Editor:
Gerhard M. Kresbach, PhD, D-79219 Staufen, Germany
Comments and suggestions for enhancements and new links are very much appreciated --- email: kresbach@kresbach.de
Life-Science News & Information
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News & Alert Services
- Analytik News Edited portal for analytical life science related information - german
- Bionity.com Search engine and database for products and news in the field of life sciences
- BioSpace Biotech and pharmaceutical news & jobs
- BioWorld Biotechnology daily news and information
- BIO-IT World Information Technology for the Life Sciences
- BIO - Biotechnology Industry Organization Biotechnology related news
- CenterWatch Access to clinical trials information
- Drug Discovery from Technology Networks News, products,and resources related to drug discovery
- EurekAlert Online, global news service operated by AAAS
- Science Media Center Germany Independent public activities to collect expert statements, produce fact sheets, and organize press briefings on topics related to medicine and life science, environment and climate, energy and technology for journalists, scientists, and sponsors
- Fachinformationszentrum Search engine to scan german research activities and to locate BMBF funded reports and publications - german
- GERiT – German Research Institutions Information about over 29,000 institutes at German universities and non-university research institutions
- HUM-MOLGEN International communication forum in human molecular genetics
- idw - Informationsdienst Wissenschaft News platform covering activities of several hundred universities and research institutions in Germany, Austria and Switzerland - german
- Life-Sciences-Germany.com Life sciences web portal for german-speaking Europe - german
- MedBioWorld Online resource portal for professional medical and biotechnology information
- PubCrawler Alerting service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases
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Science Search Engines
- GQuery NCBI Global Cross-database Search. Integrates information from databases at NCBI which include nucleotide sequences, protein sequences, macromolecular structures, whole genomes, and MEDLINE.
- ScienceResearch.com Deep web science and technology search engine
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Literature Search
- AuthorMapper Online tool for visualizing scientific research, enables document discovery based on author locations and geographic maps. Integrating content and mapping technology,
- BASE - Bielefeld Academic Search Engine Highly configurable search engine for scientific publications
- Crossref Metadata-based broad search of scientific published information and authors of scientific publications
- DART-Europe E-theses Portal European portal for electronic theses and dissertations
- DIMDI - Deutsches Institut für Medizinische Dokumentation und Information Search of publications with focus on medicine and pharmacology
- Google Scholar Access to a broad range of scientific publications
- LIVIVO Database to search scientific publications and authors
- PubMed Search of biomedical publications in MEDLINE, life science journals, and online books - NCBI / NHI
- ScienceResearch.com Real-time deep web search engine for scientific publications
- Science.gov Search for publications in over 60 databases and over 2200 selected websites from 15 federal agencies - Science.gov Alliance
- Subito Access to publications in academic libraries in Germany, Austria, Liechtenstein, and Switzerland
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On-Line Journal Aggregators and Open Access Publishers
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E-Libraries & E-Archives
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Publications - Varia
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General
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Scientific
& Linguistic Dictionaries
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Protocols
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Scientific Images & Illustrations
- BIODIC - The Ultrastructure Website Collection of high resolution electron micrographs of cells, bacteria, fungi, pollen, biological structures, etc.
- BrainInfo Maps of brains of primates
- Cells Alive Drawings, micrographs, and movies of cells and microorganisms
- Database of Macromolecular Movements Animations and movies of motions that occur in proteins and other macromolecules
- Jena Library of Biological Macromolecules Information on three-dimensional biopolymer structures with an emphasis on visualization and analysis
- Nanoworld Scanning electron, transmission electron, and optical microscopy images of microorganisms and biological structures
- PDBsum Pictorial database of 3D structures in the Protein Data Bank
- Protein Imager Tool to visualize protein structures directly in the browser
- Structural View of Biology Images of biomolecules utilizing Protein Data Bank data, focusing on the biological function of the molecules
- The Visible Human Project Complete, anatomically detailed, three-dimensional representations of the normal male and female human bodies
- Virtual Cell Animation Collection Visualization of cellular functions
- Anatomia 1522 - 1867 - Anatomical Plates from the Thomas Fisher Rare Book Library Approximately 4500 full page plates and other significant illustrations
of human anatomy selected from the Jason A. Hannah and Academy of Medicine collections in the history of medicine
- EPACT - Scientific Instruments of Medieval and Renaissance Europe Electronic catalogue of medieval and renaissance scientific instruments from the Museum of the History of Science, Oxford, the
Istituto e Museo di Storia della Scienza, Florence, the British Museum, London, and the Museum Boerhaave, Leiden.
- Images from the History of Medicine Collection including portraits, pictures of institutions, caricatures, genre scenes, and graphic art in a variety of media, illustrating the social and historical aspects of medicine
- Medicine and Madison Avenue Images and database information for various health-related advertisements printed in newspapers and magazines from the 1910s through the 1950s
- MEMS Image Gallery
Electron micrographs of micromachined devices
- Pictures of Famous Physicists Photos, drawings, stamps and other portraits of scientists
- The Edgar Fahs Smith Memorial Collection Prints, engravings,and photographic images of scientists, laboratories, and scientific apparatus
- The Periodic Table of Comic Books
Chemical elements in comic books
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Spectroscopy Databases
- BioMagResBank Repository for NMR data of proteins, peptides, and nucleic acids
- Infrared Spectra Downloadable free infrared spectra library
- IR-Spektrensammlung der ANSYCO GmbH IR spectra of gaseous state compounds - german
- MassBank Public repository of mass spectral data
- NIST Chemistry WebBook National Institute of Standards
Reference databases, covers MS, IR and UV/VIS spectra
- NMRShiftDB Open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data
- SDBS Integrated Spectral Data Base System for Organic Compounds - MS, NMR, IR, Raman, and ESR spectra
- SPECARB - Raman Spectra of Carbohydrates
Experimental database that contains Raman spectra of carbohydrates
- TeleSpec Simulation of infrared spectra, especially for compounds whose spectra are not available in any database
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Biology,
Biotechnology & Molecular Biology
- Bacteria and Viruses: How Are They Different? Basic as well as advanced information about bacteria and viruses
- Biochemistry of Metabolism Instructional materials for a studio-format course
- BioChemWeb Virtual library of biochemistry, moleculer biology and cell biology
- biolinks.de Selected and commented links to fields of biology equally relevant for science and society - german
- BiosciEdNet Digital library portal for teaching and learning the biological sciences
- BioED Online Science teachers resources from Baylor College of Medicine
- Digital Learning Center for Microbial Ecology Information on microbial ecology for students and teachers
- DNA from the beginning Animated experiments illustrating modern genetics
- Fishbase Global information database about fishes
- GBIF - Global Biodiversity Information Facility Open access database on biodiversity
- GSLC - Genetic Science Learning Center
Science education program of the University of Utah
- Giftpflanzen Poisonous plants - covering different aspects of poisons in plants and herbs, their chemistry, toxicity, antidots, as well as biological function - german
- MendelWeb Educational resource for teachers and students interested in the origins of classical genetics, introductory data analysis, elementary plant science, and the history and literature of sciencee
- MicrobeWorld Educational website providing information about basic microbiology and issues involving microbiology
- Molecular Station Science and discussion forum for molecular biology methods and protocols
