LassoPred: a tool to predict the 3D structure of lasso peptides

Random Forests

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Gradient boosting machines, a tutorial

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K-nearest neighbor

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Scoring function for automated assessment of protein structure template quality

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Template-based protein structure modeling using the RaptorX web server

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A new genome-mining tool redefines the lasso peptide biosynthetic landscape

Tietz, J. I., Schwalen, C. J., Patel, P. S., Maxson, T., Saint‐Vincent, P. M. B., Tai, H.-C., Zakai, U. I., & Mitchell, D. A. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2319 · Cited by 490 · see citing works

Lasso Peptides: An Intriguing Class of Bacterial Natural Products

Hegemann, J. D., Zimmermann, M., Xie, X., & Marahiel, M. A. (2015) · Accounts of Chemical Research · doi:10.1021/acs.accounts.5b00156 · Cited by 395 · see citing works

Microcin 25, a novel antimicrobial peptide produced by Escherichia coli

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Lasso peptides: structure, function, biosynthesis, and engineering

Maksimov, M. O., Pan, S. J., & Link, A. J. (2012) · Natural Product Reports · doi:10.1039/c2np20070h · Cited by 277 · see citing works

SaProt: Protein Language Modeling with Structure-aware VocabularyPreprint

Su, J., Han, C., Zhou, Y., Shan, J., Zhou, X., & Yuan, F. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.01.560349 · Cited by 251 · see citing works

Isolation and Structural Characterization of Capistruin, a Lasso Peptide Predicted from the Genome Sequence of Burkholderia thailandensis E264

Knappe, T. A., Linne, U., Zirah, S., Rebuffat, S., Xie, X., & Marahiel, M. A. (2008) · Journal of the American Chemical Society · doi:10.1021/ja802966g · Cited by 238 · see citing works

Application of Berendsen barostat in dissipative particle dynamics for nonequilibrium dynamic simulation

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AlphaFold predictions of fold-switched conformations are driven by structure memorization

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Precursor-centric genome-mining approach for lasso peptide discovery

Maksimov, M. O., Pelczer, I., & Link, A. J. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208978109 · Cited by 147 · see citing works

Lariatins, Antimycobacterial Peptides Produced by Rhodococcus sp. K01−B0171, Have a Lasso Structure

Iwatsuki, M., Tomoda, H., Uchida, R., Gouda, H., Hirono, S., & Ōmura, S. (2006) · Journal of the American Chemical Society · doi:10.1021/ja056780z · Cited by 139 · see citing works

Introducing Lasso Peptides as Molecular Scaffolds for Drug Design: Engineering of an Integrin Antagonist

Knappe, T. A., Manzenrieder, F., Mas‐Moruno, C., Linne, U., Sasse, F., Kessler, H., Xie, X., & Marahiel, M. A. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.201102190 · Cited by 134 · see citing works

Systematic Structure-Activity Analysis of Microcin J25

Pavlova, O., Mukhopadhyay, J., Sineva, E. V., Ebright, R. H., & Severinov, K. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m803995200 · Cited by 132 · see citing works

A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat

Liu, J., Li, D.-Z., & Liu, X. (2016) · The Journal of Chemical Physics · doi:10.1063/1.4954990 · Cited by 129 · see citing works

Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin

Braffman, N. R., Piscotta, F. J., Hauver, J., Campbell, E. A., Link, A. J., & Darst, S. A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1817352116 · Cited by 125 · see citing works

A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome

Jangra, M., Travin, D. Y., Aleksandrova, E. V., Kaur, M., Darwish, L., Koteva, K. K., Klepacki, D., Wang, W., Tiffany, M., Sokaribo, A. S., et al. (2025) · Nature · doi:10.1038/s41586-025-08723-7 · Cited by 124 · see citing works

Dynamic covalent self-assembly of mechanically interlocked molecules solely made from peptides

Schröder, H. V., Zhang, Y., & Link, A. J. (2021) · Nature Chemistry · doi:10.1038/s41557-021-00770-7 · Cited by 121 · see citing works

Anantin-A peptide antagonist of the atrial natriuretic factor(ANF). I. Producing organism, fermentation, isolation and biological activity.

