OHSU

Databases & Tools

Please use these tools to become as informed of the biology of the genes/proteins you are studying as possible. As these tools and the associated databases are continuously evolving, make a point to review your work frequently.

Toolboxes

EMBL - EBI European Bioinformatics Institute.

NCBI - National Center for Biotechnology Information

MIPS - Munich Information Center for Protein Sequences

ExPASy Great Protein Analysis Tools

BioCatalog - New molbio applications

Biome - bioscience website catalog

Biology WorkBench

Omics Gateway

Softberry

BioGPS -  resource for learning about gene and protein function

DataBases & Search Engines

dbGET

SOURCE, A unified resource for genomic and biochemical data for human, mouse, and rat genes.

GenBank

Ensemble.

Allgenes

OMIM- Online Mendelian Inheritance in Man

CGAP- Cancer Genome Anatomy Project

GENATLAS- Human genes atlas

GeneTests- Medical genetics knowledge base

GeneCards- Db integrating information on human genes

GeneLoc- Integrated map of the human genome (ex- UDB)

GDB- Human Genome Data Base.

Celera Consensus Human Genome, Celera Genomics, US 

Ensembl Human genome browser

The Gene Index Project- ex-TIGR Human Gene Indices

MGC- Mammalian Gene Collection

MGD- Mouse Genome Database.

FlyBase- Genetic and Molecular Database for Drosophila

Celera Drosophila Genome

"The Interactive Fly"

Berkeley Drosophila Genome Project

Homophila- Human Disease to Drosophila gene db

Wormbase

Caenorhabditis elegans WWW Server

Comprehensive Yeast Genome Database

Yeast Genome Database Search

Yeast Genome Database

ENZYME The Enzyme Data Bank.

COPE- Cytokines & Cells Online Pathfinder Encyclopedia

GPCRDB: Information System for G Protein-Coupled Receptors 

IUPHAR Receptor Database 

Kinomer 

Kinase.com- Genomics, evolution and function of protein kinases

Protein Kinase Resource 

Ligand-Gated Ion Channel Database 

Molecular Class-Specific Information System (MCSIS) 

Nuclear Receptor Resource (NRR) 

NucleaRDB: Information System for Nuclear Receptors 

NURSA: Nuclear Receptor Signaling Atlas 

Protein Tyrosine Phosphatases 

The SH2 Domain 

Knockout, Transgenic & Native Mutation databases

Database of Genotypes and Phenotypes (dbGaP)

C. elegans Gene Knockout Consortium,

TBASE - Transgenic/Targeted Mutation Database

Pathbase

Protein Mutant Database

RNAi Gateway

Gene Expression Databases & Tools

Gene Expression Omnibus (GEO) Datasets

Gene Expression Omnibus (GEO) Profiles

TROMER - The transcriptome analyser (TROMER) project

MDCS- Microarray Data Classification Server

CleanEx- The gene expression database and cross-dataset analysis tool

HTPSELEX- A database of in vitro selected TFBS sequences obtained with HT-SELEX

Biological Relevance of Gene Networks (BIOREL)

Expression Profiler

SCDb- Stem cell db

Stanford Microarray Database

ArrayExpress, EBI, UK

BODYMAP, Osaka Univ., Japan 

Biomolecule Interaction Growth and Expression Database (BIGED), George Church Lab, Harvard

ChipDB*, Richard Young, Whitehead Institute

SSA - The Signal Search Analysis server

ChIP-Seq - The ChIP-Seq Analysis server

Promoter Analysis

EPD Eucaryotic Promoter Database.

Transcription Factor Advisor

TFFACTOR and TFSITE - Transcription Factor Data

Protein Tools

EBI Toolbox Protein analysis tools at EBI

Protein Information Research

ExPASy links The ExPASy Life Science Directory

UniProt - Protein sequence and function

iHOP - Information Hyperlinked over Proteins

Proteomics

ExPASy Proteomics Protein analysis tools at ExPASy

Peptidome

Human 2-D PAGE Databases 

UNIMOD  "Protein Modifications For Mass Spectrometry", A list of potential amino acid modifications and mass shifts.

