This repository contains the data and codes associated with the paper-Sequence Patterns and Signatures: Computational and Experimental Discovery of Amyloid forming peptides, submitted to PNAS Nexus.
The source codes are in /code/. Compiler such as gfortran or ifort is required
/code/-This directory contains the following files and directories:
- main.f90-source code
- /lib/-This directory contains the forcefield and rotamer parameters of all the 20 natural amino acids
- comp.pdb-An example of the input PDB file needed to start the design
- input.txt-Input file to start design
- pdbfiles-This is an empty directory where the pdbfiles will be stored of the new peptides that are designed
/sequences and PDB files/-This directory contains the follwoing files:
- case1-top150-potential-candidates- File containing the top 150 peptide sequences from Case 1
- case2-top150-potential-candidates- File containing the top 150 peptide sequences from Case 2
- Px.pdb files- Protein data bank files of peptides P1, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12