paper.md

title	BioPandas: Working with molecular structures in pandas DataFrames
tags	bioinformatics computational biology protein structure analysis protein-ligand docking virtual screening
authors	name orcid affiliation Sebastian Raschka 0000-0001-6989-4493 1
affiliations	name index Michigan State University, East-Lansing, USA 1
date	31 May 2017
bibliography	paper.bib

Summary

BioPandas is a Python library that reads molecular structures from 3D-coordinate files, such as PDB [@Berman2000] [@berman2003announcing] and MOL2, into pandas DataFrames [@mckinney2010data] for convenient data analysis and data mining related tasks.

In addition to parsing protein and small molecule data into a data frame format, BioPandas provides additional utility functions for structure analysis. These functions include common computations such as computing the root-mean-squared-deviation between structures and converting protein structures into primary amino acid sequence formats.

Furthermore, useful small-molecule related functions are provided for reading and parsing millions of small molecule structures (from multi-MOL2 files [@tripos2007tripos]) fast and efficiently in virtual screening applications. Inbuilt functions for filtering molecules by the presence of functional groups and their pair-wise distances to each other make BioPandas a particularly attractive utility library for virtual screening and protein-ligand docking applications.

References