Weber, W., Fischli, W., Hochuli, E., KUPFER, E., & Weibel, E. K. (1991) · The Journal of Antibiotics · doi:10.7164/antibiotics.44.164 · Cited by 121 · see citing works

Genome mining for lasso peptides: past, present, and future

Cheung‐Lee, W. L., & Link, A. J. (2019) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/s10295-019-02197-z · Cited by 103 · see citing works

Enzymatic Reconstitution and Biosynthetic Investigation of the Lasso Peptide Fusilassin

DiCaprio, A. J., Firouzbakht, A., Hudson, G. A., & Mitchell, D. A. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.8b09928 · Cited by 93 · see citing works

Structural basis for hijacking siderophore receptors by antimicrobial lasso peptides

Mathavan, I., Zirah, S., Mehmood, S., Choudhury, H. G., Goulard, C., Li, Y., Robinson, C. V., Rebuffat, S., & Beis, K. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1499 · Cited by 93 · see citing works

Rational Improvement of the Affinity and Selectivity of Integrin Binding of Grafted Lasso Peptides

Hegemann, J. D., Simone, M. D., Zimmermann, M., Knappe, T. A., Xie, X., Leva, F. S. D., Marinelli, L., Novellino, E., Stefan Zahler, A., Kessler, H., et al. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm5004478 · Cited by 89 · see citing works

Heterologous and in Vitro Reconstitution of Fuscanodin, a Lasso Peptide from Thermobifida fusca

Koos, J. D., & Link, A. J. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.8b10724 · Cited by 79 · see citing works

Cell-Free Biosynthesis to Evaluate Lasso Peptide Formation and Enzyme–Substrate Tolerance

Si, Y., Kretsch, A. M., Daigh, L. M., Burk, M. J., & Mitchell, D. A. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c01452 · Cited by 75 · see citing works

Lasso Peptide Benenodin-1 Is a Thermally Actuated [1]Rotaxane Switch

Zong, C., Wu, M. J., Qin, J. Z., & Link, A. J. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b04830 · Cited by 75 · see citing works

An Experimental and Computational Investigation of Spontaneous Lasso Formation in Microcin J25

Ferguson, A. L., Zhang, S., Dikiy, I., Panagiotopoulos, A. Z., Debenedetti, P. G., & Link, A. J. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.08.073 · Cited by 70 · see citing works

Lasso peptides: chemical approaches and structural elucidation

Martín-Gómez, H., & Tulla‐Puche, J. (2018) · Organic & Biomolecular Chemistry · doi:10.1039/c8ob01304g · Cited by 68 · see citing works

Self-Assembly of Catenanes from Lasso Peptides

Allen, C. D., & Link, A. J. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b09454 · Cited by 65 · see citing works

Factors Governing the Thermal Stability of Lasso Peptides

Hegemann, J. D. (2019) · ChemBioChem · doi:10.1002/cbic.201900364 · Cited by 64 · see citing works

High-resolution solution structure of siamycin II: Novel amphipathic character of a 21-residue peptide that inhibits HIV fusion

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Solution structure of endothelin B receptor selective antagonist RES-701-1 determined by 1H NMR spectroscopy

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Cellulonodin-2 and Lihuanodin: Lasso Peptides with an Aspartimide Post-Translational Modification

Cao, L., Beiser, M., Koos, J. D., Orlova, M., Elashal, H. E., Schröder, H. V., & Link, A. J. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c05017 · Cited by 55 · see citing works

Thermal Unthreading of the Lasso Peptides Astexin-2 and Astexin-3

Allen, C. D., Chen, M. Y., Trick, A. Y., Le, D. T., Ferguson, A. L., & Link, A. J. (2016) · ACS Chemical Biology · doi:10.1021/acschembio.6b00588 · Cited by 54 · see citing works

Self-assembling peptide biomaterials: Insights from spontaneous and enhanced sampling molecular dynamics simulations

Williams‐Noonan, B. J., Kamboukos, A., Todorova, N., & Yarovsky, I. (2023) · Chemical Physics Reviews · doi:10.1063/5.0142302 · Cited by 52 · see citing works

AlphaFold predicts the most complex protein knot and composite protein knots

Brems, M. A., Runkel, R., Yeates, T. O., & Virnau, P. (2022) · Protein Science · doi:10.1002/pro.4380 · Cited by 50 · see citing works

Characterization of caulonodin lasso peptides revealed unprecedented N-terminal residues and a precursor motif essential for peptide maturation

Zimmermann, M., Hegemann, J. D., Xie, X., & Marahiel, M. A. (2014) · Chemical Science · doi:10.1039/c4sc01428f · Cited by 50 · see citing works

Peptidase Activation by a Leader Peptide-Bound RiPP Recognition Element

Kretsch, A. M., Gadgil, M. G., DiCaprio, A. J., Barrett, S. E., Kille, B. L., Si, Y., Zhu, L., & Mitchell, D. A. (2023) · Biochemistry · doi:10.1021/acs.biochem.2c00700 · Cited by 38 · see citing works

Rational generation of lasso peptides based on biosynthetic gene mutations and site-selective chemical modifications

Liu, T., Ma, X., Yu, J., Yang, W., Wang, G., Wang, Z., Ge, Y., Song, J., Han, H., Zhang, W., et al. (2021) · Chemical Science · doi:10.1039/d1sc02695j · Cited by 37 · see citing works

