The Biochemistry Links Resource - Tools, Guides & Tables

Links to Science Tools, Guides & Tables:

Abbreviations of Chemical Compounds - Type in an abbreviation of the name of a chemical compound to find that compound.

Amino Acids - Amino acid structure and properties.

APE - A Plasmid Editor - Full featured program (Windows, OS X and Unix) to map restriction digests, create plasmid maps, check reading frames and more.

BioABACUS - BioABACUS (Biotechnology Abbreviaion and Acronym Uncovering Service) is a searchable database of abbreviations and acronyms in Biotechnology that contains terms in such categories as: Biochemistry, Cell Biology, Computers and Internet, Diseases, Grants, Journals, Laboratories, Medicine, Molecular Biology/Genetics, Neuroscience, Other Organizations, Professional Societies and US Government. The data provided include the name of the term, its meaning, the category in which it is mostly used and, when available, a link in which additional information for the term can be found.

Biochemical Gallery - This online guide from the Johnson County Community College Virtually Biology course explains the basics of the structure and function of organic molecules, including fatty acids, carbohydrates, amino acids, proteins, and nucleic acids.

BioChemWeb - The Virtual Library of Biochemistry, Moleculer Biology and Cell Biology. Has several academic resources of biochemistry, molecular biology and cell biology compiled by the Fenteany Research Group from the University of Illinois Chicago.

Bioinformatics Research Software - Computational analysis and prediction of the function and three-dimensional structure of proteins from their amino acid sequence.

BioNet - Compendium of courseware and experience collected by BioNet members.

BioToolKit - Annotated directory of 1004 links to online molecular biology resources/bioinformatic tools for nucleic acid, genome, and protein structure analysis.

Cell's Basic Metabolism - Provides a thorough introduction to the biochemical processes that suport all living cells. Topics covered include glycolysis and the citric acid cycle, oxidative phosphorylation, ATP, and biosyntheses of various macromolecules.

Chime - Molecular Visualization Resources.

CHIMERA - Macromolecule viewing, creation of publication-quality structural images. Available for most operating systems. Runs under X11 on Mac OS X, but very simple to set up. Some learning curve (different style to VMD and RasMol), but well worth the effort. Can also be used to generate movies of your protein structures.

Codon Usage Database

Conversion of Units - Conversion of units.

EMBOSS runner - EMBOSS runner provides a GUI for use of the EMBOSS suite.

EMBOSS sequence analysis - EMBOSS is a free suite of sequence analysis tools.

ExPASy - Analysis of protein sequences and structures as well as 2-D PAGE.

Fundamental Physical Constants - Fundamental Physical Constants.

Genamics SoftwareSeek - Respository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry.

Genetic codes

Guidance for Students Project - Guidance for Students Projects.

Guide to Sequence Search - Biosequence comparison.

Hyperactive Molecules Using Chemical MIME - Use of chemical MIME to produce Hyperactive Molecules.

Introduction to Enzymes - Excerpted from a 1972 Worthington Biochemical publication, this site explains the basics of enzymes: their chemical nature, specificity, naming conventions, basic reactions, the enzyme-substrate complex, and factors affecting enzymatic activity.

Introduction to Molecular Virology - Introduction to Molecular Virology.

Jalview - Multiple alignment editor. Although this editor is written in Java, it is acceptably quick (but is probably best used on newer, faster hardware). An extremely capable and fairly user-friendly editor. Produces publication quality alignments.

JaMBW 1.1 - The Java based Molecular Biologist's Workbench.

MathMol Home Page - Designed to serve as an introductory starting point for those interested in the field of molecular modeling.

Medical Biochemistry - Topics covered include enzyme kinetics, the TCA cycle, DNA and RNA synthesis, lipoproteins, and more.

Metabolic Pathways of Biochemistry - Designed to graphically represent all major metabolic pathways, primarily those important to human biochemistry. Includes reaction pathways for carbohydrate, lipid, amino acid, and energy metabolism, as well as some coenzymes.

MSDS index - Material Safety Data Sheets.

NetBiochem - Several text-based tutorials in medical biochemistry, as well as a host of summary tables and several QuickTime animations. Topics covered include fatty acid metabolism, heme and iron metabolism, macromolecules, membranes, nucleic acids, and pourines and pyrimidines.

Periodic Table of Elements - The first periodic table published on the WWW.

The Principles of Protein Structure - Principles of Protein Structure Online Course.

Protein Explorer - Explore any 3D macromolecular structure model PDB file.

RasMol - Free molecular visualization resources.

RasMol Help - Molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules.

SI Units - International system of units.

Softberry (formerly genomic.sanger.ac.uk website) - Bioinformatics software to help identify genes and functional signals, determine gene function, decipher gene expression data and select disease-specific genes and drug target candidates.

Visual Molecular Dynamics (VMD) - Macromolecule viewing, creation of publication-quality structural images. Available for most operating systems. Runs under X11 on Mac OS X, but very simple to set up. Very quick program- useful even on older hardware. Built in support for Interactive Molecular Dynamics simulations further extend the utility of VMD.