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Given the emerging global threat of antimicrobial resistance, new methods for next-generation antimicrobial design are urgently needed.
Amino acid substitution matrices from protein blocks
S. Henikoff and J. G. Henikoff · 1992
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Hospital-acquired infections due to gram-negative bacteria
A. Y. Peleg and D. C. Hooper · 2010
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N-gram analysis of 970 microbial organisms reveals presence of biological language models
H. U. Osmanbeyoglu and M. K. Ganapathiraju · 2011
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Designing antimicrobial peptides: form follows function
C. D. Fjell, J. A. Hiss, R. E. Hancock, and G. Schneider · 2012
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Antibiotic resistance threats in the united states, 2013
CDC · 2013
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Auto-encoding variational bayes
D. P. Kingma and M. Welling · 2013
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Lamp: a database linking antimicrobial peptides
X. Zhao, H. Wu, H. Lu, G. Li, and Q. Huang · 2013
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Generative adversarial nets
I. Goodfellow, J. Pouget-Abadie, M. Mirza, B. Xu, D. Warde-Farley, S. Ozair, A. Courville, and Y. Bengio · 2014
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Generating sentences from a continuous space
S. R. Bowman, L. Vilnis, O. Vinyals, A. M. Dai, R. Jozefowicz, and S. Bengio · 2015
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Dbaasp v. 2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides
M. Pirtskhalava, A. Gabrielian, P. Cruz, H. L. Griggs, R. B. Squires, D. E. Hurt, M. Grigolava, M. Chubinidze, G. Gogoladze, B. Vishnepolsky, et al · 2015
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Satpdb: a database of structurally annotated therapeutic peptides
S. Singh, K. Chaudhary, S. K. Dhanda, S. Bhalla, S. S. Usmani, A. Gautam, A. Tuknait, P. Agrawal, D. Mathur, and G. P. Raghava · 2015
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Assessment of global incidence and mortality of hospital-treated sepsis. current estimates and limitations
C. Fleischmann, A. Scherag, N. K. Adhikari, C. S. Hartog, T. Tsaganos, P. Schlattmann, D. C. Angus, and K. Reinhart · 2016
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Gans for sequences of discrete elements with the gumbel-softmax distribution
M. J. Kusner and J. M. Hernández-Lobato · 2016
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Pep-fold3: faster de novo structure prediction for linear peptides in solution and in complex
A. Lamiable, P. Thévenet, J. Rey, M. Vavrusa, P. Derreumaux, and P. Tufféry · 2016
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Toward controlled generation of text
Z. Hu, Z. Yang, X. Liang, R. Salakhutdinov, and E. P. Xing · 2017
Ampep: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest
P. Bhadra, J. Yan, J. Li, S. Fong, and S. W. Siu · 2018
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Application of generative autoencoder in de novo molecular design
T. Blaschke, M. Olivecrona, O. Engkvist, J. Bajorath, and H. Chen · 2018
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Universal Protein Resource (UniProt)
P. EMBL-EBI, SIB · 2018
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Automatic chemical design using a data-driven continuous representation of molecules
R. Gómez-Bombarelli, J. N. Wei, D. Duvenaud, J. M. Hernández-Lobato, B. Sánchez-Lengeling, D. Sheberla, J. Aguilera-Iparraguirre, T. D. Hirzel, R. P. Adams, and A. Aspuru-Guzik · 2018
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Junction tree variational autoencoder for molecular graph generation
W. Jin, R. Barzilay, and T. Jaakkola · 2018
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drugan: an advanced generative adversarial autoencoder model for de novo generation of new molecules with desired molecular properties in silico
A. Kadurin, S. Nikolenko, K. Khrabrov, A. Aliper, and A. Zhavoronkov · 2017
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Grammar variational autoencoder
M. J. Kusner, B. Paige, and J. M. Hernández-Lobato · 2017
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Regularizing and Optimizing LSTM Language Models
S. Merity, N. S. Keskar, and R. Socher · 2017
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modlamp: Python for antimicrobial peptides
A. T. Müller, G. Gabernet, J. A. Hiss, and G. Schneider · 2017
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Seqgan: Sequence generative adversarial nets with policy gradient
L. Yu, W. Zhang, J. Wang, and Y. Yu · 2017
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Recurrent neural network model for constructive peptide design
A. T. Müller, J. A. Hiss, and G. Schneider · 2018
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Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates of bacteria
D. Nagarajan, T. Nagarajan, N. Roy, O. Kulkarni, S. Ravichandran, M. Mishra, D. Chakravortty, and N. Chandra · 2018
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In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design
W. F. Porto, L. Irazazabal, E. S. Alves, S. M. Ribeiro, C. O. Matos, Á. S. Pires, I. C. Fensterseifer, V. J. Miranda, E. F. Haney, V. Humblot, et al · 2018
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Deep learning improves antimicrobial peptide recognition
D. Veltri, U. Kamath, and A. Shehu · 2018
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