LassoProt: server to analyze biopolymers with lassos

Pawel Dabrowski-Tumanski; Wanda Niemyska; Pawel Pasznik; Joanna I Sulkowska

doi:10.1093/nar/gkw308

LassoProt: server to analyze biopolymers with lassos

Nucleic Acids Res. 2016 Jul 8;44(W1):W383-9. doi: 10.1093/nar/gkw308. Epub 2016 Apr 29.

Authors

Pawel Dabrowski-Tumanski¹, Wanda Niemyska², Pawel Pasznik³, Joanna I Sulkowska⁴

Affiliations

¹ University of Warsaw, Faculty of Chemistry, Pasteura 1, Warsaw, Poland Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.
² Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland University of Silesia, Institute of Mathematics, Bankowa 14, Katowice, Poland.
³ Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.
⁴ University of Warsaw, Faculty of Chemistry, Pasteura 1, Warsaw, Poland Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland jsulkowska@chem.uw.edu.pl.

Abstract

The LassoProt server, http://lassoprot.cent.uw.edu.pl/, enables analysis of biopolymers with entangled configurations called lassos. The server offers various ways of visualizing lasso configurations, as well as their time trajectories, with all the results and plots downloadable. Broad spectrum of applications makes LassoProt a useful tool for biologists, biophysicists, chemists, polymer physicists and mathematicians. The server and our methods have been validated on the whole PDB, and the results constitute the database of proteins with complex lassos, supported with basic biological data. This database can serve as a source of information about protein geometry and entanglement-function correlations, as a reference set in protein modeling, and for many other purposes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biopolymers / chemistry*
Databases, Protein* / standards
Internet*
Models, Molecular
Proteins / chemistry*
Proteins / metabolism
Reproducibility of Results
Software* / standards

Substances

Biopolymers
Proteins