Biophysical Sciences at UW-Madison



  • 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


Physical Properties and Their Prediction

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
  • - 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.

Mobile Applications

  • Molecules - iPhone and iPod Touch application that allows you to view RCSB Protein Data Bank molecules.
  • Scientific Mobile Applications: Chemistry