Sites of General Interest
Structures
Proteins
- Protein Data Bank (PDB) RCSB. Worldwide repository for 3-D biological macromolecular structure data.
- 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).
- 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.
- Database of Macromolecular Movements Decribes motions that occur in proteins and other macromolecules.
- 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).
- ExPASy Proteomics Server
- 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 (IMB Jena) RNA Internet links.
- RNAdraw
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. - ChemBioFinder Physical property data, 2D chemical structures, and links to other chemical information sites.
- 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
- Cn3D, NCBI (plug-in)
- FirstGlance in JMol
- GRASP Molecular visualization and analysis
- 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.
- PyMOL User-sponsored, open source. Runs on Linux, MacOS, and Windows
- RasMol, University of Massachusetts (plug-in)
- 3D Macromolecular Analysis and Kinemage Home Page, Duke University (plug-ins)
- Deep View Swiss-Pdb Viewer, GlaxoSmithKline R&D Geneva
- WebMol, EMBL-Heidelberg (Java)
- Molecules ver. 1.1 - iPhone and iPod Touch application that allows you to view RCSB Protein Data Bank molecules.