Research laboratory of William DeGrado, PhD

Resources

SuperCodons

Super Codons and Super Nucleotides allow researchers to create diversity in their DNA constructs matching a chosen amino acid distribution

Suns: The Structural Search Engine

Suns provides the missing search engine for the Protein Data Bank, complete with a Pymol interface

E(Z) Depth Potential Position Finder

Calculate the energy minimum of a sequence in standard alpha-helix conformation

MadCat

Searches for structurally similar backbone motifs in the Protein Data Bank

DrawCoil 1.0

Creates helical wheel diagrams for coiled coils of any oligomerization state and orientation.

β-Peptide Rotamer Libraries

Supplementary materials for our paper discussing rotamer libraries for beta-peptide helices. We have calculated libraries for the C3 and C2 positions for both D/L chiralities for 314, 312, 3.0 β-helices. In addition, we present a comparison of libraries computed for different secondary structure environments.

OSTRICh

Use low resolution experimental data to predict the structure of homo-oligomeric transmembrane helical bundles


See computational tools for more information.