Protein Engineering in Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs)

Do, T., & Link, A. J. (2022) · Biochemistry · doi:10.1021/acs.biochem.1c00714 · Cited by 35 · see citing works

Lasso peptide, a highly stable structure and designable multifunctional backbone

Zhao, N., Pan, Y., Cheng, Z., & Liu, H. (2016) · Amino Acids · doi:10.1007/s00726-016-2228-x · Cited by 34 · see citing works

Lasso Peptides: Exploring the Folding Landscape of Nature’s Smallest Interlocked Motifs

da Hora, G. C. A., Oh, M., Mifflin, M. C., Digal, L., Roberts, A. G., & Swanson, J. M. J. (2024) · Journal of the American Chemical Society · doi:10.1021/jacs.3c10126 · Cited by 32 · see citing works

High-Throughput Screen Reveals the Structure–Activity Relationship of the Antimicrobial Lasso Peptide Ubonodin

Thokkadam, A., Do, T., Ran, X., Brynildsen, M. P., Yang, Z. J., & Link, A. J. (2023) · ACS Central Science · doi:10.1021/acscentsci.2c01487 · Cited by 32 · see citing works

Genome Mining and Heterologous Expression Reveal Two Distinct Families of Lasso Peptides Highly Conserved in Endofungal Bacteria

Bratovanov, E. V., Ishida, K., Heinze, B., Pidot, S. J., Stinear, T. P., Hegemann, J. D., Marahiel, M. A., & Hertweck, C. (2019) · ACS Chemical Biology · doi:10.1021/acschembio.9b00805 · Cited by 30 · see citing works

Substrate interactions guide cyclase engineering and lasso peptide diversification

Barrett, S. E., Song, Y., Jordan, P., Brunson, J. K., Gordon-Nunez, J., da Cruz, G. C. M., Rosario, C. J., Okada, B. K., Anderson, K., Pires, T. A., et al. (2024) · Nature Chemical Biology · doi:10.1038/s41589-024-01727-w · Cited by 29 · see citing works

LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling

Juarez, R. J., Jiang, Y., Tremblay, M., Shao, Q., Link, A. J., & Yang, Z. J. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00945 · Cited by 25 · see citing works

Cloacaenodin, an Antimicrobial Lasso Peptide with Activity against Enterobacter

Carson, D. V., Patiño, M., Elashal, H. E., Cartagena, A. J., Zhang, Y., Whitley, M. E., So, L., Kayser-Browne, A., Earl, A. M., Bhattacharyya, R. P., et al. (2022) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.2c00446 · Cited by 21 · see citing works

AlphaKnot 2.0: a web server for the visualization of proteins’ knotting and a database of knotted AlphaFold-predicted models

Rubach, P., Sikora, M., Jarmolinska, A. I., Perlinska, A. P., & Sulkowska, J. I. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae443 · Cited by 16 · see citing works

Everything AlphaFold tells us about protein knots

Perlinska, A. P., Sikora, M., & Sulkowska, J. I. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168715 · Cited by 13 · see citing works

Antagonistic actions of Paucibacter aquatile B51 and its lasso peptide paucinodin toward cyanobacterial bloom‐forming Microcystis aeruginosa PCC7806

Cha, Y., Kim, W., Park, Y., Kim, M., Son, Y., & Park, W. (2023) · Journal of Phycology · doi:10.1111/jpy.13412 · Cited by 12 · see citing works

The Shuttling Cascade in Lasso Peptide Benenodin‐1 is Controlled by Non‐Covalent Interactions

Schröder, H. V., Stadlmeier, M., Wühr, M., & Link, A. J. (2021) · Chemistry - A European Journal · doi:10.1002/chem.202103615 · Cited by 12 · see citing works

Computational Modeling of Conformer Stability in Benenodin-1, a Thermally Actuated Lasso Peptide Switch

Yang, Z. J., Hajlasz, N., & Kulik, H. J. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c00762 · Cited by 12 · see citing works

One Descriptor to Fold Them All: Harnessing Intuition and Machine Learning to Identify Transferable Lasso Peptide Reaction Coordinates

da Hora, G. C. A., Oh, M., Nguyen, J. D. M., & Swanson, J. M. J. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c08492 · Cited by 9 · see citing works

Heterologous production of new lasso peptide koreensin based on genome mining

Fuwa, H., Hemmi, H., Kaweewan, I., Kozaki, I., Honda, H., & Kodani, S. (2020) · The Journal of Antibiotics · doi:10.1038/s41429-020-00363-5 · Cited by 9 · see citing works

Structure of a lasso peptide bound ETB receptor provides insights into the mechanism of GPCR inverse agonism

