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Appendix

From the book," Computational Biochemistry and Biophysics"


Appendix:

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 presented below. In addition, this appendix will regularly be updated.

A. Internet Resources for Topics in Selected Chapters

Related chapters are in the parentheses.

  1. Force Fields (Chapter 2)

https://rxsecure.umaryland.edu/research/amackere/research.html

  1. CHARMM: http://www.pharmacy.umaryland.edu/~alex/research.html
  2. AMBER: http://www.amber.ucsf.edu/amber
  3. GROMOS: http://igc.ethz.ch/gromos/gromos.html

http://www.ccl.net/cca/data/ff_evaluation_suite

  1. Protein Dynamics (Chapter 3)

http://www.ch.embnet.org/MD_tutorial

http://bioinfo.mbb.yale.edu/MolMovDB/db/ProtMotDB.main.html

  1. Minimization and Conformational Analysis (Chapter 4)

http://www.cooper.edu/engineering/chemechem/monte.html

  1. Structure Refinement Applications (Chapter 13)

http://www.rcsb.org/pdb/software-list.html at the Protein Data Bank

http://atb.csb.yale.edu/xplor/

Nilges Group: http://www.embl-heidelberg.de/nmr/nilges

Basics of NMR: http://www.cis.rit.edu/htbooks/nmr

CCP4: http://www.dl.ac.uk/CCP/CCP4/main.html

General Site: http://www.iucr.org/cww-top/crystal.index.html

  1. Comparative Protein Structure Modeling (Chapter 14)

Sali Group: http://guitar.rockefeller.edu/sub-pages/programs.html

  1. Statistics in Molecular and Structural Biology (Chapter 15)

Dunbrack Group: http://www.fccc.edu/research/labs/dunbrack

  1. Computer Aided Drug Designs (Chapter 16)

http://www.scripps.edu/pub/olson-web/people/gmm

http://www.chem.swin.edu.au/modules/mod4

  1. Protein Folding (Chapter 17)
  1. Membrane Simulations (Chapter 21)

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.

  1. CHARMM: Chemistry at HARvard Molecular Mechanics - General-purpose molecular dynamics computer simulation package
  1. AMBER: Assisted Model Building with Energy Refinement - General-purpose molecular dynamics computer simulation package

http://www.amber.ucsf.edu/amber

  1. GROMOS: A general-purpose molecular dynamics computer simulation package for the study of biomolecular.

http://igc.ethz.ch/gromos

  1. GROMACS: GROningen MAchine for Chemical Simulations

http://www.gromacs.org/

  1. TINKER: Software Tools for Molecular Modeling

http://dasher.wustl.edu/tinker

  1. NAMD: object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.

http://www.ks.uiuc.edu/Research/namd

  1. The Molecular Modeling Toolkit (MMTK): Program library for molecular simulation applications

http://starship.python.net/crew/hinsen/MMTK

  1. Ghemical: A molecular modelling package released under the GNU GPL.

http://bioinformatics.org/ghemical/

  1. 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.

http://www.planaria-software.com

  1. 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.)

http://laetro.usc.edu/programs/

  1. 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.

http://www.cs.sandia.gov/~sjplimp/lammps.html

  1. 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 .

http://www.webmo.net/

C. Molecular Visualization Software

Listed is a collection of visualization software, which are widely used in academic and industrial research groups.

  1. RasMol: a free program which displays molecular structure. It is easy to use and produces space-filling, colored, 3-dimensional images.

http://www.bernstein-plus-sons.com/software/rasmol

  1. MOLMOL (MOLecule analysis and MOLecule display): A molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules

http://www.mol.biol.ethz.ch/wuthrich/software/molmol

  1. WebMol: JAVA PDB Viewer to display and analyze structural information

http://www.embl-heidelberg.de/cgi/viewer.pl

  1. Swiss-Pdb Viewer: An application that provides a user friendly interface allowing simultaneous analysis of several proteins.

http://www.expasy.ch/spdbv/mainpage.html

  1. Jmol: A Free, Open Source molecule viewer and editor:

http://www.openscience.org/jmol

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.

  1. VMD (Visual Molecular Dynamics): MD generated trajectories can be read.

    http://www.ks.uiuc.edu/Research/vmd

    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 1