Software

Databases/servers with topological information about proteins

KnotProt

A database of proteins with knots and slipknots
knotprot

LassoProt

A server and database of proteins with lassos

 

LinkProt

A database of proteins with topological links

 

Plugins/programs for proteins topology identification

PyLasso

A plugin to detect lassos and to analyze their geometric structure

PyLink

A plugin to identify links
carousel_3sumABCD

 

Knot_pull

Python package for biopolymer smoothing and knot detection
knotpull

 

Server with information about mechanical properties of proteins

Bio-molecule stretching database

A database that contains information related to mechanical stretching of biomolecules
stretch

 

Prediction of proteins structures based on co-evolution methods

DCA-mol

A plugin to analyze direct evolutionary couplings
dcamol

PconsFam

A database of PFAM families modelled using the PconsFold2 pipeline

 

Server for protein backbone reconstruction

GapRepairer

Server for automatic reconstruction of missing parts of protein models
gaprepairer

 

Database and servers for chromatin analysis (knots and links)

KnotGenome

A server to detect entanglement in and between chromosomes

 

Database for genus trace (RNA and protein chains)