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Enzyme-catalyzed protein cleavage is essential for many biological functions.
Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold
J. J. Perona and C. S. Craik · 1997
Earlier work this paper cites.
Three-dimensional structure of asp189ser trypsin provides evidence for an inherent structural plasticity of the protease
E. Szábó, Z. Böcskei, G. Náray-Szabó, and L. Gráf · 1999
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The protein data bank
Helen M. Berman, John Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, and Philip E. Bourne · 2000
Earlier work this paper cites.
Determination of protease cleavage site motifs using mixture-based oriented peptide libraries
Benjamin E. Turk, Lisa L. Huang, Elizabeth T. Piro, and Lewis C. Cantley · 2001
Earlier work this paper cites.
Mechanism of the cleavage specificity of alzheimer’s disease γ \gamma -secretase identified by phenylalanine-scanning mutagenesis of the transmembrane domain of the amyloid precursor protein
S. F. Lichtenthaler, R. Wang, H. Grimm, S. M. Uljon, C. L. Masters, and K. Beyreuther · 2003
Earlier work this paper cites.
Hiv-1 incorporates and proteolytically processes human ndr1 and ndr2 serine-threonine kinases
Eric Devroe, Pamela A Silver, and Alan Engelman · 2005
Earlier work this paper cites.
Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant
W. Ma, C. Tang, and L. Lai · 2005
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Targeting proteases: successes, failures and future prospects
Boris Turk · 2006
Earlier work this paper cites.
Strategies to improve plasma half life time of peptide and protein drugs
M. Werle and A. Bernkop-Schnürch · 2006
Earlier work this paper cites.
Sitepredicting the cleavage of proteinase substrates
Jelle Verspurten, Kris Gevaert, Wim Declercq, and Peter Vandenabeele · 2009
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Developing a powerful in silico tool for the discovery of novel caspase-3 substrates: a preliminary screening of the human proteome
Muneef Ayyash, Hashem Tamimi, and Yaqoub Ashhab · 2012
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Merops: the database of proteolytic enzymes, their substrates and inhibitors
Neil D Rawlings, Alan J Barrett, and Alex Bateman · 2012
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Awsem-md: Protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing
Aram Davtyan, Nicholas P. Schafer, Weihua Zheng, Cecilia Clementi, Peter G. Wolynes, and Garegin A. Papoian · 2012
Earlier work this paper cites.
Screencap3: Improving prediction of caspase-3 cleavage sites using experimentally verified noncleavage sites
Szu-Chin Fu, Kenichiro Imai, Tatsuya Sawasaki, and Kentaro Tomii · 2014
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Hiv protease inhibitors: a review of molecular selectivity and toxicity
Zhengtong Lv, Yuan Chu, and Yong Wang · 2015
Earlier work this paper cites.
Hepatitis c virus ns3/4a protease inhibitors
John A McCauley and Michael T Rudd · 2016
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Protein frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics
R. Gonzalo Parra, Nicholas P. Schafer, Leandro G. Radusky, Min-Yeh Tsai, A. Brenda Guzovsky, Peter G. Wolynes, and Diego U. Ferreiro · 2016
Earlier work this paper cites.
Proteolytic cleavage-mechanisms, function, and "omic" approaches for a near-ubiquitous posttranslational modification
Theo Klein, Ulrich Eckhard, Antoine Dufour, Nestor Solis, and Christopher M Overall · 2018
Cited alongside, same era.
Deepcleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites
Fuyi Li, Jinxiang Chen, André Leier, Tatiana Marquez-Lago, Quanzhong Liu, Yanze Wang, Jerico Revote, A Ian Smith, Tatsuya Akutsu, Geoffrey I Webb, Lukasz Kurgan, and Jiangning Song · 2019
Cited alongside, same era.
Local frustration around enzyme active sites
Maria I. Freiberger, A. Brenda Guzovsky, Peter G. Wolynes, R. Gonzalo Parra, and Diego U. Ferreiro · 2019
Cited alongside, same era.
Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations
Jan P. Pethe, A. B. Rubenstein, and S. D. Khare · 2019
Cited alongside, same era.
