Area of research
Molecular Biology · Atomic and Molecular Physics, and Optics · protein folding alphafold
Research interest
Research interests include Protein Structure and Dynamics, Biochemical and Structural Characterization, Force Microscopy Techniques and Applications, and Enzyme Structure and Function.
Novel Knotted Solenoid fold with order-shifted coil arrangement leads to nontrivial 3<sub>1</sub> topology.
Universe of Lasso Proteins: Exploring the limit of entanglement and folding landscape of proteins predicted by AlphaFold
AlphaLasso-a web server to identify loop and lasso motifs in 3D structure of biopolymers.
Topology in soft and biological matter
Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model.
AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.
Knots and θ-Curves Identification in Polymeric Chains and Native Proteins Using Neural Networks
Theta-curves in proteins.
Knotted artifacts in predicted 3D RNA structures.
AlphaFold predicts novel human proteins with knots.
Identification of Novel CB2 Ligands through Virtual Screening and In Vitro Evaluation.
First crystal structure of double knotted protein TrmD-Tm1570 – inside from degradation perspective
Conservation of knotted and slipknotted topology in transmembrane transporters.
Proteins containing 6-crossing knot types and their folding pathways
Nucleolar Essential Protein 1 (Nep1): Elucidation of Enzymatic Catalysis Mechanism by Combined Molecular Dynamics Simulation and Quantum Chemical Calculations
Knot or Not? Sequence-Based Identification of Knotted Proteins With Machine Learning
Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding.
Identification of CB1 Ligands among Drugs, Phytochemicals and Natural-Like Compounds: Virtual Screening and In Vitro Verification.
New 6 <sub>3</sub> knot and other knots in human proteome from AlphaFold predictions
SARS-CoV-2 Papain-Like Protease Potential Inhibitors-In Silico Quantitative Assessment.
Lasso Proteins-Unifying Cysteine Knots and Miniproteins.
Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.
Mg<sup>2+</sup>-Dependent Methyl Transfer by a Knotted Protein: A Molecular Dynamics Simulation and Quantum Mechanics Study.
Knot_pull-python package for biopolymer smoothing and knot detection.
KnotProt 2.0: a database of proteins with knots and other entangled structures.
Proteins' Knotty Problems.
PconsFam: An Interactive Database of Structure Predictions of Pfam Families.
Supercoiling in a Protein Increases its Stability.
PyLink: a PyMOL plugin to identify links.
Statistical Properties of Lasso-Shape Polymers and Their Implications for Complex Lasso Proteins Function.