- NCBI Bookshelf Free access to books and documents in life science and healthcare
- PAZy - The Plastics-Active Enzymes Database Database of biochemically characterized plastic-active enzymes to be of use for plastic degradation
- Protist Information Server
Images and movie clips of protists and other microorganisms
- The Biology Project On-line interactive resources for learning biology
- The Human Body: Skin Biology and Structure Web site featuring a broad range of information about skin related structure, biology, and treatment
- Tree of Life web project Vast collection of information about biodiversity compiled in a phylogenetic tree
- TreeBASE Database of phylogenetic knowledge
- Understanding Genetics
Introduction to basic principles of genetics for a general audience
- Vascular Plant Types Catalog Database and images of approximately 92,000 vascular plant type specimens of the New York Botanical Garden
- Virtual Genetics Lab Simulation of transmission genetics that approximates, as closely as possible, the hypothesis-testing environment of genetics research
- Zbio.net Methods, information and programs
for molecular biologists - russian - german project
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Chemistry
& Analytics
- Analytical Chemistry Springboard Comprehensive list of analytical chemistry resources on the Internet
- Chemexper Search engine to locate chemicals and suppliers
- Chemical Information Sources Wikibook covering a wide range of chemistry information resources on the internet
- ChemIDplus Advanced
Database allowing users to search the NLM ChemIDplus database of over 400,000 chemicals for among others physical, chemical, and toxicological properties
- Chem1 Virtual Textbook
Comprehensive virtual textbook for General Chemistry
- Chemie.de German chemistry information service - german
- Chemistry animations and movies on the World Wide Web Link list for chemistry related animations
- Chemistry Webercises Directory
Extensive collection of links to various areas of chemistry
- Enhanced NCI Database Browser 2.2 Data base with structures, data, tools, programs and other useful information to the public
- Experimentalchemie.de Chemical experiments for teaching, educational and show purposes - german
- Global Instructional Chemistry Chemistry tutorials,
course materials, reviews, and reports
- Molecular Modeling for Organic Chemistry Lecture course aimed to introduce in a simple way into the hierarchy of computational modelling methods
- Namensreaktionen Chemical mane reactions - german
- Nobel Prize for Chemistry
Information about Nobel price winners in the field of chhemistry
- Organic Chemistry Resources Worldwide WWW resource guide for synthetic organic chemists covering literature, bench work, structural analysis, and communication
- Organic Chemistry Portal
Overview of recent topics, interesting reactions, and information on important chemicals for organic chemists
- Panopticon Lavoisier Virtual museum of the collections of the French chemist Antoine Laurent Lavoisier
- Periodic Table Resource: Tungsten, Palladium and Other Transition Metals Detailed information about transition metals
- Prof. Blumes Bildungsserver für Chemie Large
collection of chemistry related texts and experiments especially suited for educational purposes - german
- Selected Classic Papers from the History of
Chemistry Papers from the history of chemistry as html files
- Virtual Chemistry 3-D simulated laboratory for the teaching of chemistry
- Virtual Mass Spectrometry Laboratory Interactive, educational tool to teach mass spectromtery
- Yeah Science Entertaining introduction to chemistry
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Medicine
- A Nurse's Guide to the Human Body Comprehensive link list covering a multitude of functional and regulatory systems of the human body
- Anatomy of the Human Heart ACLS link list to educational resources related to the heart
- Digital Anatomist Information System
The long term goal of the Digital Anatomist project is an anatomy information system that is available from any desktop computer on the network
- Genetics Home Reference National Library of Medicine's web site for consumer information about genetic conditions and the genes or chromosomes responsible for those conditions
- MedNets Medical database designed for use by physicians, administrators, patients and the general public as a health research and information resource
- Introduction to Cardiothoracic Imaging Illustrated tutorial to heart and lung anatomy
- Medscape Online resource for medical information - Medline, Toxline, Aidsline access
- MedBioWorld Resource portal for professional medical and
biotechnology information
- Merck Manual of Medical Information--Home Edition Based on The Merck Manual of Diagnosis and Therapy, commonly referred to as The Merck Manual, transformed into commonly used English while retaining the vital information about diseases, diagnosis, prevention, and treatment
- RN to BSN Online Programs Listing of RN to BSN Programs in America
- The Internet Pathology Laboratory for Medical Education Web resource that includes over 1900 images along with text, tutorials, laboratory exercises, and examination items for self-assessment that demonstrate gross and microscopic pathologic findings associated with human disease conditions
- The Ultimate List of Anatomy and Physiology Resources Comprehensive link list covering medical, biological as well as chemical areas
- Virtual Autopsy
Mini-tutorials on aspects of anatomy
- Who
Named It? Comprehensive dictionary of medical eponyms - including bibliographic information
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Pharma
- ChemBank
Collection of data about small molecules and resources for studying their properties, especially their effects on biology
- Drug Discovery Online Site devoted exclusively to drug discovery and early-stage drug development - buyer's guide, feature stories, case studies, industry news, and newswire feeds related to the science and business of discovering new drugs
- etc.
The Enzyme Technology Consultancy - Reports for the diagnostics industry
- Global Pharmaceutical Industry - Statistics & Facts
- HTScreening.net
High throughput screening (HTS) web portal
- Medtrial.com
Information source for clinical trials
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Physics,
Maths & Engineering
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Patent-Retrieval
Databases
- DEPATISnet On-line search of patents world-wide - Deutsches Patent- und Markenamt
- Espacenet Database of the European Patent Office
- FPO Free Paternts Online search system
- FreshPatents Listing of recent US patent applications with keyword monitoring
- Google Patents Google patent search system
- Lens.org Global patent and scholarly knowledge search system
- Patent Center USPTO's patent application information retrieval system
- Patentscope World International Property Organization searchable database
- Swissreg Trademark, patent and designs register data as well as protected topographies of the Swiss Federal Institute for Intellectual Property
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Additional Patent
Information
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Trademarks
- DMPAregister Marken Database of German trademarks - german
- Markengesetz Full text of German trademark law - german
- Swissreg Marken Database of Swiss trademarks - german
- TMview Database of trademarks in Europe
- TESS USPTO's database of registered trademarks and prior pending applications
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Microarrays
- ArrayExpress
Public EBI sponsored repository for microarray based gene expression data. Currently the EBI is establishing a pilot database containing
microarray gene expression data that are available publicly
- ABRF Microarray Research Group
Microarray Research Group in the framework of the Association ob
Biomolecular Resource Facilities
- BASE
project page Open source web-based comprehensive
database server to manage the massive amounts of data generated by
microarray analysis
- BioChipNet
NMI / BMI website on biochip technologies
- Diagnostic
Microbial Microarrays Microbial microarray projects carried out at the Department of Biotechnology of the Austrian Research
Centers, Seibersdorf, Austria
- DNA Microarray Methodology - Flash Animation Animation that demonstrates how DNA microarrays are performed
- EMBL-EBI The microarray
informatics group at the EBI addresses the problem(s) of managing,
storing and analysing microarray data
- Gene-Chips
Leming Shi's Array Page
- GermOnline
Cross-species community annotation knowledgebase that provides microarray data relevant for the mitotic and meiotic cell cycle as well
as gametogenesis
- Genome Consortium for Active Teaching (GCAT)
Initiative to allow college students to work with DNA microarrays
- Lab-on-a-Chip News server
for microarray and microfluidics activities
- Longhorn
Array Database - LAD The LAD is a MIAME compliant
microarray database that operates on PostgreSQL and Linux. It is a
fully open source version of the Stanford Microarray Database (SMD),
one of the largest microarray databases.
