Inspiring Papers

On this page, I shall maintain an updated inventory of research papers, reviews, and news articles that have served as sources of inspiration for my investigations in the realm of protein topology. The primary purposes behind establishing this page are twofold: 1) to facilitate my preparation for the PhD qualification examination, and 2) to systematically curate a collection of resources beneficial to fellow researchers in this domain. Notably, papers annotated with an asterisk (*) hold pivotal significance within the scope of my research. In the course of reviewing this list, I shall generate succinct summary slides for each of the featured papers.


Readings on Knotted Proteins

Some research groups in this field that I have been following are the Sulkowska group (University of Warsaw), the Jackson group (University of Cambridge), the Yeates group (UCLA), the Mirny group (MIT), and the José group (Rice University). The Sulkowska group has published many papers on computational approaches which I have included in the list below.

  1. De novo design of knotted tandem repeat proteins (2023)
  2. Homology of homologous knotted proteins (2023)
  3. AlphaFold predicts the most complex protein knot and composite protein knots (2022)
  4. AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods (2022) Summary Slides
  5. In silico method for identifying the key residues in a knotted protein: with MJ0366 as an example (2022) *
  6. Investigation of the structural dynamics of a knotted protein and its unknotted analog using molecular dynamics (2022)
  7. A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins (2022)
  8. The protein folding rate and the geometry and topology of the native state (2022)
  9. Knotting Optimization and Folding Pathways of a Go-Model with a Deep Knot (2022)
  10. Elucidation of folding pathways of knotted proteins (2022)
  11. Homology of homologous knotted proteins (2022)
  12. Tying up the Loose Ends: A Mathematically Knotted Protein (2021)
  13. New 63 knot and other knots in human proteome from AlphaFold predictions (2021)
  14. A Topological Selection of Folding Pathways from Native States of Knotted Proteins (2021)
  15. Dynamic covalent self-assembly of mechanically interlocked molecules solely made from peptides (2021)
  16. Converging experimental and computational views of the knotting mechanism of a small knotted protein (2021)
  17. Unfolding and Translocation of Knotted Proteins by Clp Biological Nanomachines: Synergistic Contribution of Primary Sequence and Topology Revealed by Molecular Dynamics Simulations (2021)
  18. Mechanical unfolding of a knotted protein unveils the kinetic and thermodynamic consequences of threading a polypeptide chain (2020)
  19. The Folding of Knotted Proteins: Distinguishing the Distinct Behavior of Shallow and Deep Knots (2020)
  20. Knot_pull—python package for biopolymer smoothing and knot detection (2019)
  21. Computational methods in the study of self-entangled proteins: a critical appraisal (2019)*
  22. Proteins’ Knotty Problems (2019)
  23. KnotProt 2.0: a database of proteins with knots and other entangled structures (2018)
  24. Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting from the Ribosome Exit Channel (2018)
  25. Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids (2018) *
  26. Topological knots and links in proteins (2017)
  27. LinkProt: A database collecting information about biological links (2017)
  28. Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids (2017)
  29. How to fold intricately: using theory and experiments to unravel the properties of knotted proteins (2017)
  30. Knotting and unknotting of a protein in single molecule experiments (2016)
  31. In Search of Functional Advantages of Knots in Proteins (2016) *
  32. LassoProt: server to analyze biopolymers with lassos (2016)
  33. Complex lasso: new entangled motifs in proteins (2016)
  34. Identification of rare slipknots in proteins and their implications for stability and folding (2015)
  35. Mechanistic Insights into the Folding of Knotted Proteins In Vitro and In Vivo (2015)
  36. KnotProt: A database of proteins with knots and slipknots (2015) *
  37. Knotted proteins: A tangled tale of Structural Biology (2015)
  38. Effects of knot type in the folding of topologically complex lattice proteins (2014)
  39. Translocation of knotted proteins through a pore (2014)
  40. Knotting a Protein in Explicit Solvent (2013)
  41. Knotting pathways in proteins (2013)
  42. Driving the formation of molecular knots (2012)
  43. Energy landscape of knotted protein folding (2012)
  44. Conservation of complex knotting and slipknotting patterns in proteins (2012)
  45. Chemical Topology: Complex Molecular Knots, Links, and Entanglements (2011)
  46. Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins (2011)
  47. Slipknotting upon native-like loop formation in a trefoil knot protein (2010)
  48. A Stevedore’s protein knot (2010)
  49. Dodging the crisis of folding proteins with knots (2009)
  50. The Folding Mechanics of a Knotted Protein (2007)
  51. Discovery of a thermophilic protein complex stabilized by topologically interlinked chains (2007)
  52. Identification of Rare Slipknots in Proteins and Their Implications for Stability and Folding (2007)
  53. Intricate Knots in Proteins: Function and Evolution (2006)
  54. A deeply knotted protein structure and how it might fold (2000)
  55. Fit to be tied (1997)
  56. Topological Features of Protein Structures: Knots and Links (1995)
  57. Knots in Proteins (1994)
  58. Are there knots in proteins? (1994) *


Readings on AI

  1. Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models (2023)
  2. Advancing mathematics by guiding human intuition with AI (2021) Summary Slides
  3. Highly accurate protein structure prediction with AlphaFold (2021) *
  4. DeepMind’s AI helps untangle the mathematics of knots (2021)
  5. Deep learning methods in protein structure prediction (2020)
  6. Improved protein structure prediction using potentials from deep learning (2020)
  7. Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening (2018)


Readings on Topology

  1. Biomolecular Topology: Modelling and Analysis (2022)
  2. Invariants of Bonded Knotoids and Applications to Protein Folding (2022)
  3. Macromolecular topology engineering (2021)
  4. Handbook of Discrete and Computational GeometryApplications to structural molecular biology (2017)
  5. Interactive Knot Theory with KnotPlot (2002) *
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