Prof. Joanna Sulkowska
Interdisciplinary Laboratory of Biological Systems Modelling
Prof. Joanna I. Sulkowska

Projects & Software

Open-source databases, servers, and tools for studying the topology of proteins, genomes, and biomolecules.

Databases & Servers

Protein Topology
AlphaKnot AlphaFold
AlphaKnot 2.0
Knot & knotoid detection across AlphaFold proteomes.
AlphaLasso AlphaFold
AlphaLasso
Lasso topology classified across AlphaFold structures.
KnotProt
KnotProt 2.0
Reference database of knotted proteins from the PDB.
LassoProt
LassoProt
Covalent lasso motifs, classified by piercing number.
LinkProt
LinkProt
Topologically linked loops in protein structures.

Plugins & Packages

Topology Identification
Package
Topoly
Knot polynomials (Alexander, Jones, HOMFLY) for polymers.
PyLasso Plugin
PyLasso
Lasso detection with 3D visualization in PyMOL/VMD.
PyLink Plugin
PyLink
Topological link identification and visualization in PyMOL.
Knot_pull GitHub
Knot_pull
Topology simplification via iterative chain pulling.

Chromatin & Genome Topology

Genomics
KnotGenome Server
KnotGenome
Knots & links in chromatin fiber from polymer models.

Mechanical Properties

Molecular Mechanics
BSDB
BSDB — Bio-molecule Stretching Database
Force-extension data from coarse-grained simulations.
Genus
Genus for Biomolecules
Topological genus of proteins and RNA via minimal surfaces.

Structure Prediction

Co-evolution Methods
DCA-mol Server
DCA-mol
Evolutionary couplings from MSA for structure prediction.
PconsFam
PconsFam
Contact-assisted models for thousands of Pfam families.
GapRepairer Server
GapRepairer
Reconstructs missing backbone fragments in PDB structures.

Computing Infrastructure

HPC Resources
Horda Cluster
Primary HPC cluster for large-scale topology simulations.
LSSCB Cluster
Shared HPC infrastructure for structural bioinformatics.
HORDA resources

HORDA supports large-scale topology simulations, molecular modelling, and analysis workflows used across lab research projects.

View available resources →
228 physical CPUs 348 virtual CPUs
22 GPUs
736 GB RAM
around 45 TB shared storage
Available software
Amber 18 (with AmberTools) CUDA 11.5 CUDA 12.2 Gromacs 2023.1 Gromacs with CP2K 2023.1 Python 3.9 Python 3.10 Python 3.11 SageMath 9.5-4