- Microarrays
Research Today Free monthly online journal that
collates and summarizes the latest research about Microarrays,
including details on experiments, designs, statistics, analysis,
software
- microarrays.com
Vanderbilt microarray core facility
- MicroArray Quality Control (MAQC) Project
The project involves six FDA Centers, major providers of microarray
platforms and RNA samples, EPA, NIST, academic laboratories, and other
stakeholders. It aims to establish QC metrics and thresholds for
objectively assessing the performance achievable by various microarray
platforms and evaluating the advantages and disadvantages of various
data analysis methods
- MUSC DNA Microarray Database
Repository for DNA microarray data generated by MUSC investigators. At
the discretion of the contributors, DNA microarray data is placed into
the public domain and can be viewed and downloaded via the web
interface - Medical University of South Carolina
- ProteomicsSURF
- Microarrays Comprehensive list of links to DNA and
protein microarray activities and literature
- University
of Geneva Hospitals - Genomic Research Laboratory
Microarrays in prokariotic research
- Y.F.
Leung's Functional Genomics - Microarray List of
links to microarray related activities
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Field
Flow Fractionation
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Mass
Spectrometry
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Nanotechnology
- CC
NanoChem Center of competence nanotechnology -
german interdisciplinary network of nanotechnology activities
- Exploring the Nanoworld
Educational website to investigate the frontiers of the nanoworld
- Nanomat
Superregional NETWORK for Nanotechnology Materials - sponsored by the
german Ministry of Research
- Nanonet
Information on aspects of the nanoworld - sponsored by the bmb+f
(german federal research department) and the VDI (german engineering
association)
- NAS Computational Molecular Nanotechnology
Survey of NASA Ames molecular nanotechnology activities - publications,
images, links
- Nanotechnology
Database Up-to-date sources of information on
nanotechnology in the following areas: major research centers, funding
agencies, major reports and books
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Global
- 2Can
Support Portal Bioinformatics Introductions to
basic concepts in molecular and cell biology and bioinformatics. The
main emphasis is placed on making it as easy as possible for the user
to understand which tools and databases are available from the EBI and
from sites belonging to its collaborators
- BIOINFORMATICS.PHRMA.ORG
Page of the Pharmaceutical Research and Manufacturers of America
- bioinformatik.de
Webdirectory for bioinformatics
- CMS
Molecular Biology Resource Compendium of electronic
and Internet-accessible tools and resources for Molecular Biology,
Biotechnology, Molecular Evolution, Biochemistry, and Biomolecular
Modeling. Among others: PCR primer selection, primer databases, PCR
reaction setup, and PCR protools - Prediction of melting transitions of
dsRNA, DNA or RNA/DNA hybrids
- HSLS Online Bioinformatics Resources
Collection Annotated information and guided links to more than 1500 open sources bioinformatics databases and software tools
- The Elements of Bioinformatics Summarizing a large range of bioinformatics tools via a periodic table like structure
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Microarrays
- A 'module map' showing conditional activity
of expression modules in cancer Integrated analysis of a compendium of 1975 published microarrays spanning 22 tumor types. Expression profiles in different tumors are described in terms of the
behavior of modules, sets of genes that act in concert to perform a specific function.
- BRB
ArrayTools Integrated package for the visualization
and statistical analysis of DNA microarray gene expression data - NCI
- Cyber-T
Statistics program with a web interface that can be conveniently used
on high-dimensional array data for the identification of statistically
significant differentially expressed genes. It employs statistical
analyses based on simple t-tests that use the observed variance of
replicate gene measurements across replicate experiments, or
regularized t-tests that use a Bayesian estimate of the variance among
gene measurements within an experiment - University of California,
Irvine, Functional Genomics Center
- CMS
Molecular Biology Resource Compendium of electronic
and Internet-accessible tools and resources for Molecular Biology,
Biotechnology, Molecular Evolution, Biochemistry, and Biomolecular
Modeling. Among others: PCR primer selection, primer databases, PCR
reaction setup, and PCR protools - Prediction of melting transitions of
dsRNA, DNA or RNA/DNA hybrids
- DNA-Chip Analyzer (dChip)
Software package implementing model-based expression analysis of
oligonucleotide arrays and several high-level analysis procedures -
Harvard School of Public Health
- GEDA Gene Expression Data
Analysis Tool Users can perform a number of simple transformations,
finds differentially expressed genes using a variety of simple tests
and performs agglomerative clustering on the samples using the retained
genes as features with a user-selected clustering algorithms -
University of Pittsburgh Cancer Institute
- GEDS Gene Expression Data
Simulator - University of Pittsburgh Cancer institute
- GenMAPP
Gene MicroArray Pathway Profiler - Computer application designed to
visualize gene expression data on maps representing biological pathways and groupings of genes
- GeneXPress GeneXPress is
a visualization and analysis tool for gene expression data, integrating
clustering, gene annotation, and sequence information. It allows to
load clustering results and automatically analyze them for significance
of functional groups through correlation with functional annotations
(e.g. Gene Ontology) and for enrichment of motif binding sites (e.g.
TRANSFAC motifs).
- Genomics
and Bioinformatics Group (GBG) web site
Bioinformatic program packages, microarray data analysis information,
and molecular databases for genomic and proteomic research: MatchMiner,
GoMiner, MedMiner, CIMminer, MIMminer
- GSCope Suite of
bioinformatics software packages: SOM clustering and gene-ontology
analysis of microarray data, integrated viewer for biomolecular network
graphs, viewing and analyzing expression data on biological pathways
- High-density
Array Pattern Interpreter (HAPI)
Method for interpreting the conceptual
similarities of a cluster or group of genes that have been identified
by a statistical methods such hierarchical clustering, Self-Organizing
Maps, "gene shaving", k-means clustering, etc.
