Physics, biophysics
- Free energy landscape of proteins with nontrivial topology
- Protein folding from the point of view of kinetic theory
- Mechanical properties of proteins, reaction rate theory
- Protein dynamics: coarse-grained modeling, implicit solvent simulation
- Maximum entropy models
Useful links:
- Spin glasses and the statistical mechanics of protein folding
- Theory of protein folding
- A theoretical physicist looks at protein structure
Bioinformatics
- Direct coupling analysis, statistical model for the variability within a set of phylogentically related biological sequences
- Evolutionary pressure, multiple sequence alignment (MSA), maximum likelihood estimation (MLE)
- Protein structure prediction
- Development of algorithmic methods to identify tangled structures in proteins
- Construction of databases: KnotProt, LinkProt; servers: LassoProt, GapRepairer; plugins for Pymol and VMD
Applied mathematics
- Knot theory: knotted and slipknotted proteins, complex lasso proteins, links
- Application of minimal surface to biomolecules, orientable surface, Seifert surface
- RNA topology, chord diagram
Biochemistry
- Insights into catalysis by a knotted TrmD tRNA methyltransferase
- Protein-ligand interactions
- Drug design
