{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Complex analysis example" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Analyze a complex of two strands intended to form a bipedal walker with a duplex torso and single-stranded legs (Shin and Pierce, J Am Chem Soc, 2004).\n", "\n", "Material: DNA \n", "Temperature: 23 C\n", "\n", "Calculate the partition function, equilibrium pair probability matrix, MFE proxy structure(s), and a set of suboptimal structures within a specified free energy gap.\n", "\n", "These calculations can alternatively be performed using Utilities commands (see the Utilities example notebook). " ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "# Import NUPACK Python module\n", "from nupack import *" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "Complex results:
Complex | \n", "Pfunc | \n", "ΔG (kcal/mol) | \n", "MFE (kcal/mol) | \n", "
---|---|---|---|
(a+b) | \n", "4.1688e+30 | \n", "-41.492 | \n", "-38.547 | \n", "