- L2L Microarray Analysis Tool Tool for discovering hidden biological significance in microarray expression data
- Module Map Tool to parse
microarray data to identify groups of genes that work in concert during
normal activities or in cancerogeneous cells
- OligoArray
2.0 Software that computes gene specific
oligonucleotides for genome-scale oligonucleotide microarray
construction
- ONCOMINE
Camcer Microarray Database Bioinformatics
infrastructure for cancer genomics research that provides tools to
query and visualize cancer microarray data for a gene or cancer type of
interest
- ProMAT - Protein Microarray Analysis Tool
Software module for data analysis of protein microarrays
- PubGene
Web Tools On-line packages for up-to-date gene
data, protein and mutation data, import and export options, clustering
methods, disease, process, and function associations and advanced
graphics
- TM4
Online Suite of tools that consist of Microarray
Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System
(MIDAS), and Multiexperiment Viewer(MeV), as well as a Minimal
Information About a Microarray Experiment(MIAME)-compliant MySQL
database - TIGR
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Oligonucleotide Primer
Synthesis / Positioning
- ALIGN Query ALIGN query
using sequence data at the GENESTREAM network server IGH Montpellier, F
- ExonPrimer
Perl script that helps to design intronic primers for the PCR
amplification of exons - Tim Strom, Institute for Human Genetics,
Technical University of Munic
- GeneFisher Interactive
PCR primer design - University of Bielefeld, D
- IDT SciTools
Oligonucleotide sequence designer tools - for primers, RNAi and
microarray probes
- LALIGN Query LALIGN query
using sequence data at the GENESTREAM network server IGH Montpellier, F
- NetPrimer Free web-based
interface using the latest primer design algorithms - Premier Biosoft
- OligoAnalyzer
Oligonucleotide parameter calculator from IDT BioTools
- Oligo Calculation Oligonucleotide parameter calculator from Genset
- Oligonucleotide Properties Calculator
Comprehensive calculator with open algorithms
- OligoCalc Oligonucleotide melting point calculator
- PRIDE Primer Design for large-scale projects in sequencing, PCR, and DNA array design
- The Primer Generator Automated generator of primers for site-directed mutagenesis
- Primer3web Pick primers from
a DNA sequence - Whitehead Institute for Biomedical Research
- Primer Design Java applet
by Luca Ida Giovanni TOLDO
- Primer
Selection Interface to a PCR primer selection program based on xprimer - University of Minnesota
- POLAND Prediction of melting transitions of dsRNA, DNA or RNA/DNA hybrids
- Primer Selection Interface to a primer selection program based on Xprimer
- QPPD
The Quantitative PCR Primer Database (QPPD) provides information about primers and probes that can be used to quantitate human and mouse mRNA by reverse transcription polymerase chain reaction (RT–PCR) assays. All data has been gathered from published articles, cited in
PubMed.
- Tinoco Plots Simple tool to investigate possible secondary structure elements in RNA or DNA single strands
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Nucleic
Acid Structures & Sequences
- Beacon Designer Free Edition Free on-line qPCR design software that can be used to screen SYBR® Green primers and TaqMan® probes for possible secondary structures such as dimers or hairpins
- Bioinformatics Software Packages Mayo Clinic's software packages to analyze, visualize and interpret genomic data
- GeneDesign
Web-based program for the design of synthetic genes. It consists of
several modules that automate the tasks associated with the
manipulation of synthetic sequences
- InstaSeq Tool to search
the World-Wide-Web for any fragment of DNA, RNA or Protein Sequence
- RNA mfold RNA folding
server of Michael Zuker, Washington University in St. Louis -
calculation of secondary RNA structures
- SEQUEROME Web-based
sequence profiling tool of BLAST results allowing to extract the
maximum out sequence alignment reports
- Sfold Sfold predicts probable RNA secondary structures, assesses target
accessibility, and provides tools for the rational design of RNA-targeting nucleic acids
- SMS
Collection of JavaScript programs for generating, formatting, and
analyzing short DNA and protein sequences
- UNAFold Unified Nucleic Acid Folding and hybridization package - access to mfold & DINAMelt RNA & DNA folding calculation software
- VISTA
Comprehensive suite of programs and databases for comparative analysis
of genomic sequences
- WatCut On-line tool for
restriction analysis, silent mutation analysis, and SNP analysis
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Proteins
- AbMiner
Relational database of information on antibodies that we have screened
specificity against the NCI-60 cancer cell lines. The database includes
results of screenings by western blot, practical information for
purchase, identifiers such as UniGene cluster and gene name for each
antibody, and out-links to major public bioinformatics resources
- BIND
Biomolecular Interaction Network Database - a database designed to store full descriptions of interactions, molecular complexes and pathways
- DeepView
Visualization, comparison, analysis, and modeling of proteins - former
SwissPDB Viewer
- Molecular Docking Web
Software for automated docking and scoring of flexible ligands to
receptors
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Prediction
of Biological Function
- AmiGO
HTML-based browser for Gene Ontology - established by the Gene Ontology
Consortium
- BioModels
Database The BioModels Database is a new effort to develop a data resource that will allow biologists to store, search and retrieve published mathematical models of biological interests. The models in the BioModels Database are annotated and linked to relevant data resources, such as publications, databases of coumpounds and pathways, controlled vocabularies, etc.
- eGOn
eGOn (explore Gene Ontology) is a tool that facilitates use of biological background knowledge in analysis of genes selected from high throughput analysis like e.g microarray analysis. Lists of identifiers containing i.e. differentially expressed genes, are submitted to our annotation database, and eGOn automatically extends the list with Gene Ontology (GO) terms annotated to these genes.
- E-Cell
The E-Cell Project is an international research project aiming at
developing necessary theoretical supports, technologies and software
platforms to allow precise whole cell simulation.
- Gepasi
Software package for modeling biochemical systems. It simulates the
kinetics of systems of biochemical reactions and provides a number of
tools to fit models to data, optimize any function of the model,
perform metabolic control analysis and linear stability analysis.
- GRAM - Genetic RegulAtory Modules
Algorithm that identifies modules, collections of genes that share
common regulators as well as expression profiles. The algorithm
combines direct information from DNA binding experiments with indirect
functional information from expression experiments.
- LocusLink
Single query interface to curated sequence and descriptive information
about genetic loci. It presents information on official nomenclature,
aliases, sequence accessions, phenotypes, EC numbers, MIM numbers,
UniGene clusters, homology, map locations, and related web sites.
