Databases and portal sites:

DBget Integrated database retrieval system for major biological databases	UniProt Most comprehensive, high-quality and freely accessible resource of protein sequence and functional information
EMBL Nucleotide Sequence Database Europe’s primary nucleotide sequence resource	GenBank Sequence Database Annotated collection of all publicly available DNA sequences by NIH
UniParc Comprehensive and non-redundant database that contains most of the publicly available protein sequences	KEGG Collection of online databases dealing with genomes, enzymatic pathways, and biological chemicals
OMIM Comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes	SWISS-MODEL Database of annotated three-dimensional comparative protein structure models
Protein Data Bank The single worldwide repository of information about the 3D structures of large biological molecules	PDB Select Non-redundant selection of a representative set of PDB chains
NCI Small Molecule Database Database of >250000 small molecules with screening results for human tumour cell lines and HIV antiviral screens
WolframAlpha Ambitious project to make all systematic knowledge immediately computable and accessible to everyone. Try asking for "Answer to life, the universe and everything"

Databases for literature searching:

PubMed Free search engine for accessing the MEDLINE database of citations, abstracts and full text articles on life sciences of the United States National Library of Medicine	GoPubMed Knowledge-based search of scientific literature
PubNet Publication network graph utility for visualsation of literature-derived networks	arXiv "The Archive" is the most comprehensive archive for open access scientific papers in the fields of mathematics, physics, astronomy, computer science, quantitative biology and statistics
wipo Full-text search in over 1.7 million published international patent applications from the first publication in 1978	EPO/espacenet Database of the European Patent Office
STN International online database service that provides global access to published research journal, literature, patents, structures, sequences, properties and other data	OJOSE Free scientific search engine enabling you to make search-queries in different databases
THM University of Applied Sciences, Online services of the library of the University of Applied Sciences in Giessen	Justus Liebig University, Giessen Online services of the library of the Justus Liebig University in Giessen

Life science informatics software:

Expasy Proteomics Tools Huge collection of protein-related online tools and software	EMBL Bioinformatics services of the European Molecular Biology Laboratory
JCell Java based framework to reconstruct genetic interactions from microarray data	phyre Software to predict 3D protein structure by the Structural Bioinformatics Group of the Imperial College, London
Relibase Database system for searching, storing and analysing 3D structures of protein-ligand complexes	PDB Gate @ Cheminformatics.ch Website, created by passionate cheminformaticians to provide new cheminformatics solution free of charge to the public
AffinDB Database of affinity data for structurally resolved protein–ligand complexes from the Protein Data Bank
DrugScore Web-based user interface for the knowledge-based scoring functions DrugScore/CSD and DrugScore/PDB	OSIRIS On-the-fly calculation of various drug-relevant properties
JOELib Cheminformatics library: Assignment of atom types, substructure search, descriptor calculation, Java3D molecule visualization	MOPAC (Molecular Orbital PACkage) Semiempirical quantum chemistry program based on Dewar and Thiel’s NDDO approximation
CORINA 3D structure generator for small and medium sized molecules	JME Molecular Editor Java applet which allows to draw and edit molecules and reactions and to depict molecules directly within an HTML page
marvin Collection of tools for drawing, displaying and characterizing chemical structures, substructures and reactions	moloc Molecular modeling package designed with emphasis on high interactivity
FlexX Predicts the geometry of the protein-ligand complex for a protein with known three-dimensional structure and a small ligand molecule	Gold Program for calculating the docking modes of small molecules in protein binding sites

General software:

KNIME Open source modular data pipeling platform	JavaNNS Flexible simulator for many types of artificial neural networks
EvA2 Evolutionary Algorithms workbench	SiSense Prism Data visualisation and business intelligence software