Biomolecules: Databanks, Visualisation and Computations -Internet resources


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Internet resources for the lecture

1. Data Banks and other basic resources

2. Interesting internet pages on particular topics

3. Programs

4. Chime or other plugin teaching resources

2. Data banks and basic resources:

Protein Data Bank: The protein structure database

World Wide Protein Data Bank: The The world wide protein structure database

BRENDA: - The Comprehensive Enzyme Information System

EBI: - European Bioinformatics Institute

Human Protein Atlas: Swedish page containing information on more than 1500 antibodies and 1200000 images from all parts of the body.

ExPASy - Swiss-Prot and TrEMB

EMBL - The European Molecular Biology Laboratory

Humane Genome Project

AHo's Amazing Atlas of Antibody Anatomy: Well sorted list of antibodies available.

Humane Genome Project

World Index of Molecular Visualization Resources

2. Interesting internet pages on particular topics:

-Bioinformatics and Structure

Bioinformatics.org: The Open-Access Institute

Charite Bioinformatics group

Columba - Protein Structure Annotation Database

Nucleic Acid Database (NDB)

-Protein Engineering resources

Wikipedia entry -Protein Engineering

The Plückthun Lab Homepage -University of Zurich

MRC Centre for Protein Engineering

Biologische Chemie TUM - Prof. Skerra

ZLab Protein Engineering Hub -Boston University

- Aptamer resources

Wikipedia entry -Aptamers

University of Bonn, -Prof. Famulok

Fa. NOXXON Berlin -gespiegelte Aptamere

3. Programs :

Note: This list merely contains those programs that were used during the class and does not intend to be a comprehensive list of available programs.

-Protein Data Bank file viewers:

Rasmol: first generation pdb and molecule viewer: Very nice to get a first glimpse on a protein. Also includes scripting capabilities, but this is somewhat complicated to handle. Runs under Windows and Linux

Molsee: Tcl/Tk -Script for the GUI -control of Rasmol. Runs under Unix / Linux

Chime: Browser Plug-in derived from Rasmol. Unfortunately it only works for some browsers under MS Windows, like Netscape 4.7x and Explorer. For usage with Netscape 7/8, Mozilla and Firefox see comments
. http://www.umass.edu/microbio/rasmol/
For testing your chime installation, you may take a look at my protein gallery

VMD (Visual Molecular Dynamics): VMD is agreat program for viewing pdb - files and molecular dynamics simulations (in connection with NAMD), Includes many structure visualization modes, many presentation choices. Easy scripting capability based on TCL/TK or python. There are scripts available that add button capabilities to the program, which faciliates demonstrations during lectures and seminars. This program will be dominantly used in the class. Runs under Windows, Unix/Linux and Mac

SPDBV (Deep view Swiss pdb viewer): Also an advanced program with capabilities partly exceeding those of VMD, however, the graphical presentation is not as nice as with VMD. Runs under Windows and Linux.

Chimera: visualization and molecular modeling system, also with docking plug-ins. Runs under Windows, Unix/Linux and Mac

Pymol: a newcomer written in python which looks promising. Easy creation of presentations, in some ways similar to VMD. Runs under Windows, Unix/Linux and Mac

-Program aimed at visualizing small molecules and outputs from calculations:

The molecule visualization programs use the output data from molecule calculation programs, such as Gaussian, Gamess, Mopac6 or others. Since these calculations on a high-quality level take a considerable time and are complicated to operate, the input and output files from computations will be provided and can directly be used in the visualization programs.

Molden: great program, shows structure, orbitals, electron density etc. Also shows vibrational spectrum (Raman, IR) and correspondingly the animated vibrational modes. Runs under Unix/Linux.

Molekel: similar to molden, shows structure, orbitals, electron density etc. Also shows animated vibrational modes, but does not include a drawn spectrum. Runs under Unix/Linux and Windows.

gOpenMol: nice program, shows structure, orbitals, vibrations etc. . For Windows and Unix / Linux.

Facio: 3D-Graphics program for Molecular Modeling and Visualization of Quantum Chemical Calculations For Windows only.

-Calculation programs and GUIs to these programs:

NAMD / VMD : Molecular mechanics calculation package. Uses VMD as GUI. Runs under Unix/Linux, Windows and MAC.

Oscail / Móílín : A very nice GUI from Prof. P. McArdle, National University of Ireland, Galway, for drawing molecules and submitting jobs for calculation using Tinker, Mopac6, Wingamess and Iconc. Mopac6 and Iconc (Prof. G. Calzaferri) is included, Tinker and Wingamess (Prof. Alex Granovsky) have to be installed independently. Runs under Windows.

Gamess / Wingamess : The ab-initio free program. Several versions (Gamess-UK, Gamess-US) and multiple compilations are available for Windows and Unix. The version used in the class can be found here:

Tinker / Force Field Explorer: Modular molecular mechanics calculation package with FFE as GUI from Prof. Jay W. Ponder, Washington University, St. Louis) . Runs under Unix/Linux and Windows.

HEX : Docking program (Dave Ritchie, University of Aberdeen). Runs under Unix/Linux, Windows and MAC.

FAST: FAST Alignment and Search Tool -Boston University. Runs in the Internetbrowser or offline under Linux and Mac

3. Specific chime or other plugin teaching resources to be used during the lecture :

( For information on installing chime as plug-in with Netscape 7/8, Mozilla and Firefox,
klick here )

Please note: Chime is not freeware, and MDL, that developed chime is not really updating it any longer and does not publish the source code. This clearly demonstrates the disadvantage of 'cost free' programs that do not come with a open source licence, for example that are not governed by GPL. I only included these links, since many authors still offer very nice Chime-based presentations (including me, I do not have the time to rewrite those). Do not create new scripts with Chime, there are much better alternatives, especially JMOL. This is Java -based, goes without additional plug-in installation and is platform -independent. More to this topic under the following page:
Molecular Visualization Resources -Eric Martz

Highlights of Biochemistry, FB Biologie, Uni Hamburg (also in German)

Molecular Models for Biochemistry at Carnegie Mellon University

Stryer, Berg, Tymoczko, Biochemistry, 5th ed.

MH-Hannover, Biophys. Chemie, AK Manstein

Protein Gallery, P. Schellenberg

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For questions, please contact:
Peter Schellenberg, phone (+351) 253-604074

Peter Schellenberg May, 09th, 2008