/FASPR-backup

THIS IS A FORK. an ultra-fast and accurate program for deterministic protein sidechain packing

Primary LanguageC++MIT LicenseMIT

ATTN: This is a fork

The original is at https://github.com/tommyhuangthu/FASPR I just forked it in case the original gets taken down one day.

FASPR is a method for fast and accurate protein side-chain packing, which is an important step in protein structure prediction and protein design.

Copyright (c) Xiaoqiang Huang Yang Zhang Lab Dept. of Computational Medicine and Bioinformatics Medical School University of Michigan Email: tommyhuangthu@foxmail.com, xiaoqiah@umich.edu

FAQ

  1. How to use the program? Usage: ./FASPR -i input.pdb -o output.pdb [-s sequence.txt]

-i: input a pdb backbone for packing. There should be no missing main-chain atoms (N, CA, C and O). If side-chain atoms are included in input.pdb, they are ignored by FASPR.

-o: the repacked structure output by FASPR (in standard PDB format). The residue positions are kept identical to the input pdb file

-s: (optionally) pack a new sequence on the backbone of the input.pdb file. The sequence should be written as one-single line of one-letter alphabet of amino acid types, e.g.:

ACDEFGHIKLMNPQRSTVWYYWVTSRQPNMLKIHGFEDCA

for the input sequence, only 20 canonical amino acids are allowed.

When the input sequence is the same as the one extracted from the PDB structure, the amino acid side-chain conformations is repacked. When the input sequence is different from that extracted from PDB, mutations will be introduced. Therefore, FASPR can be used to construct mutant models very efficiently.

If you want to fix the conformation of some residues during packing, you can specify those residue in low-case letters and the others in upper-case letters, e.g.: acdefghiklmnpqrstvwyYWVTSRQPNMLKIHGFEDCA

NOTE

Please remember to put the executable FASPR program and the binary Dunbrack rotamer library 'dun2010bbdep.bin' in the same directory. Otherwise, the program will prompt "error! cannot find rotamer library dun2010bbdep.bin". Do not change the name of 'dun2010bbdep.bin' because it is hard coded in the source code.

  1. How to build the program for speed? Build the executable program from the source code using the following command: g++ --ffast-math -O3 -o FASPR src/*.cpp or (if the above command does not work): g++ -O3 -o FASPR src/*.cpp

  2. In which OS can I run FASPR? FASPR can be run in any OS if it is buit following the way as mentioned above.

  3. Please report bugs to Dr. Xiaoqiang Huang at the above emails.

  4. FASPR is open-source software under the MIT license.

REFERENCE

If FASPR is useful to your work, please cite:

[1] Xiaoqiang Huang, Robin Pearce, Yang Zhang, FASPR: an open-source tool for fast and accurate protein side-chain packing. Bioinformatics (2020) 36: 3758-3765. [2] Xiaoqiang Huang, Robin Pearce, Yang Zhang. Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries. J. Chem. Inf. Model. 2020; 60:410-420.