Comparative analysis of cleavage specificities of immobilized porcine pepsin and nepenthesin ii under hydrogen/deuterium exchange conditions
Towards prototype-based self-explainable graph neural network, 2022
Enyan Dai and Suhang Wang · 2022
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Proteinbert: a universal deep-learning model of protein sequence and function
Nadav Brandes, Dan Ofer, Yam Peleg, Nadav Rappoport, and Michal Linial · 2022
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Protein representation learning by geometric structure pretraining
Zuobai Zhang, Minghao Xu, Arian Jamasb, Vijil Chenthamarakshan, Aurelie Lozano, Payel Das, and Jian Tang · 2022
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High-resolution de novo structure prediction from primary sequence
Ruidong Wu, Fan Ding, Rui Wang, Rui Shen, Xiwen Zhang, Shitong Luo, Chenpeng Su, Zuofan Wu, Qi Xie, Bonnie Berger, Jianzhu Ma, and Jian Peng · 2022
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The road to death: Caspases, cleavage, and pores
Vishva M Dixit · 2023
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Jie Zheng, Timothy S. Strutzenberg, Adrian Reich, Venkatasubramanian Dharmarajan, Bruce D. Pascal, Gogce C. Crynen, Scott J. Novick, Ruben D. Garcia-Ordonez, and Patrick R. Griffin · 2020
Cited alongside, same era.
Procleave: Predicting protease-specific substrate cleavage sites by combining sequence and structural information
Fuyi Li, Andre Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, A. Ian Smith, Tatiana Marquez-Lago, Jian Li, and Jiangning Song · 2020
Cited alongside, same era.
Learning from protein structure with geometric vector perceptrons
Bowen Jing, Stephan Eismann, Patricia Suriana, Raphael JL Townshend, and Ron Dror · 2020
Cited alongside, same era.
Modular combination of proteolysis-responsive transcription and spherical nucleic acids for smartphone-based colorimetric detection of protease biomarkers
Fang Liu, Ru Chen, Wenlu Song, Liangwen Li, Chunyang Lei, and Zhou Nie · 2021
Cited alongside, same era.
Towards self-explainable graph neural network, 2021
Enyan Dai and Suhang Wang · 2021
Cited alongside, same era.
Deepdigest: prediction of protein proteolytic digestion with deep learning
Jinghan Yang, Zhiqiang Gao, Xiuhan Ren, Jie Sheng, Ping Xu, Cheng Chang, and Yan Fu · 2021
Cited alongside, same era.
Prottrans: Toward understanding the language of life through self-supervised learning
Ahmed Elnaggar, Michael Heinzinger, Christian Dallago, Ghalia Rehawi, Yu Wang, Llion Jones, Tom Gibbs, Tamas Feher, Christoph Angerer, Martin Steinegger, et al · 2021
Cited alongside, same era.
E (n) equivariant graph neural networks
Vıctor Garcia Satorras, Emiel Hoogeboom, and Max Welling · 2021
Cited alongside, same era.
Prosperousplus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction
Fuyi Li, Xudong Guo, Cong Wang, Tatsuya Akutsu, Geoffrey Webb, Lachlan Coin, Lukasz Kurgan, and Jiangning Song · 2023
Later among the works it cites.
Deepneuropepred: A robust and universal tool to predict cleavage sites from neuropeptide precursors by protein language model
Lei Wang, Zilu Zeng, Zhidong Xue, and Yan Wang · 2023
Later among the works it cites.
One transformer can understand both 2d & 3d molecular data, 2023
Shengjie Luo, Tianlang Chen, Yixian Xu, Shuxin Zheng, Tie-Yan Liu, Liwei Wang, and Di He · 2023
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A unified framework of graph information bottleneck for robustness and membership privacy, 2023
Enyan Dai, Limeng Cui, Zhengyang Wang, Xianfeng Tang, Yinghan Wang, Monica Cheng, Bing Yin, and Suhang Wang · 2023
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Uniprot: the universal protein knowledgebase in 2025
The UniProt Consortium · 2024
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Clipzyme: Reaction-conditioned virtual screening of enzymes, 2024
Peter G. Mikhael, Itamar Chinn, and Regina Barzilay · 2024
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Reactzyme: A benchmark for enzyme-reaction prediction, 2024
Chenqing Hua, Bozitao Zhong, Sitao Luan, Liang Hong, Guy Wolf, Doina Precup, and Shuangjia Zheng · 2024
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Accurately predicting enzyme functions through geometric graph learning on esmfold-predicted structures
Yujie Song, Qiang Yuan, Shuo Chen, et al · 2024
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Academic license, 2025
BioRender.com · 2025
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HARMONY: A multi-representation framework for RNA property prediction
Junjie Xu, Artem Moskalev, Tommaso Mansi, Mangal Prakash, and Rui Liao · 2025
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Protap: A benchmark for protein modeling on realistic downstream applications, 2025
Shuo Yan, Yuliang Yan, Bin Ma, Chenao Li, Haochun Tang, Jiahua Lu, Minhua Lin, Yuyuan Feng, Hui Xiong, and Enyan Dai · 2025
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