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Current drug discovery is expensive and time-consuming. It remains a challenging task to create a wide variety of novel compounds with desirable pharmacological properties and cheaply available to low-income people. In this work, we develop a generative network complex (GNC) to generate new drug-like molecules based on the multi-property optimization via the gradient descent in the latent space of an autoencoder. In our GNC, both multiple chemical properties and similarity scores are optimized to generate and predict drug-like molecules with desired chemical properties. To further validate the reliability of the predictions, these molecules are reevaluated and screened by independent 2D fingerprint-based predictors to come up with a few hundreds of new drug candidates. As a demonstration, we apply our GNC to generate a large number of new BACE1 inhibitors, as well as thousands of novel alternative drug candidates for eight existing market drugs, including Ceritinib, Ribociclib, Acalabrutinib, Idelalisib, Dabrafenib, Macimorelin, Enzalutamide, and Panobinostat.
It remains a challenging task to generate a vast variety of novel compounds with desirable pharmacological properties. In this work, a generative network complex (GNC) is proposed as a new platform for designing novel compounds, predicting their phys
The tertiary structures of functional RNA molecules remain difficult to decipher. A new generation of automated RNA structure prediction methods may help address these challenges but have not yet been experimentally validated. Here we apply four pred
The flexibility in gap cost enjoyed by Hidden Markov Models (HMMs) is expected to afford them better retrieval accuracy than position-specific scoring matrices (PSSMs). We attempt to quantify the effect of more general gap parameters by separately ex
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected near 5 million people and led to over 0.3 million deaths. Currently, there is no specific anti-SARS-CoV-2 medication.
The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA persistence leng