- Onto-Express
Tool to automatically translate lists of genes found to be
differentially regulated in the condition under studyl into functional
profiles characterizing the impact of the condition studied
- Pandora
Protein ANnotation Diagram ORiented Analysis - protein-clustering tool
to help to identify their mode-of-action
- PubGene
Web tools for the analysis of expression data in the context of
literature or sequence associations
- The
ConSurf server Identification of Functional Regions
in Proteins by Surface-Mapping of Phylogenetic Information
- Virtual
Cell Modeling cell biological processes. The
approach associates biochemical and electrophysiological data
describing individual reactions with experimental microscopic image
data describing their subcellular locations. A transparent mathematics
framework develops numerical simulations, and results can be analyzed
as images. Developed by the National Resource for Cell Analysis and
Modeling (NRCAM)
- 3d
Mind Tools Tools for modeling pharmacological
activity using neuronal networks
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Varia
- Argo
Java Tool for visualizing and manually annotating whole genomes
- BioLinux
Free bioinformatics software tools
- Chemical
Structure Searching Servers Access to National
Library of Medicine's information databases on drugs, pesticides,
environmental pollutants, and other potential toxins
- ELECTRAS Web-based
electronic data analysis service for the mathematical analysis of
numerical data sets
- Interactive Statistical Pages
Powerful, conveniently-accessible, and free multi-platform statistical
software package. Links to online statistics books, tutorials,
downloadable software, and related resources
- IUBio
Archive for Biology Data and Software Indiana
University archive of biology data and software, established in 1989 to
promote public access to freely available information, primarily in the
field of molecular biology
- NCBI
Structure The Structure Group at NCBI has created an
up-to-date database of 3-dimensional macromolecular structures along
with a rich set of tools for comparing and visualizing structures and
sequences, searching for similarities, and associating these data with
other information sources such as taxonomy and literature databases
- Visual
Molecular Dynamics Free downloadable software
package for modeling proteins, lipid bilayers, and nucleic acids
- Webcutter Determination
of the restriction maps - automatic sequence search-and-entry from
NCBI's GenBank
- 2D and
3D Structural Information from DTP About half a
million structures of the Developmental Therapeutics Program of the NCI
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File
Formats
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Genomics, Proteomics
& Transcriptomics
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Global Access to Databases
- Blast Search BLAST Search
using sequence data at the GENESTREAM network server IGH Montpellier,
France
- Databases
on Medicine and Molecular Biology Comprehensive
annotated link list to genomics, pharmacology, toxicology and related
databases
- Entrez, The Life Science Search Engine
Cross-database search page for all NCBI Web and FTP sites - NCBI
- Entrez Nucleotide Access
to Genbank - NCBI
- FASTA Search FASTA Search
using sequence data at the GENESTREAM network server IGH Montpellier,
France
- GenBank Database Query
Text and Similarity Searching - National Center for Biotechnology
Information
- GeneStream2
Nucleic acid sequences from Genbank, EMBL, Genbank-new, EMBL new and
GB-expressed sequence tag databases are concatenated and duplicate
entries removed to produce a single dataset. The current size of the
non-redundant database is over 3.0 million sequences. Its size requires
that access to search this data base by some search programs is
resticted to a mail only service.
- OLCODIBS
- On Line Colection of Databases in the Biological Sciences
Broad structured collection of links to life science databases
- Sequence
Retrieval System EMBL service for a combined search
of SWISS-PROT, EMBL, TrEMBL, GenBank, etc.
- SSEARCH Search SSEARCH
Search using sequence data at the GENESTREAM network server IGH
Montpellier, France - email service only
Back to Genomics, Proteomics & Transcriptomics
Genomics
- addgene
Non-profit plasmid repository operating a plasmid repository for the research community
- ARS Genome Database Resource
Set of agricultural genome databases. They include plant genes,
chromosome maps, DNA fingerprints, beneficial traits, and crop varieties
- Atlas of Nucleic Acid Containing Structures
Extremely comprehensive database of the Nucleic Acid Database Project
covering DNA structures, RNA structures, unusual structures,
protein/DNA complexes, and protein/RNA complexes
- Bacteriophage Home Page Bacteriophage T4 and other phages home page - Evergreen State College
- BGMUT
- Blood Group Antigen Gene Mutation Database
Database of variations in the genes that encode antigens of blood group
systems
- Cancer
Genome Anatomy Project Survey of commonly used
approaches to high throughput, comprehensive analysis of relative
transcript expression levels
- Caenorhabditis
elegans WWW Server Webserver for Caenorhabditis
elegans research
- Cancer Cell Line Project
Characterization of 600 tumor cell lines with respect to in vitro
acquired additional genetic abnormalities
- CGEMS
- Cancer Genetic Markers of Susceptibility
Genome-Wide Association Study (GWAS) on over 500,000 genetic variants
to determine their role in cancer susceptibility
- Consensus CoDing Sequence (CCDS) project
Annotated high quality core set of human protein-coding regions
- Cyanosite Webserver for
cyanobacterial research
- Comparative
RNA Web Site Information on structure and evolution
of especially ribosomal and transfer RNAs
- DG
CST - Disease Genes Conserved Sequence Tags Database
collection of conserved sequence elements, identified by a systematic
genomic sequence comparison between a set of human genes involved in
the pathogenesis of genetic disorders and their murine counterparts
- DHGP -
Deutsches Humangenomprojekt German Human Genome
Project - Resource Center
- DHGP - Deutsches Humangenomprojekt German Human Genome
Project - Resource Center
- DNASU Central repository for plasmid clones and collections. Currently over 200,000 plasmids including 75,000 human and mouse plasmids are stored and distributed
- DISC
DNA Information and Stock Center, National Institute of Agrobiological
Resources,
Tsukuba, Japan
- EGAD
- The Expressed Gene Anatomy Database Non-redundant
set of human transcript (HT) sequences and non-human transcript (ET)
sequences
- EST Clone
Resources American Type Culture Collection (ATTC)
cDNA collection including clones deposited by TASC/I.M.A.G.E.
- E.coli
Index Comprehensive guide to information relating to
Escherichia coli
- FVII
Mutation Database Searchable database covering
mutations of Factor VII
- genepaint.org
Digital atlas of gene expression patterns in the mouse
- Gene Expression Database Query
Database of human and mouse gene activities in various cells and
tissues - Novartis Research Foundation
- Genlink
Multimedia database resource for human genetics - Washington University
St. Louis
- GeneSeeker
Search engine to interrogate different databases simultaneously, given a known human genetic location and expression/phenotypic pattern
- genome
gateway Comprehensive genomics web resource
established by Nature and Nature Genetics
- Genome
Reviews Standardised and comprehensively annotated
view of the genomic sequence of organisms with completely deciphered
genomes - EMBL-EBI
- Genetic Association Database
Archive of human genetic association studies of complex diseases and
disorders
- geo
- Gene Expression Omnibus Public gene expression
data collection - launched by NCBI. Gene expression data repository and
online resource for the retrieval of gene expression data from any
organism or artificial source. Gene expression data from multiple
platforms, including spotted microarray, high-density oligonucleotide
array , hybridization filter and serial analysis of gene expression
(SAGE) data, will be accepted, accessioned, and archived as a public
data set.
- GOLD
- Genomes OnLine Database Information covering
complete and ongoing genome projects around the world
- Gottschling Lab Homepage
Collection of core yeast protocols
- GeneCards Concise
information about the functions of all human genes that have an approved symbol (gene listing)
- Gramene
Curated, open-source, Web-accessible data resource for comparative
genome analysis in the grasses
- HapMap
Multi-country effort to identify and catalog genetic similarities and
differences in human beings. The haplotype map of the human genome, the
HapMap, will describe the common patterns of human DNA sequence
variation.
