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APPENDIX I
List of Software Programs and Web Sites Useful for
Each Chapter
This table lists Web sites that are particularly relevant to specific chapters. The
list is not all-inclusive, but it does include popular and especially helpful URLs.
Individual chapters also contain detailed lists of associated Web sites. Additional
Web sites for each chapter are available on the books Companion Website,
which can be found at http://www.chemplace.com.

Chapter No.

Name

1
1

Description

URL

Sigma-Aldrich

MSDS

www.sigma-aldrich.com

Swarthmore
College

Scientific posters

http://www.swarthmore.edu/NatSci/
courrin1/posteradvice.htm

1-3

Rainin

Pipetting

http://www.rainin.com

1-3

Graphpad

Statistics

http://www.graphpad.com/prism/
Prism.htm

1-3

Journal of Chemical
Education
Resource Shelf

List of all current

biochemistry
textbooks

http://www.umsl.edu/divisions/artscie
nce/chemistry/books/welcome.html

1-3

ChemDraw

Chemical structure
drawing program

http://www.cambridgesoft.com

1-11

Intute

Best Web sites

http://www.intute.ac.uk/
biologicalsciences

1-11

BioChemWeb

Biochemistry library

http://www.biochemweb.org

2-11

Protocol-Online

Your labs reference

book

http://www.protocol-online.org

2-11

Protein Data
Bank (PDB)

Protein structures
determined by X-ray
and NMR

http://www.rcsb.org/pdb

2-11

ChemBioFinder

Life science solutions

http://www.chembiofinder.com

2-11

NCBI Molecules
to Go

Structures of
biomolecules

http://molbio.info.nih.gov.cgi-bin/pdb

2-11

PyMol Molecular
Viewer

Structures of
biomolecules

http://pymol.org

2-11

Chimera Molecular
Modeling System
(UCSF)

Advanced molecular
modeling

http://www.cgl.ucsf.edu/chimera

2-11

Biomolecules Alive

Instructional material

http://www.biomoleculesalive.org

2-11

Entrez Browser
of NCBI

Database searching including PubMed literature

http://www.ncbi.nlm.nih.gov/Entrez
(continued)

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332 Appendix I
Chapter No.

Name

Description

URL

2-11

MEDLINE (PubMed)

U.S. National Library

of Medicine

http://www.nlm.nih.gov

2-11

International Union
of Biochemistry and
Molecular Biology
(IUBMB)

Nomenclature

http://www.chem.qmul.ac.uk/iubmb

Biological Magnetic
Resonance
Data Bank

NMR data of
biomolecules

http://bmrb.wisc.edu

Science of
Spectroscopy

Spectroscopy
applications
and techniques

http://www.scienceofspectroscopy
.info/index.htm

DynaFit

Ligand binding

http://www.biokin.com

SigmaPlot

Enzyme kinetics
module

http://www.sigmaplot.com/products/
sigmaplot/enzyme-mod.php

Enzyme Structures
Database

Enzyme structures in
Protein Data Bank

http://www.biochem.ucl.ac.uk/bsm/
enzymes/index.html

8-11

IUBMB Enzyme List

Catalog of enzymes

http://www.chem.qmul.ac.uk/iubmb/
enzyme

8-11

Worthington
Enzyme Manual

Properties of enzymes

http://www.worthington-biochem
.com/index/manual/html

8-11

BRENDA

A comprehensive
enzyme information
system

http://www.brenda-enzymes.info

9-10

European
Bioinformatics
Institute (EBI)

DNA sequences

http://www.ebi.ac.uk

9-10

GenBank of the
NCBI

Nucleotide sequence
database

http://www.ncbi.nlm.nih.gov/Genbank

9-10

EMBL

Nucleotide sequence
database

http://www.ebi.ac.uk

9-10

The Institute for

Genomic Research

Collection of genomic
databases

http://www.ebi.ac.uk/genomes/index.
html

9-11

Enzyme Database
of ExPASy

Enzyme names and

numbers

http://www.expasy.ch/enzyme

9-11

The Broad Institute

of MIT and Harvard

Genomics

http://www.broadinstitutes.org

10

REBASE-The
Restriction Enzyme
Database

Restriction enzyme
directory and action

http://rebase.neb.com

10

Fermentas

Restriction enzymes

http://www.fermentas.com
(continued)

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Appendix I 333
Chapter No.

Name

Description

URL

11

Munich Information
Center for Protein
Sequences (MIPS)

Protein sequences

http://www.helmholtz-muenchen.de/
en/mips

11

Protein Information
Resource (PIR)

Database searching
for proteins

http://pir.georgetown.edu

11

Swiss-Protein

Protein sequences

http://ca.expasy.org/sprot