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Atkins & de Paula: Physical Chemistry: 8e

Chapter 19

Databases
Tutorials
Software

Databases

CRC Handbook of Chemistry and Physics
http://www.hbcpnetbase.com/
Data may be accessed after purchasing a personal or institutional subscription.

Database of Macromolecular Movements
http://molmovdb.org
A collection of movies describing motions in proteins and other macromolecules. Also available are freeware and server-based tools for structural analysis.

LIPIDAT
http://www.lipidat.chemistry.ohio-state.edu/
A database of thermodynamic properties of lipids.

NDB
http://ndbserver.rutgers.edu/
A database of nucleic acid structures.

RCSB Protein Data Bank
http://www.rcsb.org/pdb
A database of structures of proteins obtained by X-ray diffraction or NMR spectroscopy. For best viewing of the three-dimensional structures, install a molecular visualization plug-in (such as MDL Chime, Protein Explorer, or RasMol).

Tutorials

Protein Structure
http://www.med.unibs.it/~marchesi/proteins.html
Introduction to protein structure.

Protein Explorer
http://beta.rcsb.org/pdb/pe/explorer/pe_tut.htm
Tutorial on how to use the Protein Explorer programme.

MALDI-TOF
http://www.abrf.org/ABRFNews/1997/June1997/jun97lennon.html
MALDI-TOF mass spectrometry.

Electrophoresis Simulation Site
http://www.rit.edu/~pac8612/electro/E_Sim.html
Run an electrophoresis gel online with this simulation.

Colloids
http://pharmlabs.unc.edu/colloids/pretext.htm
An introduction to colloids.

Software

AMBER Server: Molecular Mechanics over the Web
http://amber.scripps.edu/index.html
This free interactive utility allows the user to predict the secondary structure of a polypeptide by molecular mechanics simulations using the AMBER force field.

CORINA
http://www2.chemie.uni-erlangen.de/software/corina/free_struct.html
Interactive molecule builder and energy minimizer.

MDL Chime
http://www.mdl.com/products/framework/chime/
A free browser plug-in for molecular visualization.

PredictProtein
http://www.embl-heidelberg.de/predictprotein/predictprotein.html
A web-based service for prediction of protein structures.

Protein Explorer
http://www.umass.edu/microbio/chime/pe/protexpl/frntdoor.htm
A free browser plug-in for molecular visualization, based on RasMol.

RasMol
http://www.umass.edu/microbio/rasmol/
A free browser plug-in for molecular visualization.