Resources/Links

Keating Lab Resources

    SYNZIPs – Synthetic heterodimeric coiled-coils
    CLEVER V1.0
        CLEVER(.zip) – Sequence based approximation of protein energies
        CLEVER manual(.pdf) – user manual
    AVID – Annotation Via Integration of Data
    DrawCoil – a program for producing coiled-coil helical wheel diagrams

Dissertations

•Scott Chen, “Design of Protein-Protein Interaction Specificity Using Computational Methods and Experimental Library Screening”, link
•Aaron Reinke, “Determining Protein Interaction Specificity of Native and Designed bZIP Family Transcription Factors”, link
•Nora Zizlsperger, “Investigation of coiled-coil interactions between proteins of the spindle pole body”, link
•Emiko Fire, “Flexibility and specificity of the interaction of MCL-1 with BIM BH3”, link
•Karl Gutwin, “Computational prediction of coiled-coil interaction structure specificity”, link
•James Apgar, “Modeling the flexibility of alpha helices in protein interfaces : structure based design and prediction of helix-mediated protein-protein interactions”, link
•Gevorg Grigoryan, “Computational approaches for the design and prediction of protein-protein interactions”, link
•Christina Taylor, “Redesigning specificity in miniproteins”, link

Links

 

Literature Search

PubMed

Web of Science

 

Journals

Nature 
Science 
Cell 
Nature Structural & Molecular Biology
Protein Science 
Journal of Biological Chemistry 
Journal of Molecular Biology 
Journal of the American Chemical Society
Proceedings of the National Academy of Sciences 
Protein Engineering, Design and Selection 
Structure 
Biochemistry 
Proteins: Structure, Function and Bioinformatics
ACS Synthetic Biology

 

Web Calculators & Suppliers 

MS Adduct List
Protein Calculator
MGH Sequencing
IDT - OligoAnalyzer
Hampton

Lab & Affiliate Websites

Keating Lab wiki
Cell Decision Processes Center 
CSBi
National Centers for Systems Biology Portal

 

Calendars

MIT Biology Dept. Calendar
Broad Institute Calendar
Whitehead Institute Calendar
MIT Biological Engineering Dept. Calendar
MIT Chemistry Dept. Calendar

 

Coiled Coil Analysis

Paircoil2
Paircoil
Multicoil scoring form
COILS
Marcoil
bZIP coiled-coil scoring form
SOCKET:  detecting coiled coils in structures