Phospepsort - Digest Phosphorylated Peptide Sequences

Protein Similarity & Motif Searches

PIR- Protein Identification Resource Database.

PROSITE- Protein Motifs Database.

SBASE- Library of Protein Domains

ProDom- A comprehensive set of protein domain families.

MOTIF- Search Patterns in Protein Sequences

PMOTIF- Search Protein Motifs

SwissProt- Protein Sequence Database.

BLOCKSDatabase of Highly Conserved Regions in Proteins.

FSSP- Families of Structurally Similar Proteins.

HSSP- Homology-Derived Structures of Proteins.

Pfam- The Pfam database is a large collection of protein families.

Domain Interaction Map (DIMA)- Interaction predictions

Functional Annotation Tool (FUNAT)- Functional class based on sequence

CDD- Conserved Domain Database, NCBI, US

CATH- Protein Structure Classification, University College, London, UK

COG- Clusters of Orthologous Groups of Proteins, NCBI, US. 

SMART- Simple Modular Architecture Research Tool

SCANPS - Scan Protein Sequence

PPSearch

PROPSEARCH - Protein Sequence Search for Structural Homolog

ProLink - Integrated Database of Protein Structure, Sequence Homology, and Functional Pattern Information.

PSORT - Predict Protein Sorting Signals

TMAP - Identification of Transmembrane Segments

Domain Club Browser Protein domain combinations that correlate with evolutionary change.

LOCATE: Subcellular Localization Database 

Structural Tools

3D Domains Database

Protein Explorer, Chime,RasMol & InterPro

META II PredictProtein server

3D-Dock Suite : FTDock, RPScore and MultiDock

CPHmodels server

Dali

Finding 3-D similarities in protein structures: using combinatorial extension (CE)

MaxSprout

PROSPECT

Protein-nucleic acid interaction server

ASTRAL compendium for sequence and structure analysis, Stanford Univ. US 

Structural Biology Knowledgebase

Enzyme Structures Database

NDB Nucleic Acid Structural Database.

Molecular Visualization Freeware

PredictProtein - Predict Protein Secondary Structure

PHD - Predict Protein Secondary Structure

PredictProtein - Predict Protein Secondary Structure

PSSP - Protein Secondary Structure Prediction

SOPM - Self Optimized Prediction Method for Prediction of Protein Secondary Structure

Protein Motions - DataBase of Protein Movement

SCOP - Structural Classification of Proteins

Sleuth - Amino Acid Conformation and Solvent Accessibility

Biological Macromolecule Crystallization Database 

Orientations of Proteins in Membranes database 

Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) 

Stephen White Laboratory at UC Irvine 

Ontology, Interactome Databases & Tools

Reactome

Database of Interacting Proteins 

Gene Ontology (GO) Consortium

BIOCARTA- gene interaction in dynamic graphical models.

Biochemical Pathways, Boehringer Mannheim

CGAP Cancer Gene Anatomy Project, NCBI, US  

BRITE Biomolecular Relations in Information Transmission and Expression

NCI's Pathway Interaction Database

Center for Cancer Systems Biology

KEGG Pathway database

CluSTr Index Proteins grouped by structural similiarities

IntEnz Enzymes grouped by function

BBID Biological Biochemical Image Database,

The MIPS Mammalian Protein-Protein Interaction Database (MPPI)

MPact: Representation of Interaction Data at MIPS

The Negatome Reference Database

Mammalian protein complexes at MIPS

BIND- Biomolecular Interaction Network Database

DIP- Database of Interacting Proteins

MINT- Molecular INTeraction database

IMEx

PSICQUIC View

ARNIE: AVEXIS Receptor Network with Integrated Expression

STRING protein-protein interaction network

HPRD- Human Protein Reference Database

IntAct

BioGRID- General Repository for Interaction Dataset

PPI- JCB Protein-Protein Interaction Website

PMD- Protein Mutant db

Database of Ribosomal Crosslinks (DoRCs), Max Planck Institut, Berlin

Metabolic Database- Metabolic Reactions and Pathways

Human Protein Reference Database (HPRD) 

Signal Transduction

WWW Virtual Library - signal transduction

Nature - The Signaling Gateway

ROSPath 

Post-Translational Protein Modification Databases

Scansite - Searches for binding motifs and phosphorylation sites.