- Harvard
Medical School - George M. Church Laboratory & Lipper Center
for Computational Genetics Computational &
comparative functional genomics
- Hembase
Information about genes transcribed in blood cells
- HemoPDP The Hematopoiesis
Promoter Database (HemoPDB) is as a publicly available, web-based
information resource focused on transcriptional regulation in
hematopoiesis
- Human
Genome Project Information Information about the
U.S. and worldwide Human Genome Project, research in progress site
- Human
Genome Resources Links to key genomic databases,
maps, and markers for all 23 pairs of human chromosomes. LocusLink -
starting place for a quick summary of all top-level information about a
gene. Launched by the National Center for Biotechnology Information
(NCBI)
- hum-molgen
Communication forum in human molecular genetics
- IDbases
- databases for immunodeficiency-causing mutations
Large collection of databases for immunodeficiency-causing mutations
- International
Sequencing Consortium Large-scale Sequencing Project Database
Web site to provide a single, central site for the scientific community and the public to have access to up-to-date information about animal, plant and other eukaryotic genomic sequencing projects
- Mapping the Icelandic Genome
An ANTHROPOLOGY of the scientific, political, economic, religious, and ethical issues surrounding the deCode project and its global
implications
- Mouse Encyclopedia Index About 20000 end sequenced cDNA
clones compiled by the Genome Exploration Research Group of RIKEN (Japan)
- National
Center for Biotechnology Information - Genes and Disease Map
Physical maps with identified disease-causing genes
- NCBI
Reference Sequence Project Non-redundant collection
of naturally-occurring biological molecules
-
NDB - Nucleic Acid Database Project Atlas of nucleic acid containing structures, archives, searching options
- NIA/NIH
Mouse Genomics Home Page NIA Mouse cDNA Project / NIA Mouse t-complex Genome Sequencing Project
- Oncogenomics Normal Tissue Database
High-density gene expression database derived from 42,000 clone cDNA microarrays containing 18,927 unique genes for 158 normal human samples from 19 different organs of 30 different individuals
- PheLiGe Web-service that provides access to publicly available results from human genetic association studies and among others allows for exploration of genome-wide and regional associations, finding phenotypes associated to a genetic variant, and comparison of associations patterns between different traits
- PhosPhAt Arabidopsis Protein Phosphorylation Site Database
- PicSNP
Catalog of non-synonymous SNP (Single Nucleotide Polymorphism)
- Probe Database The NCBI
Probe Database is a public registry of nucleic acid reagents designed
for use in a wide variety of biomedical research applications, together
with information on reagent distributors, probe effectiveness, and
computed sequence similarities
- PubMatrix
Tool to rapidly and systematically compare any list of terms against
any other list of terms in PubMed. It reports back the frequency of
co-occurrence between all pairwise comparisons between the two lists as
a matrix table. Lists of terms can be anything: gene names, diseases,
gene functions, authors etc.
- RDP -
Robosomal Database Project Provision of ribosome
related data services to the scientific community, including online
data analysis, rRNA derived phylogenetic trees, and aligned and
annotated rRNA sequences
- repairGenes
Site containing information about DNA repair genes from a set of
selected species. The information is organised by organism and by
biological process term as defined by the Gene Ontology (GO) project
- RestrictionMapper On-line restriction mapping
- RiboWEB The RiboWEB is a
knowledge base containing templates (or structured representations) for
the most common experiments used to study the structure of RNA/Protein
complexes. It is currently populated with information (almost 5800
individual observations) from 150 articles about the 30S ribosomal
subunit in procaryotes
- RNA
Interference siRNA Database and Resources for RNA
Interference Studies
- rrnDB
Searchable database documenting variation in ribosomal RNA operons (rrn) in Bacteria and Archaea
- SAGEmap
Information on SAGE libraries and access to the data produced from
these libraries
- SAGE
Genie SAGE Genie uses a new analytical method of
reliably matching SAGE tags to known genes. Based on this tag to gene
mapping, the website visualizes human gene expression analysis in
tissues or individual libraries using displays that are highly intuitive
- SAGE -
Serial Analysis of Gene Expression Genzyme molecular
oncology (GMO) homepage for academic SAGE applications
- SEGE - Single Exonic Genes in Eukaryotes
Database Collection of gene sequences that are
annotated to have single exon structure in Genbank feature table
- SNPs.com
A site dedicated to the creation, collection and dissemination of
information pertaining to single nucleotide polymorphisms (SNPs),
sponsored by Orchid Biocomputer, Inc
- The
Genome Channel Atlas for finding genes - links to
sequencing centers for 24 organisms
- The
tmRNA Website Links to tmRNA sequences of about 250
bacteria
- TubercuList
Collection and integration of various aspects of the genomic
information from M. africanum, M. bovis, M. bovis BCG, M. canetti, M.
microti, and above all, M. tuberculosis. TubercuList provides a
complete dataset of DNA and protein sequences derived from the paradigm
strain M. tuberculosis H37Rv, linked to the relevant annotations and
functional assignments.
- UKNCC
United Kingdom National Culture Collection
- The
Whole Mouse Catalog The Web site serves as a central
place to find numerous Internet resources of particular interest to
scientific researchers using mice or rats in their work
- Virtual
Genome Center Access to tools and databases for
molecular biologists
- BacMap Interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes
- Botanical Databases
- coliBASE
Online database for E. coli, Salmonella and Shigella comparative
genomics
- CUTG Codon usage
tabulated from gene bank
- dbSNP
NIH database of human genetic variation
- DDBJ
- DNA Data Bank of Japan All known nucleotide and
protein sequences
- EBI
Databases European Bioinformatics Institute
- EMBL
Nucleotide Sequence Database All known nucleotide
and protein sequences
- Ensembl
Annotated information on eucariotic genomes
- GDB -
The Genome Database International collaboration in
support of the Human Genome Project
- GenBank
All known nucleotide and protein sequences
- Genewindow
DNA browser that allows to scroll through a particular gene nucleotide
by nucleotide, identifying SNPs and other landmarks like protein-coding
segments
- GOBASE
GOBASE is a taxonomically broad organelle genome database that
organizes and integrates diverse data related to organelles with a
focus on the mitochondrial and chloroplast subset of data
- HGMG -
Human Gene Mutation Database at the Institute of Medical Genetics in
Cardiff Database of known (published) gene lesions
responsible for human inherited disease
- HGVbase
HGVbase (Human Genome Variation database)is a database of intra-genic
(promoter to end of transcription) single nucleotide polymorphisms -
hosted by the Center for Genomics and Bioinformatics, Karolinska
Institute, Stockholm, Sweden
- HIV
Sequence Database Access to databases, alignments,
and tools and interfaces produced at Los Alamos National Laboratories
- HuGEIndex Database The
Human Gene Expression Index (HuGE Index) aims to provide a
comprehensive database to aid in understanding the expression of human
genes in normal human tissues
- Integrated
Microbial Genomes (IMG) Access to nearly 300 draft
or completed genome sequences from archae and bacteria
- IMAGE
consortium database Query The world's largest public
collection of genes
- Jackson
Laboratory Mouse Genome Database Collection of mouse
genetic and phenotypic data
- KSD
- Kinase Sequence Database Collection of protein
kinase sequences grouped into families by homology of their catalytic
domains. The aligned sequences are available in MS Excel format, as
well as in HTML
- Mammalian
Gene Collection (MGC) New effort by the NIH to
generate publicly accessible full-length complementary DNA
(cDNA)resources. The project entails the production of cDNA libraries
and sequences, database and repository development, as well as the
support of research forimproved library construction, sequencing, and
analytic technologies
- Mitomap
v. 3.1 Human mitochondrial genome database;
structure - function correlation
- Mobile
group II introns Resource to identify and catalog
group II introns
- NONCODE
Database of noncoding RNAs
- OMIM
Online Mendelian inheritance in man - catalog of human genes and genetic disorders
- PeptideAtlas
Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments
- RTPrimerDB
- Real Time PCR Primer and Probe Database Public
database holding real time PCR primers and probes for popular
chemistries (Intercalating Dyes, Hydrolysis Probes, Hybridisation
Probes, Molecular Beacons) to prevent time-consuming primer design and
experimental optimisation
- snoRNA-LBME-db
Database of human C/D box and H/ACA modification guide RNAs
- Stanford University - Saccharomyces Genome
Database Scientific database of the molecular
biology and genetics of the baker's (or budding) yeast
- STACKdb Database of
virtual human transcripts, based on GenBank Data
- Subviral
RNA Database About 1300 nucleotide sequences for
viroids and related solo RNA molecules
- The Gene Expression Database (GXD)
The Gene Expression Database is a community resource for gene
expression information from the laboratory mouse. GXD stores and
integrates different types of expression data and makes these data
freely available in formats appropriate for comprehensive analysis.
