George Georgiou Research Group

Protocols:

Buffer Ph and Recipes, editable version (intranet only, if inaccessible access our lab directory first)

Buffer design  interactive recipes from EMBL Heidelberg

Error Prone PCR calculation sheet  based on: M. Fromant et all Biochemistry 224, 347-353 (1995)

Antibody Homology Modeling

ELISA

FACS

Making Heat Shock Competent Cells

Heat Shock Plasmid Transformation

In vitro Transcription/Translation

Purifying Inclusion Bodies vis His-Tag and Nickel Columns

Osmotic Shock

PCR Primer Design

Western Blot Analysis

Silver Staining

Protocol links:

• Antibodies: From Design to Assay
• Lab Protocols- quick index
• Lab. Protocol 1
• Lab Protocols 2
• Molecular Biology Protocols
• Molecular Biology Shortcuts - Protocols
• NHGRI Microarray Project: Experimental Protocols
• NIST Chemistry WebBook of Organic & Inorganic Compounds
• NWFSC Molecular Biology Protocols
• Protocols at Indiana University
• Protocols from Ambion, Inc.
• Technical Tips Online
• Wash U Mol Biol Protocols
• Methods: A Companion to Methods in Enzymology
• http://www.molbiol.edu.ru/eng/protocol/

 

Other Resources:

• Amino Acids
  from the FU Berlin
• Amino Acid Information  
  from EMBL, Heidelberg
• Webcutter
  free online software for restriction mapping nucleotide sequences - from Yale University

• Primerfinder 
  online primer design program - from the Univ. of Texas-SW Med. Ctr.

• Online Analysis Tools 
  Analysis of nucleotide and protein sequence data, Primers.....

• WAM - Web Antibody Modelling 
  an online facility for generating a 3D model of an antibody Fv from its sequence

• Thermodynamics of Enzyme Catalyzed Reactions
  from the NIST

• Molecular Biology glossary 
  from the University of North Carolina

• Protein engineering glossary
  from the Biomedical Center, Uppsala, Sweden 

• Useful calculation tools: 
  cell growth, DNA concentration, and much more.. - from "Practical Molecular Biology")

• PDB to MultiGIF Page:
  creates animated gif files out of pdb files - from the DKFZ (German Cancer Research Center), Heidelberg" 

• Worthington Enzyme Manual
  enzymes and related biochemicals

• Combinatorial Codons
  allows the user to input desire probabilities for each amino acid and/or stop codons and outputs required percentages of bases (A,G,C or T) necessary for each of the three codon positions

• Bio Mail
  searches Pub Med on a regular bases and send you the results as an e-mail
  

 

Databases:

• Image Library of Biological Molecules (Jena)

• PDB:The Protein Data Bank

• REBASE The Restriction Enzyme Database

• Kabat Database 
  database of protein of immunological interest

• MGT Database 
  Marie-Paule LeFranc's Immunogenetics database at the EBI. This is a database of nucleic acid sequence information on immunoglobulins, T-cell receptors and MHC/HLA.

• VBase 
  Ian Tomlinson's database of human V region gene sequences.

• PMD 
  protein mutant database

• Codon Usage Database
  from the Kazusa DNA Research Institute

• ABG: Directory of 3D structures of antibodies 
  A directory of information on 3D structures of antibodies publicly available in the PDB, from the Instituto de Biotecnologia, UNAM in Mexico.

• NCBI's Molecular Modelling Database

• The WWW Virtual Library Biotechnology Section Databsaes 
  

 

Chemistry Tools:

• Chemland 
  a huge collection of Java applets to calculate and explore various chemical properties, reactions... (click here to download Windows version)

• Periodic Table of Elements 
  from los Alamos National Laboratory

• Molecular Weight Calculator
  from the FU Berlin

• NIST Chemistry WebBook

• pKa of Common acids and pKb of Common Bases
  from Merck Chromatography
• Buffers: Ph and Recipes,  editable version (intranet only)
  
  

General Tools:

• Mathematical Notation for Orders of Magnitude
  from UC Berkeley

• Conversion of Units Calculator
  from the FU Berlin

• Bio Mail
  searches Pub Med on a regular bases and send you the results as an e-mail

• Useful calculation tools: 
  cell growth, DNA concentration, and much more.. - from "Practical Molecular Biology"

  Software:

• Bioedit
  free DNA Sequence alignment, analysis and much more

• DNA Tools
  free DNA analyzing software

• pDRAW32
  free DNA cloning, sequence analyses, restriction side finding, plasmid/DNA plotting software

• Rasmol
  free powerful Protein display and manipulation program 

• Protein Explorer FrontDoor
  free powerful Protein display and manipulation program 

• Web Lab Viewer Lite
  free powerful Protein display and manipulation program 

• Swiss PDB Viewer
  free Protein display and manipulation program 

• RNAstructure
  analyzes RNA sequences for probable secondary structure

Chemland 
Helps to calculate and explore various chemical properties, reactions...

Software-collections:

• Genamics SoftwareSeek - Molecular Biology and Biochemistry ...
  database of freely-distributable and commercial tools for use in molecular biology and biochemistry...  

• Free Software for Molecular Biology 
  Gopher site listing over 150 free software programs in molecular biology and related areas - from Indiana Univ. Program files found at: gopher://iubio.bio.indiana.edu:70/11/IUBio-Software+Data/molbio

• The BioCatalog
  the BioCatalog is a software directory of general interest in molecular biology and genetics (EMBL)
  

Link-collections:

• Amos' WWW links page
  huge collection of Biology related tools and information sources

• Stefan Dübel Antibody link page

• Antibody related companies
  from Stefan Dübel's page 

• SciSeek
  science Search Engine

• Molecular Toolbox 
  Links to programs and databases for online analysis of DNA, RNA and protein sequences

• Molecular Biology shortcuts 
  Links and general Information for Molecular Biologists 

• Links to Bioinformatics Resources 
  from Rutgers University 

• Chemie.De 
  An electronic gateway to numerous resources on the Web for chemists and chemical engineers worldwide.

• The World Wide Web Virtual Library,  Biotechnology Information Directory, Pharmaceutical Companies