Laboratory Procedures

Protocol template file

General Procedures

• Standard Cell Prep
• Preparation of Competent Cells (old)
• Getting DNA sequenced
• Isolating Inclusion Bodies
  
• Making Competent Cells
• MALDI
• Amino Acid Analysis
• Minimal Media Recipe
• Sterile Technique
• Thrombin Cleavage
• Western Blotting and Immunostaining
• Limited proteolysis
• Thermal melt using CD
• Calculating denaturant concentration by r.i.
• Theoretical simulations and considerations for Kd measurement and calculation
• Protocol for growing labeled protein

DNA Processing Assemblies

• RPA-AB Purification
• T-Antigen Purification
• DNA primase Exp. / Purification

Calcium-Binding Proteins

• Lab Guidelines
• Calbindin D_9k Prep
• updated Calbindin D_9k Prep
• Calmodulin Prep
• S100A2 Prep
• S100A6 Prep
• S100B Prep
• S100A8/A9 Prep
• Production of Calbindomodulin Mutants
• Centrin Prep
• Purification Protocol for HCentrin2
• CDPK prep
• Competitive Chelator Method for Calcium-Binding Constants (Updated version)
• Phenyl Sepharose Binding Assay for Calbindin Mutants
• Preparing Chelexed water
• Walter's notes about NMR with EDTA

NMR and Computational Wisdom

• Beginner's guide to data collection on Bruker instruments using xwinnmr

Other NMR Data Processing

• Removing off-resonance water line
• Handling ¹³C resonances at spectrum edge
• Tips on getting Modelfree up and running
• Overlaying multiple spectra in colors
• Summary of common commands used in Bruker pulse programming
• Description of some automated backbone and NOE assignment packages

Calculating Structures

• Chazin Lab "how to"

Analysis and Comparison of Structures

• Randy's InsightII Tips
• Electrostatic Surface calculation with UHBD and display with AVS 
• Contact maps with CHARMM
• Distance difference matrices with DISCOM
• Randy's DISCOM Tips
• Calculating Interhelical Angles with signs using Interhlx, a program written by Kyoko Yap
• Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids-PDF format
• Displaying Protein Surfaces With Dino

UNIX and Other Computing Topics

• UNIX Tips
• Randy's UNIX Tips
• Basic procedures in PostgreSQL, a database management system 
• Using the DBI and DBD:Pg Perl modules to access PostgreSQL databases

Software Manuals

• MSI Online Docs (Vandy only)
• Facelift - multidimensional baseline correction
• Our own experience
• NAB
• xv
• Garry Gippert's programs
• ACE/gr-also known as xmgr or xvgr

Javascript and Perl Utilities

• Perl scripts for use in structure calculations