Sites of General Interest

• CMS Molecular Biology Resource
• IMB Jena Image Library of Biological Macromolecules
• Bioinformatics (bioinformatik.de)
• NMR Information Server
• UW-Madison Libraries Top Ten (Literature) Databases

Structures

Proteins

• Protein Data Bank (PDB) RCSB. Worldwide repository for 3-D biological macromolecular structure data.
• 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).
• Swiss 3-D Image 3-D protein image database.

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.
• 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

• BEILSTEIN/GMELIN CROSSFIRE Preparations, properties, and reactions of organic and inorganic/organometallic compounds. Licensed access for UW-Madison students, faculty, and staff. Client required. To launch Beilstein/Gmelin from a campus library workstation, click HERE. The client may be installed on local workstations for access outside campus libraries. See Remote Access and Client Distribution for more information about local installation.
  For search help, see Beilstein and Gmelin Help.
• 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

See The "Top 5" 3D Molecular Visualization Technologies

• Chimera, University of California, San Francisco
• 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
• MolMol Molecular analysis and display. Also other tools from Institute for Molecular Biology and Biophysics. Zurich.
• 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
• PyMOL User-sponsored, open source. Runs on Linux, MacOS, and Windows
• Proteopedia collaborative 3D encyclopedia of proteins & other molecules
• RasMol, University of Massachusetts (plug-in)
• Swiss-Pdb Viewer Deep View, GlaxoSmithKline R&D Geneva
• VMD - Visual Molecular Dynamics for displaying, animating, and analyzing large biomolecular systems using 3-D graphics
• WebMol, University of California - San Francisco (Java)
• Molecules ver. 1.1 - iPhone and iPod Touch application that allows you to view RCSB Protein Data Bank molecules.