Useful Biology Websites

 

§http://www.iedb.org/

The IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases. It offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species. Epitopes involved in infectious disease, allergy, autoimmunity, and transplant are included.

http://www.proteinatlas.org/

§http://bio-hpc.eu/software/blind-docking-server/

The website provides a web-based server that automatically performs the docking

§  http://www.antibodyresource.com/

Database for resource on antibodies which provides the research community with comprehensive information about antibodies.

§  http://pax-db.org/#!home

Database for Relative Protein Abundance in different organisms including human. Very useful to eliminate false results from LCMS results (due to high abundance).

§  http://www.proqinase.com/

A very good company to source for most recombinant active kinases and mutants.

§  http://www.reactionbiology.com/webapps/main/pages/LaunchKir.aspx

Reaction Biology provides an exclusive web-based kinome mapping solution to present enzyme inhibition data. Click on the button below and the Java App will load. See the Hints file in the app for instructions.

§  http:/www.addgene.org/pgvec1

Addgene is a non-profit organization dedicated to promoting sharing of plasmid constructs described in published literature. Addgene stores original plasmid samples submitted by scientists and distributes them for use in advancing life science research.

§  http://www.hprd.org/

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain   architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data. HPRD has been created using an object oriented database in Zope, an open source web application server, that provides versatility in query functions and allows data to be displayed dynamically.

§  http://www.proteinkinase.de/html/protein_kinase_inhibitors.html

Commercial sources for small molecule kinase inhibitors.

§  http://merops.sanger.ac.uk/

Comprehensive proteases database (including substrates and inhibitors)

§  http://www.wormbook.org/chapters/www_transformationmicroinjection/transformationmicroinjection.html#d0e388

Microinjection set-ups and protocols

·       http://ptp.cshl.edu/index.shtml

This website aims to provide a peer-reviewed compendium on Protein Tyrosine Phosphatases (PTPs) that integrates sequence and structure information with cellular and biological function. Together with our analyses published in Mol & Cell Biol (2001), FASEB Journal (2004) and Methods (2005), it provides a resource for annotation and classification of the classical, tyrosine-specific PTPs.

§  http://www.phosphatase.net/

a useful website for phosphatase

§     http://phospho.elm.eu.org/

The Phospho.ELM database contains a collection of experimentally verified Serine, Threonine and Tyrosine sites in eukaryotic proteins. The entries, manually annotated and based on scientific literature, provide information about the phosphorylated proteins and the exact position of known phosphorylated instances.

§      http://smart.embl-heidelberg.de/

§   http://www.ebi.ac.uk/Tools/InterProScan/

§     http://pfam.sanger.ac.uk/

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)

§     http://www.ensembl.org/index.html

Ensembl is a joint project between EMBL – EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust.

§     http://www.cellsignal.com/reference/domain/index.html

§     http://www.cazy.org/

The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.

§     http://pawsonlab.mshri.on.ca/index.php?option=com_content&task=view&id=30&Itemid=63

Pawson lab protein interaction domain map.

§     http://sh2.uchicago.edu/

The SH2 domain website at the Piers lab, University of Chicago

§     http://www.phosphosite.org/

It is the intention of the scientists who are designing and implementing PhosphoSite to provide an accurate and comprehensive source of information about mammalian protein phosphorylation sites. Our goal is to identify and organize information about all in vivo phosphorylation sites in human and mouse proteomes and to provide information and resources that will facilitate phosphorylation research

§    http://horfdb.dfci.harvard.edu/

hORFeome v5.1 represents a central resource of cloned human ORFs which can be transferred easily to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10Kb base pairs, and (excluding the RT-PCR rescued ORFs) contains 1,502 genes with multiple splice-variants and 814 polymorphic genes.

§     http://locate.imb.uq.edu.au/

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications.

§     Chromatin Biology related

§  http://www.abcam.com/index.html?pageconfig=resource&rid=11924

§  http://202.97.205.61/hhmd/

§ http://www.cellsignal.com/reference/pathway/histone_modification.html#biotinylation

§    Genecards – http://www.genecards.org/

About GeneCards®: GeneCards is a searchable, integrated, database of human genes that provides concise genomic related information, on all known and predicted human genes. The GeneCards human gene database extracts and integrates a carefully selected subset of gene related transcriptomic, genetic, proteomic, functional and disease information, from dozens of relevant sources. It provides robust user-friendly access to up-to-date knowledge. GeneCardsovercomes barriers of data format heterogeneity, and uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each gene, and provides the means to obtain a deep understanding of biology and medicine. Information is featured in 18 GeneCards sections as shown below.

§     http://mordred.bioc.cam.ac.uk/timbal

A database containing known small molecule PPI inhibitors of different classes of proteins/domains.

§ http://bioinformatics.oxfordjournals.org/content/early/2013/08/19/bioinformatics.btt483

Subject: HippDB: A database of readily targeted helical protein-protein interactions

 

Commercial Sources for Recombinant Enzymes

§  http://www.jenabioscience.com/

§  http://www.bioclon.com/

§  http://www.upstate.com

 

Common Biology Protocols

·       96-well DNA minipreps and PCR purification (protocol, intro)

·       TLC Stains (1, 2, 3)

·       Distill Anhydrous solvents

·       Flash Column

·       Slide preparations

·       Slide, spotting and detection-1

·       Slide, spotting and detection-2

·       Slide, spotting and detection-3

·       Slide, spotting and detection-4

·       Quest 210 prtocols

·       Position-Scanning-Mix AA table

·       Growth of Hela Cells

 

Useful Biology Websites

§  http://pax-db.org/#!home

Database for Relative Protein Abundance in different organisms including human. Very useful to eliminate false results from LCMS results (due to high abundance).

