comparative (homology) modelling.
http://www.cbs.dtu.dk/services/CPHmodels

Membrane Protein Transmembrane Secondary Structure Prediction Server
http://www.pref.etfos.hr/split

Protein Structure Prediction Center - Critical assessment of structure prediction.
http://www.predictioncenter.llnl.gov

Coiled Coils - Coiled Coil Prediction from Protein Sequences
http://www.york.ac.uk/depts/biol/units/coils/coilcoil.html

PHD - Protein Prediction (at EMBL)
http://www.embl-heidelberg.de

The ProDom Protein Domain Database
http://www.protein.toulouse.inra.fr/prodom.html

TMHMM Server - Prediction of transmembrane alpha-helices
http://www.cbs.dtu.dk/services/TMHMM

TMpred - Transmembrane prediction
http://www.ulrec3.unil.ch/software/TMPRED_form.html

DAS - Transmembrane prediction.
http://www.sbc.su.se/~miklos/DAS/maindas.html


Molecular Visualization

World Index of molecular visualization resources
http://www.molvis.sdsc.edu/visres/index.html

Rasmol-The most widely used molecular  visualization tool
Tutorials on Rasmol - Rasquik , Rastut
http://www.umass.edu/microbio/rasmol

Protein Explorer -Similar to Rasmol and based on Rasmol, Requires Chime Plug in
http://www.molvis.sdsc.edu/protexpl/frntdoor.htm

VMD - Visual Molecular Dynamics - Molecular visualization program for displaying, animating, and analyzing
http://www.ks.uiuc.edu/Research/vmd

MolMol - MOLMOL is a molecular graphics program with special emphasis on NMR structures
http://www.molbio.ethz.ch/wuthrich/software/molmol

Swiss-PdbViewer - Another visualization software, Works with SwissMode outputs
http://www.us.expasy.org/spdbv


Feature Prediction:

Prosite - Database of protein families and domains including functional patterns
http://www.expasy.org/prosite

CANSITE - Scan your protein for potential signalling effector and adaptor sites
http://www.scansite.mit.edu

PhosphoBase - A database of phosphorylation sites with a phosphorylation prediction program
http://www.cbs.dtu.dk/databases/PhosphoBase

PredictNLS - an automated tool for the analysis and determination of Nuclear Localization Signals (NLS).
http://www.cubic.bioc.columbia.edu/predictNLS

SignalP Server - Predictions of signal peptide cleavage sites in AA sequences from prokaryotes and eukaryotes.
http://www.cbs.dtu.dk/services/SignalP


Lab Safety:

Agency for toxic substances and disease registry
http://www.atsdr.cdc.gov/mrls/index.html


Patent, Bioethics and Legal Issues:

US patent Office - File and search patent
http://www.uspto.gov

Bioethics.net  - provides a wide range of topics and resources
http://www.bioethics.net

Biotechology Law Web server
http://www2.ari.net/foley/homepage.html


Software:

EMBOSS  -The European Molecular Biology Open Software Suite EMBOSS is a package of high-quality FREE Open Source software for sequence analysis (Linux)
http://www.hgmp.mrc.ac.uk/Software/EMBOSS

Antheprot - Integrated package of most of the methods designed for protein sequence analysis
http://www.antheprot-pbil.ibcp.fr

Genamics Software Seek  - Repository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry
http://www.genamics.com/software

Scion Image  - Gel analysis program ( Image analysis similar to NIH image)
http://www.scioncorp.com/framesfr_scion_products.htm

PREDATOR download
http://www-db.embl-heidelberg.de/jss/servlet/de.embl.bk.wwwTools.GroupLeftEMBL/argos/predator/down_predator.html

MEMSAT download - Transmembrane prediction
http://www.cs.ucl.ac.uk/staff/d.jones/memsat.html


General:

Sigmaplot - Scientific Graphing (require license)
http://www.spss.com/SPSSBI/Sigmaplot

Design Expert - Design of Experiments (require license)
http://www.statease.com

Statistical -  Statistical analyses ( require license)
http://www.statsoftinc.com

Octave - Similar to Matlab, used for mathematical modelling of biological processes and variety of other applications (Runs on Linux)
http://www.octave.org

Open office- Office Suite (Free GNU - Available for Windows and Linux - same as Star office)
http://www.openoffice.org

Adobe Acrobat Reader - Reads Portable Document Format ( PDF) files
http://www.adobe.com/products/acrobat/readermain.html


Endnote - Reference Manager
http://www.endnote.com