Sites of General Interest

• CMS Molecular Biology Resource
• Chemical Entities of Biological Interest (ChEBI) - dictionary of 'small molecular entities'.
• IMB Jena Image Library of Biological Macromolecules
• NMR Information Server
• UW-Madison Libraries Top 10 (Literature) Databases

Structures

Proteins

• Protein Data Bank (PDB) RCSB. Worldwide repository for 3-D biological macromolecular structure data.
• Binding Database - experimental data on the noncovalent association of molecules in solution, determine binding constants.
• Database of Macromolecular Movements Decribes motions that occur in proteins and other macromolecules.
• DB-SPIRE - Database for Structure-based Protein Interaction REsearch. AIST. Iincludes motif sites of all protein structures in PDB
• Entrez Structure Molecular Modelling Database contains 3-D macromolecular structures (subset of Protein Data Bank).
• ExPASy Proteomics Server (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics
• PIR (Protein Information Resource). Georgetown University Medical Center. Includes Protein Family Classification System and iProClass database. iProClass provides reports for UniProtKB (merged data from Swiss-Prot, TrEMBL and PIR-PSD) and unique NCBI Entrez protein sequences in UniParc (comprehensive non-redundant protein sequence collection). Also includes links to over 90 biological databases, including databases for protein families, functions and pathways, interactions, structures and structural classifications, genes and genomes, ontologies, literature, and taxonomy.
• Prosite ExPASy Database of protein domains,families and functional sites
• PROWL Interactive protein analysis.
• SCOP: Structural Classification of Proteins Structural and evolutionary relationships between all proteins with known structures.
• UniProt Protein knowledgebase consisting of Swiss-Prot (manually annotated and reviewed) and TrEMBL (automatically annotated and not reviewed).

Nucleic Acids

• Protein Data Bank (PDB) RCSB. Worldwide repository for 3-D biological macromolecular structure data.
• Nucleic Acids Database (NDB) Repository of three-dimensional structural information .
• MFOLD : RNA Sequence folding, DNA Sequence folding. UNAFold Web Server, RNA Institute, University of Albany, SUNY.
• RNA World Website (Leibniz Institute for Age Research - Fritz Lipmann Institute - FLI) RNA Internet links.

Viruses

• Protein Data Bank (PDB). RCSB. Worldwide repository for 3-D biological macromolecular structure data.
• VIPER - VIrus Particle ExploreR Descriptions of icosahedral virus structures in the Protein Data Bank.

Physical Properties and Their Prediction

• Reaxys (formerly Beilstein/Gmelin CrossFire): Preparations, properties, and reactions of organic and inorganic/organometallic compounds. Licensed access for UW-Madison students, faculty, and staff.
• ChemSpider Database of Chemical Structures and Property Predictions - searchable chemistry information repository
• CRC Handbook of Chemistry and Physics Chemical and physical data. Licensed access for UW-Madison students, faculty, and staff.
• ExPASy (Expert Protein Analysis System) Proteomics server of the Swiss Institute of Bioinformatics (SIB)
• PSA Protein Structure Prediction Server Predicts probable secondary structures and folding classes for a given amino acid sequence.
• MFOLD RNA Sequence folding
• MFOLD DNA Sequence folding

Visualization Tools

• Chimera, University of California, San Francisco. Extensible program for interactive visualization and analysis of molecular structures and related data.
• Cn3D, NCBI (plug-in)
• FirstGlance in JMol
• GRASP (Graphic Representation and Analysis of Structural Properties)
• JMOL open-source Java viewer for chemical structures in 3D
• 3D Macromolecular Analysis and Kinemage Home Page, Duke University (plug-ins) - especially MolProbity - Web service for all-atom contact and geometrical analysis of your model
• MolviZ.org - Molecular Visualization Resources all free and open source collected by Eric Martz,
• PyMOL User-sponsored, open source. Runs on Linux, MacOS, and Windows. View, render, animate, export, present 3D data in PowerPoint with AxPyMOL plugin. Licensed by UW-Madison for faculty, staff, and students. Download from DoIT Tech Store. Help: PyMol Wiki.
• Proteopedia collaborative 3D encyclopedia of proteins & other molecules
• RasMol, University of Massachusetts (plug-in)
• Swiss-Pdb Viewer Deep View, GlaxoSmithKline R&D Geneva
• VMD - University of Illionois at Urbana-Champaign. Visual Molecular Dynamics for displaying, animating, and analyzing large biomolecular systems using 3-D graphics.

Mobil Applications

• Molecules ver. 1.1 - iPhone and iPod Touch application that allows you to view RCSB Protein Data Bank molecules.
• Chemistry on the Mac
• Scientific Mobil Applications: Chemistry