§  http://www.proqinase.com/

A very good company to source for most recombinant active kinases and mutants.

§  http://www.reactionbiology.com/webapps/main/pages/LaunchKir.aspx

Reaction Biology provides an exclusive web-based kinome mapping solution to present enzyme inhibition data. Click on the button below and the Java App will load. See the Hints file in the app for instructions.

§  http://www.addgene.org/pgvec1

Addgene is a non-profit organization dedicated to promoting sharing of plasmid constructs described in published literature. Addgene stores original            plasmid samples submitted by scientists and distributes them for use in advancing life science research.

§  http://www.hprd.org/

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain   architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data. HPRD has been created using an object oriented database in Zope, an open source web application server, that provides versatility in query functions and allows data to be displayed dynamically.

§  http://www.proteinkinase.de/html/protein_kinase_inhibitors.html

Commercial sources for small molecule kinase inhibitors.

§  http://merops.sanger.ac.uk/

Comprehensive proteases database (including substrates and inhibitors)

§  http://www.wormbook.org/chapters/www_transformationmicroinjection/transformationmicroinjection.html#d0e388

Microinjection set-ups and protocols

·       http://ptp.cshl.edu/index.shtml

This website aims to provide a peer-reviewed compendium on Protein Tyrosine Phosphatases (PTPs) that integrates sequence and structure information with cellular and biological function. Together with our analyses published in Mol & Cell Biol (2001), FASEB Journal (2004) and Methods (2005), it provides a resource for annotation and classification of the classical, tyrosine-specific PTPs.

·       http://www.phosphatase.net/

a useful website for phosphatase

·       http://phospho.elm.eu.org/

The Phospho.ELM database contains a collection of experimentally verified Serine, Threonine and Tyrosine sites in eukaryotic proteins. The entries, manually annotated and based on scientific literature, provide information about the phosphorylated proteins and the exact position of known phosphorylated instances.

·       http://smart.embl-heidelberg.de/

·       http://www.ebi.ac.uk/Tools/InterProScan/

·       http://pfam.sanger.ac.uk/

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)

·       http://www.ensembl.org/index.html

Ensembl is a joint project between EMBL – EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust.

·       http://www.cellsignal.com/reference/domain/index.html

·       http://www.cazy.org/

The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.

·       http://pawsonlab.mshri.on.ca/index.php?option=com_content&task=view&id=30&Itemid=63

Pawson lab protein interaction domain map.

·       http://sh2.uchicago.edu/

The SH2 domain website at the Piers lab, University of Chicago

·       http://www.phosphosite.org/

It is the intention of the scientists who are designing and implementing PhosphoSite to provide an accurate and comprehensive source of information about mammalian protein phosphorylation sites. Our goal is to identify and organize information about all in vivo phosphorylation sites in human and mouse proteomes and to provide information and resources that will facilitate phosphorylation research

·       http://horfdb.dfci.harvard.edu/

hORFeome v5.1 represents a central resource of cloned human ORFs which can be transferred easily to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10Kb base pairs, and (excluding the RT-PCR rescued ORFs) contains 1,502 genes with multiple splice-variants and 814 polymorphic genes.

·       http://locate.imb.uq.edu.au/

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications.

·       Chromatin Biology related

o   http://www.abcam.com/index.html?pageconfig=resource&rid=11924

o   http://202.97.205.61/hhmd/

o   http://www.cellsignal.com/reference/pathway/histone_modification.html#biotinylation

 

·       Genecards – http://www.genecards.org/

About GeneCards®: GeneCards is a searchable, integrated, database of human genes that provides concise genomic related information, on all known and predicted human genes. The GeneCards human gene database extracts and integrates a carefully selected subset of gene related transcriptomic, genetic, proteomic, functional and disease information, from dozens of relevant sources. It provides robust user-friendly access to up-to-date knowledge. GeneCardsovercomes barriers of data format heterogeneity, and uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each gene, and provides the means to obtain a deep understanding of biology and medicine. Information is featured in 18 GeneCards sections as shown below.

·       http://mordred.bioc.cam.ac.uk/timbal

A database containing known small molecule PPI inhibitors of different classes of proteins/domains.

 

Ÿ  http://bioinformatics.oxfordjournals.org/content/early/2013/08/19/bioinformatics.btt483

Subject: HippDB: A database of readily targeted helical protein-protein interactions

 

Commercial Sources for Recombinant Enzymes

§  http://www.jenabioscience.com/

§  http://www.bioclon.com/

§  http://www.upstate.com

 

Common Biology Protocols

·       96-well DNA minipreps and PCR purification (protocol, intro)

·       TLC Stains (1, 2, 3)

·       Distill Anhydrous solvents

·       Flash Column

·       Slide preparations

·       Slide, spotting and detection-1

·       Slide, spotting and detection-2

·       Slide, spotting and detection-3

·       Slide, spotting and detection-4

·       Quest 210 prtocols

·       Position-Scanning-Mix AA table

·       Growth of Hela Cells