Jamie's Open source code
Artemis - Computation of
torsional (dihedral angles) in peptide molecular structures
Languages: Python [ Github
Dihedral angles (also known as Torsional angles) in peptides are measured between select
atoms in neighboring residues and yield important information about the structural
conformation of the residues in the peptide (secondary structure). There are three such
dihedral angles that can be measured: φ, ψ, and ω.
The φ (Phi) angle is measured from the C of
one residue to the C of the next residue.
The ψ (Psi) angle is measured from the N of one residue to the N of the next.
The ω (Ohmega) angle is measured from the C) of one residue to the C) of the next.
(Left) φ, ψ, and ω dihedral angles in a peptide.
Image courtesy Dr. Landry, Tulane.edu
- Hadoop framework for the Protein Databank
Hadoop Streaming/Bash [ Zenodo/Github
A framework that facilitates parallel execution of protein structure analysis tools to be carried out
on the entire (or subsets of) the Protein Databank (PDB) using the Apache Hadoop platform. Our design
enables structural Biologists to use the Hadoop platform without having to explicitly write MapReduce code. It
is easily scalable and uses a mapper architecture that functions on a stand
alone basis or can be extended to include further Map