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
presented below. In addition, this appendix will regularly be
updated.
A. Internet Resources for
Topics in Selected Chapters
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.
ArgusLab:
Interactive 3D molecular Builder to build and manipulate complex structures. Suite of computational methods, both quantum mechanical and molecular mechanical, for calculating ground and excited states properties.
MOLARIS:
A macromolecular simulation program designed to study the functions of proteins ranging from ligand binding to free energy profiles of enzymatic reactions using the Empirical Valence Bond (EVB) approach and the Free Energy Perturbation (FEP) method. (from Dr. Arieh Warshel's lab.)
LAMMPS:
LAMMPS is a classical molecular dynamics (MD) code created for simulating molecular and atomic systems such as proteins in solution, liquid-crystals, polymers, zeolites, or simple Lenard-Jonesium. It was designed for distributed-memory parallel computers and runs on any parallel platform that supports the MPI message-passing library or on single-processor workstations.
WebMO:
WebMO is a classical molecular dynamics (MD) code created for WebMO is a World Wide Web-based interface to computational chemistry packages. WebMO is available for free and can be installed on nearly any unix or Linux system. WebMO Pro is a commercial add-on to the freeware WebMO computational chemistry package. It features a variety of powerful enhancements that are suitable for serious education, commercial, or research-level users
.
MOLMOL (MOLecule analysis and MOLecule
display): A molecular graphics program for displaying,
analyzing, and manipulating the three-dimensional
structure of biological macromolecules
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 (Visual Molecular Dynamics): MD
generated trajectories can be read.
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