Shihoya, W., Akasaka, H., Jordan, P. A., Lechner, A., Okada, B. K., Costa Machado da Cruz, G., Sano, F. K., Tanaka, T., Kawahara, R., Chaudhari, R., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57960-x · Cited by 8 · see citing works

Progress in Molecular Dynamics Simulations of Mechanically Interlocked Polymers

Wang, Y., Liu, G., Deng, J., & Yan, X. (2025) · Macromolecules · doi:10.1021/acs.macromol.5c02674 · Cited by 12 · see citing works

Progress and Challenges in the Biosynthesis and Chemical Synthesis of Lasso Peptides

Khatri, B., Lay, T., & Craik, D. J. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.5c10593 · Cited by 9 · see citing works

LassoESM a tailored language model for enhanced lasso peptide property prediction

Mi, X., Barrett, S. E., Mitchell, D. A., & Shukla, D. (2025) · Nature Communications · doi:10.1038/s41467-025-63412-3 · Cited by 7 · see citing works

Biosynthesis, Structure, and Antibiotic Properties of Gelatinamin A, a Triculamin‐Like Lasso Peptide

Svenningsen, T., Merrild, A., Wang, F., Hansen, F. D., Johnson, T. G., Iwase, R., Viennet, T., Larsen, M. K., Link, A. J., & Tørring, T. (2026) · ChemBioChem · doi:10.1002/cbic.70378 · Cited by 3 · see citing works

Harnessing artificial intelligence for antimicrobial discovery and optimization

Clements, A. E., Fieldhouse, M. R., & Walker, A. S. (2026) · Current Opinion in Microbiology · doi:10.1016/j.mib.2026.102724 · Cited by 3 · see citing works

Lasso Peptide Syanodin I: Loop-Pulling Two-Step Thermal Unthreading Mechanism

Santos-Fernandez, M., Fouque, K. J. D., Karki, U., Blond, A., Zirah, S., Chapagain, P. P., Hegemann, J. D., & Fernandez-Lima, F. A. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.5c04118 · Cited by 2 · see citing works

Tangled Tail of Mechanically Interlocked Peptides

Johnson, T. G., & Link, A. J. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.6c05395 · Cited by 2 · see citing works

Alliesthesia-Informed Machine Learning for Predicting Dynamic Thermal Comfort in Intermittent Convective Cooling Environments

Wang, T., Huang, W., Yan, H., Zhao, S., Sun, R., Guo, Y., & Li, Y. (2026) · Environments · doi:10.3390/environments13030147 · Cited by 1 · see citing works

FhuA-SbmA-driven resistance pathway to microcin Y triggers transcriptomic reprogramming and virulence enhancement in Salmonella Typhimurium

Yu, L., Zhang, J., Han, Y.-H., Zeng, Z., Chen, Q., Ke, W., & Cao, W. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.150111

Predicting lasso peptide structure with LassoPred

Ouyang, X., Ran, X., Zhu, D., & Yang, Z. J. (2026) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2026.01.037

“Lariocidin and ribosome-targeting lasso peptides as emerging antimicrobial agents against multidrug-resistant bacteria”

Mahdy, A., Alam-ElDein, K. M., Amin, I., Mohamed, H. H., Abuelhaded, K., Hamdy, M., Elhemiely, A. A., El-Zahraa, F., Ibrahim, A. K., Gadelmawla, M. H. A., et al. (2026) · The Journal of Antibiotics · doi:10.1038/s41429-026-00954-8

Predicting 3D Structures of Lasso PeptidesPreprint

Ouyang, X., Ran, X., Xu, H., Zhao, Y., Link, A. J., & Yang, Z. J. (2024) · ChemRxiv · doi:10.26434/chemrxiv-2024-q3rn0-v2 · Cited by 1 · see citing works

Predicting lasso peptide structure with LassoPred

Ouyang, X., Ran, X., Zhu, D., & Yang, Z. J. (2026) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2026.01.037

HighFold-Lasso: Topology-Guided Prediction of Lasso Peptide Structures Using AlphaFold3Preprint

Cao, S., Zhang, C., Yang, H., Ge, Y., Hou, H., Ning, Z., Wu, Y., Mo, J., Guo, J., Li, C., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.10.14.759041

LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling

Juarez, R. J., Jiang, Y., Tremblay, M., Shao, Q., Link, A. J., & Yang, Z. J. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00945 · Cited by 25 · see citing works

LassoESM a tailored language model for enhanced lasso peptide property prediction

Mi, X., Barrett, S. E., Mitchell, D. A., & Shukla, D. (2025) · Nature Communications · doi:10.1038/s41467-025-63412-3 · Cited by 7 · see citing works