Jamie J. Alnasir


  Jamie J. Alnasir MPharm(Hons), PhD candidate, IT Consultant, Photographer, amateur tennis player...


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Jamie's Open source code


Artemis - Computation of torsional (dihedral angles) in peptide molecular structures

Languages: Python [ Github download ]

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


PDB-Hadoop - Hadoop framework for the Protein Databank

Languages: Hadoop Streaming/Bash [ Zenodo/Github download ]

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 Reduce operations.


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