Weill Cornell Medicine Samuel J. Wood Library

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Molecular Biology and Bioinformatics Resources

WCM, Cornell & NYC Area Resources

Library Materials and Services

Molecular Biology Databases & Tools

Structure Visualization Software

Note: The Library staff does not provide technical support for this software

  • Cn3D 3-D structure viewer - Cn3D is a visualization tool for biomolecular structures, sequences, and sequence alignments. Cn3D is typically run from a WWW browser as a helper application for NCBI's Entrez system, but it can also be used as a standalone application. Cn3D reads only ASN.1 data files from the MMDB database. Tutorials and help are available.
  • RasMol - RasMol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol (UNIX and Win32 versions) can read MMDB ASN.1 files. See also: Introduction to RasMol
  • Protein Explorer, a RasMol-derivative - The Protein Explorer (PE) enables you to explore the 3D structure of any macromolecule - proteins, DNA, RNA, carbohydrates - and complexes, such as those between transcriptional regulatory proteins and DNA, or enzymes and drugs. See also: Tutorial for Protein Explorer
  • MAGE/Official Kinemage Homepage - A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Kinemages are viewed and explored by using a simple graphics program called MAGE.
  • MolviZ.Org - Molecular Visualization Resources, all free and open source.

Advanced Structure Manipulation Programs

  • MOLMOL (MOLecule analysis and MOLecule display) - MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. The program runs on UNIX and Windows NT/95/98/2000 and is freely available.

  • Visual Molecular Dynamics (VMD) - VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.

Tutorials & Training Materials

Other Resource Collections

  • 123Genomics - Hundreds of genomics-related bookmarks in categories: careers, courses, news, research labs, databases, scientific societies, protocol guides, microarrays, sequence databases & analysis, publications, and diseases & disorders.