Appendix: Useful Internet Resources
It is well known that the resources available on the Internet are in constant flux, with new sites appearing on a daily basis and established 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, and established tools, 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 to provide material representative of the tools useful to researchers in the fields of biochemistry and biophysics.
Most 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 be regularly updated at the following web site:
http://yuri.harvard.edu/ watanabe or http://www.geocities.com/masakatsu w/index.html
A.Internet Resources for Topics in Selected Chapters
1.Force Fields (Chapter 2)
•MacKerell group: https://rxsecure.umaryland.edu/research/amackere/ research.html
•Popular empirical force field web sites:
CHARMM: http://www.pharmacy.umaryland.edu/ alex/research.html AMBER: http://www.amber.ucsf.edu/amber/
GROMOS: http://igc.ethz.ch/gromos/gromos.html
• Force field evaluation suite: http://www.ccl.net/cca/data/ff evaluation suite/
2.Protein Dynamics (Chapter 3)
•Quick guide to molecular simulations (see Online tutorials, below): http://www.tc.cornell.edu/Visualization/Staff/richard/Courses/biobm631
•Molecular movements database:
http://bioinfo.mbb.yale.edu/MolMovDB/db/ProtMotDB.main.html
3.Minimization and Conformational Analysis (Chapter 4)
•Monte Carlo methods:
http://zarbi.chem.yale.edu/programs/mcpro/mc toc.htm
4.Structure Refinement Applications (Chapter 13)
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•Software for structure determination and analysis: http://www.rcsb.org/pdb/software-list.html
•X-PLOR: A program for structure determination from crystallographic or NMR data: http://atb.csb.yale.edu/xplor
•NMR:
Nilges group: http://www.embl heidelberg.de/nmr/nilges Basics of NMR: http://www.cis.rit.edu/htbooks/nmr/
•X-ray crystallography:
CCP4: http://www.dl.ac.uk/CCP/CCP4/main.html
General site: http://www.iucr.org/cww-top/crystal.index.html
5.Comparative Protein Structure Modeling (Chapter 14)
•Sali’s group: http://guitar.rockefeller.edu/sub-pages/programs.html
6.Statistics in Molecular and Structural Biology (Chapter 15)
Dunbrack group: http://www.fccc.edu/research/labs/dunbrack/
7.Computer-Aided Drug Designs (Chapter 16)
•Tropsha group: http://mmlin1.pha.unc.edu/ jin/QSAR/
•Molecular docking:
http://www.scripps.edu/pub/olson-web/people/gmm/
•Quantitative structure–activity relationship (QSAR): http://www.chem.swin.edu.au/modules/mod4
8.Protein Folding (Chapter 17)
•Becker’s group: http://www.tau.ac.il/ becker/index.html
•Friesner’s group: http://www.chem.columbia.edu/cbs/protein/protein.html
•Okamoto’s group: http://konf2.ims.ac.jp/research.html
9.Membrane Simulations (Chapter 21)
•Tobias’s group: http://www.chem.uci.edu/research/faculty/dtobias.html
•van Gunsteren’s group:
http://www.nmr.chem.ruu.nl/%7Eabonvin/ToT/lukas/index lukas.html
•Feller’s group: http://persweb.wabash.edu/facstaff/fellers/
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
http://yuri.harvard.edu/
http://master2.lobos.nih.gov/Charmm/
http://www.scripps.edu/brooks/charmm docs/charmm.html
2.AMBER (Assisted Model Building with Energy Refinement): General-pur- pose molecular dynamics computer simulation package
http://www.amber.ucsf.edu/amber/
3.GROMOS: A general-purpose molecular dynamics computer simulation package for the study of biomolecules http://igc.ethz.ch/gromos/welcome.html
4.GROMACS (GROningen MAchine for Chemical Simulations)
http://rugmd0.chem.rug.nl/ gmx/
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5.TINKER: Software tools for molecular modeling http://dasher.wustl.edu/tinker/
6.NAMD: Object-oriented molecular dynamics code designed for high performance simulation of large biomolecular systems
http://www.ks.uiuc.edu/Research/namd/
7.MMTK (Molecular Modeling ToolKit): Open Source Program library for molecular simulation applications http://starship.python.net/crew/hinsen/MMTK/
C.Molecular Visualization Software
Listed is a collection of visualization software packages that are widely used in academic and industrial research groups.