There is particular emphasis on endogenous gene expression during mouse
development
- TIGR
databases Databases of The Institute for Genomic
Research: The TIGR Microbial Database, The TIGR Parasites Database,
TIGR Gene Indices, The TIGR Arabidopsis thaliana Database, The
Expressed Gene Anatomy Database, Sequences, Sources, Taxa
- The
Genetics of Cancer Information resource to help to
understand the genetic basis of cancer and to interpret new discoveries
in the field of cancer genetics
- UniGene
Non-redundant, gene-oriented clusters
Alternative Splicing Databases
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Proteomics
- Bioinformatic Harvester Harvester caches and cross-links public bioinformatic databases and prediction servers to provide fast access to protein specific bioinformatic information
- CCSB Interactome Database Information about efforts to map the human interactome
- DBSubLoc - Database of Protein Subcellular
Localization Database of protein subcellular localization that contains proteins from SWISS-PROT and PIR, is annotated with respect to subcellular localization and is classified and categorized by cross reference to taxonomies and gene ontology
- DSDBASE - disulphide database
Database on disulphide bonds in proteins that provides information on
native disulphides and those which are stereochemically possible
between pairs of residues in a protein
- EMBL
Protein and Peptide Group Protein and peptide group
WWW server of the European Molecular Biology Laboratory
- Enzyme
Enzyme nomenclature database
- Enzyme Structures Database
Contains close to 4000 known enzyme structures that have been deposited
in the Brookhaven Protein Data Bank
- ExactAntigen
Comprehensive gene-specific and species-specific information resource
for reagents (antibodies, ELISA, siRNA, recombinant proteins,
chemicals, and tissue arrays), researchers, and patents
- HPMR
Site dedicated to studies on plasma membrane receptors in the human
genome, combining text-based and sequence-based search tools. The web
site categorizes major groups of human plasma membrane receptors based
on protein sequences, evolutionary relationships, and published
literature
- IntAct Open source database system and analysis tools for molecular interaction data
- InterPro
Database of protein families, domains and functional sites in which
identifiable features found in known proteins can be applied to unknown
protein sequences
- IMGT
Server ImMunoGeneTics database, an integrated
database specialising in Immunoglobulins (Ig), T cell receptors (TcR)
and Major Histocompatibility Complex (MHC) molecules of all vertebrate
species
- LPFC - A Library of Protein Family Cores
Database of proteins classified into families of structures
- LOCATE
subcellular location database Curated database that
houses data describing the membrane organization and subcellular
localization of proteins from the RIKEN FANTOM3 mouse protein sequence
set
- MEROPS
Peptidase database of the Babraham Institute in Cambridge / UK -
catalog of more than 900 proteases among others with structural data
and occurrance in organisms
- Meta-MEME
Motiv-based hidden Markov modeling of biological sequences - software
toolkit for building and using motiv-based hidden Markov models of DNA
and proteins. The input to Meta-MEME is a set of similar protein
sequences.
- MIA -
Molecular Information Agent The Molecular
Information Agent (MIA) is a web server that searches biological
databases to find the existing information about a macromolecule. At
the present time, the MIA supports search by molecule identification
number, gene symbol, sequence, and key word.
- MSRS
Website Searchable database of antibodies and probes
including antibody, host, antigen species, label,...
- MOWSE Search Form Rapid
identification of proteins by peptide-mass fingerprinting
- MPDB Membrane Protein Database
On-line, searchable, relational database with select structural and
functional information on membrane proteins and peptides
- National
Center for Biotechnology Information Gateway to
protein and DNA databases
- Natural
System of Gene Families from Complete Genomes
Clusters of orthologous groups (COGs) were delineated by comparing
protein sequences encoded in 8 complete genomes, representing 6 major
phylogenetic lineages
- Nuclear
Protein Database (NPD) Searchable database of
information on proteins that are localised to the nucleus of vertebrate
cells
- NURSA -
Nuclear Receptor Signaling Atlas Resource for
information relating to key aspects of orphan nuclear receptor biology
- PDB
WWW Home Page USA Archive of experimentally
determined three-dimensional structures of biological macromolecules
- PEPTIDE MASS SEARCH
Searches the protein database for multiple peptides of individual
proteins
- Pfam
- Protein families database of alignments and HMMs
Large collection of multiple sequence alignments and hidden Markov
models covering many common protein domains and families
- PhosphoSite
Curated, sequence-oriented protein database dedicated to in vivo
phosphorylation sites
- PRIDE
- PRoteomics IDEntifications database Public
repository for protein and peptide identifications together with the
evidence supporting these identifications
- PrionDB
Molecular specific information system for prion proteins
- PROLYSIS Protease and
protease inhibitor Web server at the University of Tours, France -
Introduction to proteases and their inhibitors, including assays and
enzyme kinetics
- ProteinDBS
Real-time database search and similarity rankings of 3D protein
structures
- Protein
Prospector Tools for mining sequence databases in
conjunction with mass proteometry experiments
- Proteome
Alliance Page of the Project of the German Research
Ministry "Proteom-Analyse des Menschen". This project focusses on the
development of research tools and their clinical application in human
proteome analysis
- proteomicsSURF
Covers bioanalytical approaches in the field of proteomics covering
microarrays, spectroscopy, spectrometry, and bioinformatics
- PROTONET
Global classification of the proteins into hierarchical clusters
- PROW - Protein Reviews on the Web
International WWW Resource/Journal on Human Proteins - NCBI
- PROWL
Protein information retrieval on-line world wide web lab
- The
Human Serum Proteome Comprehensive human serum
proteomic database
- UniProt
UniProt (Universal Protein Resource) is the world's most comprehensive
catalog of information on proteins. It is a central repository of
protein sequence and function created by joining the information
contained in Swiss-Prot, TrEMBL, and PIR.
