FIBOS Case Study

Description

FIBOS is an R and Python package designed to estimate the packing density of biomolecules.

In this case study, we perform in R a comparative analysis of packing densities between experimentally determined structures and those predicted by AlphaFold (AF).

Additionally, we include the codes used to generate the supplementary materials for the article.

Files

1. FIBOS-study-case-main.R: Main R script used in the case study

2. FIBOS-study-case-fun.R: R file containing auxiliary functions used by FIBOS-study-case.main.R

3. FIBOS-supp-main.R: Main R script used for producing supplementary material

4. FIBOS-supp-fun.R: R file containing auxiliary functions used by FIBOS-supp.main.R

Packages and Instalation Details

FIBOS R: https://github.com/insilico-unifei/fibos-R.git
FIBOS Python: https://github.com/insilico-unifei/fibos-py.git

Authors

• Carlos Silveira (carlos.silveira@unifei.edu.br)
  Herson Soares (d2020102075@unifei.edu.br)
  Institute of Technological Sciences,
  Federal University of Itajubá,
  Campus Itabira, Brazil.

• João Romanelli (joaoromanelli@unifei.edu.br)
  Institute of Applied and Pure Sciences,
  Federal University of Itajubá,
  Campus Itabira, Brazil.

• Patrick Fleming (Pat.Fleming@jhu.edu)
  Thomas C. Jenkins Department of Biophysics,
  Johns Hopkins University,
  Baltimore, MD, USA

References

Fleming PJ, Richards FM. Protein packing: Dependence on protein size, secondary structure and amino acid composition. J Mol Biol 2000;299:487–98.

Pattabiraman N, Ward KB, Fleming PJ. Occluded molecular surface: Analysis of protein packing. J Mol Recognit 1995;8:334–44.