1.RasMol: A free program that displays molecular structure. It is easy to use and produces space-filling, colored, three-dimensional images.
http://www.bernstein-plus-sons.com/software/rasmol/
2.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/
3.WebMol: JAVA PDB viewer to display and analyze structural information. http://www.embl-heidelberg.de/cgi/viewer.pl
4.Swiss-Pdb Viewer: An application that provides a user-friendly interface allowing simultaneous analysis of several proteins.
http://www.expasy.ch/spdbv/mainpage.html
5.WebLab ViewerLite (Freeware from Molecular Simulation, Inc.): A fully Microsoft Windows integrated program allowing for 3D molecular visualization and the generation of high quality rendered images.
http://www.msi.com/download/index.html
6.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 multiframe XYZ format and to animate the computed normal modes from ab initio quantum chemistry packages.
7.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, and lipid bilayer assemblies. It may be used to view more general molecules, as VMD can read several different structural file formats and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation.
8.gOpenMol: Graphical interface of computational chemistry http://www.csc.fi/ laaksone/gopenmol/gopenmol.html
gOpenMol can be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities, and electrostatic potentials from programs like the Gaussian.
9.Molscript: A program for displaying molecular 3D structures in both schematic and detailed representations. http://www.avatar.se/molscript/.
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10.List of other free or public domain software that is relevant to visualizations: http://www.ahpcc.unm.edu/ aroberts/main/free.htm
D.Computational Biophysics Related at the National Institutes of Health (NIH)
1.General home page: http://webasaurus.dcrt.nih.gov//molbio/
2.Scientific resources: http://helix.nih.gov/science/
3.Sequence and molecular databases: http://helix.nih.gov/science/databases.html
4.Center for Molecular Modeling: http://cmm.info.nih.gov/modeling/
5.Molecular biology software list: http://bimas.dcrt.nih.gov/sw.html
E.Molecular Biology Software Links
1.Resource site for biotechnology—Molecular biology, bioinformatics, biophys-
ics, and biochemistry—A well-organized web site: http://www.ahpcc.unm.edu/ aroberts/
2.Molecular surface package: http://www.best.com/ connolly/
3.Biotechnological software and internet journal: http://www.davincipress.com/bsj.html
4.Computational chemistry web site: http://www.ccl.net/chemistry/
F.Online Tutorials
1.Molecular dynamics:http://cmm.info.nih.gov/intro simulation/course for html.html http://www.chem.swin.edu.au/modules/mod6.
2.Monte Carlo method:
http://www.cooper.edu/engineering/chemechem/MMC/tutor.html. http://www.cooper.edu/engineering/chemechem/monte.html
3.Bioinformatics:
http://www.iacr.bbsrc.ac.uk/notebook/wwwresource/bioinformaticcourses392.htm http://biotech.icmb.utexas.edu/pages/bioinfo.html.
4.Molecular modeling workbook:
http://www.ch.ic.ac.uk/local/organic/mod/Chem99.pdf
G.Additional Resource List for Computational Chemistry and Molecular Modeling Software
1.The Center for Molecular Modeling at NIH: http://cmm.info.nih.gov/modeling/software.html
2.Laboratory of Structural Biology at NIEHS: http://dir.niehs.nih.gov/dirlmg/strFxn.html
3.BioMolecular research tools—A collection of WWW links to information and
services useful to molecular biologists:
http://www.public.iastate.edu/ pedro/research tools.html
4.Center for Scientific Computing in Finland: http://www.csc.fi/ laaksone/docs/stuff.html
5.Rolf Claessen’s chemistry index:
http://www.claessen.net/chemistry/soft mod en.html
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6.Software for structure determination and analysis at the Protein Data Bank: http://www.rcsb.org/pdb/Modeling
7.W. L. Jorgensen group at Yale: http://zarbi.chem.yale.edu/
H.Databases of Biological Molecules
1.Protein Data Bank: http://www.rcsb.org/pdb/
2.IMB Jena Image Library of Biological Macromolecules: http://www.imb-jena.de/IMAGE.html
3.Nucleic Acid Database: http://ndbserver.rutgers.edu/NDB/
4.Cambridge Structural Database: http://www.ccdc.cam.ac.uk
5.Molecules R Us: http://molbio.info.nih.gov/cgi-bin/pdb
6.ExPASy (Expert Protein Analysis System) molecular biology server: http://www.expasy.ch
7.Lists of useful databases (including the Genome database) http://www.gdb.org/gdb/hgpresources.html