- WEB
P.A.G.E Phoretix´ World-Wide Collaboration
in 2D Gel Electrophoresis: On-Line Databases
- 2D
Gel Databases World-Wide Phoretix´ links
to 2D gel databases on the internet
- Brookhaven
Protein Database Originated by the Brookhaven
National Laboratory, now hosted at the Research Collaboratory for
Structural Bioinformatics
- ExPASy
University and Hospital of Geneva WWW server, database entry point for
SWISS-PROT, PROSITE, SWISS-2DPAGE, SWISS-3DIMAGE, ExPASy Tools
- Cogent - Complete Genome Tracking Database
Single resource containing predicted peptides from all publicly
available fully sequenced genomes
- Human Mitochondrial Protein Database
The Human Mitochondrial Protein Database (HMPDb) provides comprehensive
data on mitochondrial and human nuclear encoded proteins involved in
mitochondrial biogenesis and function. This database consolidates
information from SwissProt, LocusLink, Protein Data Bank (PDB),
GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man
(OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP,
Neuromuscular Disease Center and Human 2-D PAGE Databases
- HPRD -
Humane Protein Reference Database 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
OMIM genes have been annotated
- MEROPS - the Peptidase Database Information resource for peptidases and their protein inhibitors
- STACKdb Database of
virtual human transcripts, based on GenBank Data
- SWISS-PROT
Annotated protein sequence database - EBI site
- SWISS-PROT
and TrEMBL Annotated protein sequence database -
ExPASy site
- UAB Proteomics Database
Repository for the storage and linkage of two-dimensional gel images
and the associated information obtained through mass spectrometry
analysis
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Glycomics
- Carbhyd Links to information on carbohydrate structures, biochemistry, and related
graphics tools for modeling sugar molecules
- Complex Carbohydrate Magnetic Resonance Database - CCMRD Solid-state NMR database for complex carbohydrates
- Complex Carbohydrate Research Center - CCRC On-line neural net recognition system for GC profiles and NMR spectra
- Glycominds Database Glycomics database that compiles information about glycoconjugated molecules - including their structures, functions, and interactions with other molecules
- GlyCosmos Web portal aiming to integrate the glycosciences with the life sciences; providing information about genes, proteins, lipids, pathways and diseases
- GLYCOsciences.de (SweetDB)
Databases and bioinformatics tools for glycobiology and glycomics
- GlycoSuiteDB Annotated
and curated relational database of glycan structures containing most
published O-linked glycans, and N-linked glycans in the literature from
years 1990-2000. Information is available concerning the glycan type,
linkage and anomeric configuration, mass and composition.
- NetOGlyc
The web server returns probable O-glycosylation sites of mammalian
mucin glycoproteins based on the predictions of a neuronal network
- Sugabase Links to various
glyco-related directories and databases
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Lipids
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Pathways
- BBID-Biological Biochemical Image Database Searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships
- Biocarta Pathways On-line maps depicting dynamic graphical models of gene interactions
- Biocatalysis/Biodegradation Database Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic chemical compounds
- BioCyc Database Collection Collection of Pathway/Genome
Databases. Prediction of metabolic pathways of completely sequenced organisms, prediction of which genes code for missing enzymes in metabolic pathways, and prediction of operons
- Biozon Unified biological resource on DNA sequences, proteins, complexes and cellular pathways
- BRENDA Comprehensive enzyme information system
- CST Pathways Pathway diagrams assembled by CST scientists and outside experts to provide succinct and current overviews of selected signaling pathways
- Database of Cell Signaling Information on the components of cellular signaling pathways and their relations to one another, organized into pathways called Connections Maps, Free registration required
- GenePath Web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks
- iHOP
- information hyperlinked over proteins Network accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research.
- Interactive Pathways & Processes R&D System's collection of pathway visualizations that can be explored interactively
- KEGG - Kyoto Encyclopedia of Genes and Genomes Database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information
- Reactome Open-source, curated and peer reviewed pathway database
- Roche Chemical Pathways Searchable charts covering metabolic pathways and cellular and molecular processes
- The Signaling Gateway UCSD Signaling Gateway Molecule Pages providing essential information on over thousands of proteins involved in cellular signaling
- WikiPathways Curated platform covering biological pathways
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Pharmacology
- BindingDB
Database of measured binding affinities for biomolecules, genetically
or chemically modified biomolecules, and synthetic compounds
- ChemMine
Compound mining database that facilitates drug and agrochemical
discovery and chemical genomics screens
- Clinical Pharmacology Comprehensive information on all FDA-approved drugs and OTC pharmaceuticals - indications, effects, and side effects
- PharmGKB
- The Pharmacogenetics and Pharmacogenomics Knowledge Base
Central repository for genetic and clinical information about people
who have participated in research studies at various medical centers in
the PGRN. In addition, genomic data, molecular and cellular phenotype
data, and clinical phenotype data are accepted from the scientific
community at large.
- RXList
Information about the top 200 US prescriptions Dispensed
- Self-Organizing Map of NCI Antiviral Screen
Compounds Searchable database about antiviral
compounds
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Pharmacogenetics
- Cancer
- COSMIC - Catalog of Somatic Mutations in
Cancer Contains information on publications, samples
and mutations. Includes samples which have been found to be negative
for mutations during screening therefore enabling frequency data to be
calculated for mutations in different genes in different cancer types
Back to Genomics, Proteomics & Transcriptomics
Physiome
- PhenomicDB
Multi-species genotype/phenotype database
- Physiome
Project The Physiome Project is a worldwide effort
to define the physiome through the development of databases and models
which will facilitate the understanding of the integrative function of
cells, organs, and organisms
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Systems
Biology
- Protein
Lounge Interactive web-based databases and software
to cope with the complexity of systems biology
- The BioGRID Comprehensive database of protein and genetic interactions
Back to Genomics, Proteomics & Transcriptomics
Toxicology
& Drug Metabolism
- DSSTox
The Distributed Structure-Searchable Toxicity (DSSTox) Database Network
provides a community forum for publishing standard format,
structure-annotated chemical toxicity data files for open public access
- Eurotox
Homepage of the International Union of Toxicology
- Genetic
Association Database Archive of human genetic
association studies of complex diseases and disorders. The goal of this
database is to allow the user to rapidly identify medically relevant
polymorphism from the large volume of polymorphism and mutational data,
in the context of standardized nomenclature
- OSIRIS Property Explorer
The OSIRIS Property Explorer allows to draw chemical structures and
calculates on-the-fly various drug-relevant properties whenever a
structure is valid
- IUTOX
Homepage of Eurotox, the Association of European Toxicologists and
European Societies of Toxicology
- TOXNET
Access to different toxicology related databases
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Regulatory
Affairs
- ORA - Office of Regulatory Affairs
FDA site featurung among others compliance policy guides, regulatory
procedures manual and other FDA compliance documents and information
like 21 CFR Part 11
- 21CFRPart11.com
The web site provides access to information on
the 21 CFR Part 11 rule and also maintains an email list that actively
discusses issues and concerns with industry peers and government
regulators. The site features the latest conference, meeting and
seminar information as well as links to vendors and consultants.
GMP and ISO 9001
- GMP Navigator GMP related
news and information - hosted by Concept Heidelberg
- ISO Online The source of
ISO 9000 and more than 13 700 International Standards for business,
government and society
Material Safety Data Sheets
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