PhosphoSitePlus- Tools for many PTMs

PhosphoPep - a database of protein phosphorylation sites identified by mass spectrometry.

Phosphorylation Site Database 

Cell Signaling Technologies phosphoprotein database

RESID Home– Post-translational modifications

The CAspase Substrate dataBAse Homepage (CASBAH) 

PHOSIDA Posttranslational Modification Database 

Delta Mass- A Database of Protein Post Translational Modifications

META II PredictProtein server

DSDBASE- Disulfide database (derived from 3D data)

GlycoSuiteDB- Db of glycan structures

LIPID MAPS- LIPID Metabolites And Pathways Strategy

GlycateBase- Database of glycation data for epsilon amino groups of lysines

O-GlycBase- O-glycosylated proteins db

Phospho.ELM- Phosphorylation sites db

PhosphoSite- Db of phosphorylation sites in human and mouse proteomes

DOLOPDb of bacterial lipoproteins

UbiProt- Db of ubiquitylated proteins

RESID- Db of Amino Acid Modifications

Delta Mass- Db of mass of Post-Translational Modifications

Signaling Gateway

UNIMOD  "Protein Modifications For Mass Spectrometry", A list of potential amino acid modifications and mass shifts.

Phospepsort- Digest Phosphorylated Peptide Sequences

Phospho.ELM - Database of both experimentally verified and manually annotated serine, threonine, and tyrosine phosphorylation sites.

Human Protein Reference Database (HPRD) 

virPTM: Viral Post-Translational Modification Database 

Cancer-Specific Tools

The Cancer Genome Atlas

CGAP Cancer Gene Anatomy Project, NCBI, US  

Progenetix CGH database - Molecular Cytogenetics in Leukemia and Cancer

Cancer Chromosomes

Human Protein Atlas - Displays the expression and localization of proteins in a large variety of normal human tissues and cancer cells

Cell Migration Gateway

Cancer Trials: Authoritative, comprehensive information and breaking news about cancer clinical trials and research.

Tumor Gene Database

Cancer Genetics Web

COSMIC- Somatic mutations in Cancer.

Drug Screening & Development

NIH Molecular Libraries Program

Harvard Screening Facility

PDSP Drug Database 

Sites of Interest to the Zundel Lab

NCI

OncoLink

National Comprehensive Cancer Network

VHL Family Alliance

ROSPath 

HIF  Pathway

Protocols & Bench Tools

Protocols on the WWW Lots of scientific methods and recipes

Microarrays.org

Virtual Library

MicroArray software

Nature Methods

YouTube - Molecular Biology Methods

Lab Tube.tv

The Miner Suite of web bioinformatic apps

REBase Restriction Enzyme Database.

Primer Selection - Select Primers

VecBase - Cloning Vector Sequence Database.

VECTOR - Cloning Vector Database

Gel Separation Chart - Pre-cast gel separation parameters

Ray Deshaies Lab Protocols

Other Good Resource-Listing Sites

Biotech Resources

MolBio Links

Qed Links

Sanger Institute

NCI software downloads

Protocol Links

Science Gateway

Cell & Molecular Biology Online

Protocol-Online

Molecular Biology Protocols

Axiovert 40c/cfl Inverted Microscope Demonstration Video

Health & Safety

OHSU EHRS

Volunteer Links (If you have this much time, see Dr. Z for another project!)

Volunteer at the Cancer Center!

Volunteer at OHSU Hospitals & Clinics

Camp Ukandu & Camp Tapawingo, Summer camping experience for cancer patients.

Jobs, Training & Fellowships

RRS

Naturejobs.com

Cell - Careers

Science Careers

Science Humor

Impact: Earth! Send Comets hurtling toward Terra!

Off the Mark - Mark Parisi

The Cartoons of S. Harris

The Scientific Cartoonist

Science Humor

More Science Humor

Jokeomics

Batting Penguins - The science is in vectoring bat to penguin of course!