the goodman group
university of cambridge  


   computational biological chemistry

The Silicon Graphics Teaching Laboratory
has been replaced by the
Chemi cal Information Laboratory
and this information is for historical interest only

Computational Biological Chemistry

The Silicon Graphics Teaching Laboratory provides a wide range of programs, including many that are specifically intended for the study of biological chemistry. This page outlines the programs which were written with biological applications in mind. A complete list of the programs licensed in the laboratory is also available.

A few of the facilities available are illustrated in the following thumbnail pictures, all of which were created using programs in the laboratory. Click on any of the small pictures to see a larger version and a brief explanation. The pictures illustrate methods of investigating peptides, drug-design, explicit and implicit solvent models, and molecular dynamics studies of oligosaccharides.

eadfrith macromodel cerius
EadfrithMacroModelCerius
sybyl molscript XED
Sybyl/GridMolscriptXed/Cosmic
sugar Dynamics solvent
Oligosaccharides
Continuum Solvent
Oligosaccharides
Dynamics
Ligand Binding
Explicit Solvent

Programs Available

Advice on the use of all the following programs is available online. If the instructions need to be expanded or corrected, please E-mail detailed suggestions to jmg11@cam.ac.uk.

Molecular Modelling Programs

  • These programs are able to do almost any sort of biological chemistry modelling. Insight is the only major program which is not available at the moment. However, MSI intend to merge Insight with Cerius2 as soon as possible.
  • MacroModel 5.5
  • Sybyl
  • Cerius2
  • Xed/Cosmic

Databases


Drug Design

  • Dock A program to design receptors for enzyme active sites
  • GASP Genetic Algorithms to align molecules and so aid in the identification of a pharmacophore (consult Jack Bikker, jab44@cam.ac.uk, http://mrical.ch.cam.ac.uk:8090/)
  • Grid: Determines energetically favourable binding sites for ligands
    (Documentation is only available from SGTL)
  • Delphi A program to calculate, display and analyse electrostatic potentials of macromolecules

Molecular Graphics


Miscellaneous

  • ANSIG Interpretation of NMR spectra
    (Documentation is only available from SGTL)
  • Babel A program to convert between different molecular modelling file formats.



© Goodman Group, 2005-2017; privacy; last updated October 24, 2017

department of chemistry University of Cambridge