Cool Science Links

Searching Tools | Chemistry Tools | Molecular Biology Tools | Genomics and Proteomics Tools | Protein Structure | Scientific Resources | Literacy Tools | Databases | Kinases | Protein-Protein Interactions

Searching Tools

 

ISI The Web of Knowledge

 

PubMed

 

Yale University Medical School online journals

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Chemistry Tools

 

Periodic Table – an interactive source of information about the elements

 

Organic Chemistry Resources – a toolbox for synthetic chemistry

 

Aldrich Substructure Search – search for commercial compounds with a particular substructure

 

Pharmacology Central – chemical structures of pharmacological agents

 

VassarStats – statistical tools

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Molecular Biology Tools

 

IDT SciTools - A suite of tools to help with design and analysis of oligonucleotides

 

Sorvall Rotor Calculator

 

The Antibody Resource - a guide to commercial antibody suppliers

 

ExPASy Translate Tool – how to translate a DNA/RNA sequence into protein

 

Sequence Manipulation Site – format and analyze DNA and protein sequences

 

BLAST and ClustalW – DNA and protein sequence alignment tools

 

Primer Design and Primer Generator – PCR primer design

 

RestrictionMapper – map restriction sites and predict fragment sizes

 

Consurf – locate variable and conserved regions within proteins

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Genomics and Proteomics Tools

 

Ensembl – browse the human, mouse, fly, & zebrafish genomes

 

EMBL Bioinformatics – genome database searching & analysis

 

Express Yourself – An integrated platform for processing microarray data

 

Yale Microarray Database – a web-based archive and retrieval system for storage of microarray data. The microarray convoluter (MAC) program listed under tools is useful for tracking each gene spotted on the array.

 

PFAM - a collection of multiple sequence alignments and hidden Markov models covering many common protein domains.

 

Harvard Institute of Proteomics - information about high-throughput protein expression protocols as well as FLEXGene, a publicly available and well-maintainted repository of cDNA clones.

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Protein structure tools

 

PDB server

 

RasMol - 3D Structure Viewer

 

CNS - Crystallographic/NMR Refinement Software

 

Swiss-Prot PDB Viewer

 

O webpage - program for viewing electron density representations of x-ray structures

 

DINO – freeware that creates surface potential maps

 

CCP4 Main Page - Freeware, a collection of scripts used for many of the
computational jobs involved in crystallographic data refinemen

 

INSIGHT - our licensed modeling software

 

SCOP - structural classification of proteins

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Scientific Resources

 

Biological Information Resource – Links to quality-checked biomedical websites

 

Alliance for Cellular Signaling – Signaling maps & protein information pages

 

Cell Biology Resource – General info, databases, protocols, vendors

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Literacy Tools

 

Encyclopedia Britannica

 

Oxford English Dictionary

 

The elements of style

 

Yale Writing Prose

 

Yale Web Style Guide

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Databases

 

NCBI – DNA and protein sequence database

 

Protein Information Resource – Protein sequence and classification database

 

PicSNP – Catalog of human SNPs

 

BioMagResBank – NMR data for proteins, DNA, and RNA

 

NBD Server – DNA and RNA information database

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Kinases

 

Protein Kinase Resource – Kinase sequences, protocols, structures, discussion boards

 

Phosphorylation Site Database – Determine protein phosphorylation sites

 

Scansite – Search for phosphorylation sites & SH2/14-3-3/etc binding sites

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Protein-protein interactions

 

BIND – bimolecular interaction network database

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