Updated on September 17th, 2005
It is well known that the resources available on the Internet are in constant flux, with new sites appearing on a daily basis, as well as available sites disappearing almost as frequently. This also holds true for the dedicated tools used in biochemical and biophysical studies. New tools are constantly becoming available, while established tools are becoming obsolete. Such rapid change makes it difficult to stay current with the state of the art technologies in the areas of bioinformatics and computational biochemistry and biophysics.
To help the reader keep abreast of these advances we present a list of useful WWW sites in this appendix. Realistically, this list should be updated on a daily basis as many of the tools offered on the Internet are made available not only by large organizations and research groups but also by individual researchers. The goal, therefore, has not been to provide a nearly complete guide to the WWW but rather material representative of the tools useful to researches in the fields of biochemistry and biophysics.
Most of web sites listed contain links to
other web sites. This "hyperconnectivity" is what makes
the WWW a virtually unlimited information source, which we hope
you will be able to exploit to expand the limited list of sites
A. Internet Resources for Topics in Selected Chapters
Related chapters are in the parentheses.
- CHARMM: http://www.pharmacy.umaryland.edu/~alex/research.html
- AMBER: http://www.amber.ucsf.edu/amber
- GROMOS: http://igc.ethz.ch/gromos/gromos.html
http://www.rcsb.org/pdb/software-list.html at the Protein Data Bank
Nilges Group: http://www.embl-heidelberg.de/nmr/nilges
Basics of NMR: http://www.cis.rit.edu/htbooks/nmr
General Site: http://www.iucr.org/cww-top/crystal.index.html
Sali Group: http://guitar.rockefeller.edu/sub-pages/programs.html
Dunbrack Group: http://www.fccc.edu/research/labs/dunbrack
- Tropsha Group: http://mmlin1.pha.unc.edu/~jin/QSAR
- Molecular Dokcing:
- Quantitavive Structure Activity Relationship (QSAR)
- Becker Group: http://www.tau.ac.il/~becker/index.html
- Okamoto Group: http://konf2.ims.ac.jp/research.html
- Tobias Group: http://www.chem.uci.edu/research/faculty/dtobias.html
B. Molecular modeling and simulation packages
Listed is a collection of general-purpose molecular dynamics computer simulation packages for the study of molecular systems. The packages include a wide variety of functionalities for the analysis and simulation of biomolecules. In addition, they contain integrated force fields.
C. Molecular Visualization Software
Listed is a collection of visualization software, which are widely used in academic and industrial research groups.
Jmol can be also used to animate the results of simulations that are in a multi-frame XYZ format, and to animate the computed normal modes from ab initio quantum chemistry packages.
VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid-bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read sevearl different strucutral file formats and display the contained structure. VMD provides a w