scholarly journals Molecular Design of Soluble Zein Protein Sequences

2020 ◽  
Vol 118 (3) ◽  
pp. 45a
Author(s):  
Mohammad Madani ◽  
Anna Tarakanova
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Johannes Linder ◽  
Georg Seelig

Abstract Background Optimization of DNA and protein sequences based on Machine Learning models is becoming a powerful tool for molecular design. Activation maximization offers a simple design strategy for differentiable models: one-hot coded sequences are first approximated by a continuous representation, which is then iteratively optimized with respect to the predictor oracle by gradient ascent. While elegant, the current version of the method suffers from vanishing gradients and may cause predictor pathologies leading to poor convergence. Results Here, we introduce Fast SeqProp, an improved activation maximization method that combines straight-through approximation with normalization across the parameters of the input sequence distribution. Fast SeqProp overcomes bottlenecks in earlier methods arising from input parameters becoming skewed during optimization. Compared to prior methods, Fast SeqProp results in up to 100-fold faster convergence while also finding improved fitness optima for many applications. We demonstrate Fast SeqProp’s capabilities by designing DNA and protein sequences for six deep learning predictors, including a protein structure predictor. Conclusions Fast SeqProp offers a reliable and efficient method for general-purpose sequence optimization through a differentiable fitness predictor. As demonstrated on a variety of deep learning models, the method is widely applicable, and can incorporate various regularization techniques to maintain confidence in the sequence designs. As a design tool, Fast SeqProp may aid in the development of novel molecules, drug therapies and vaccines.


2020 ◽  
Author(s):  
Cristina Garcia-Iriepa ◽  
Cecilia Hognon ◽  
Antonio Francés-Monerris ◽  
Isabel Iriepa ◽  
Tom Miclot ◽  
...  

<div><p>Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 180,000 deaths all over the world, still lacking a medical treatment despite the concerns of the whole scientific community. Human Angiotensin-Converting Enzyme 2 (ACE2) was recently recognized as the transmembrane protein serving as SARS-CoV-2 entry point into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the complex and of the effects of possible ligands. Moreover, binding free energy between ACE2 and the active Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein is evaluated quantitatively, assessing the molecular mechanisms at the basis of the recognition and the ligand-induced decreased affinity. These results boost the knowledge on the molecular grounds of the SARS-CoV-2 infection and allow to suggest rationales useful for the subsequent rational molecular design to treat severe COVID-19 cases.</p></div>


2019 ◽  
Author(s):  
Yujie Tu ◽  
Junkai Liu ◽  
Haoke Zhang ◽  
Qian Peng ◽  
Jacky W. Y. Lam ◽  
...  

Aggregation-induced emission (AIE) is an unusual photophysical phenomenon and provides an effective and advantageous strategy for the design of highly emissive materials in versatile applications such as sensing, imaging, and theragnosis. "Restriction of intramolecular motion" is the well-recognized working mechanism of AIE and have guided the molecular design of most AIE materials. However, it sometimes fails to be workable to some heteroatom-containing systems. Herein, in this work, we take more than one excited state into account and specify a mechanism –"restriction of access to dark state (RADS)" – to explain the AIE effect of heteroatom-containing molecules. An anthracene-based zinc ion probe named APA is chosen as the model compound, whose weak fluorescence in solution is ascribed to the easy access from the bright (π,π*) state to the closelying dark (n,π*) state caused by the strong vibronic coupling of the two excited states. By either metal complexation or aggregation, the dark state is less accessible due to the restriction of the molecular motion leading to the dark state and elevation of the dark state energy, thus the emission of the bright state is restored. RADS is found to be powerful in elucidating the photophysics of AIE materials with excited states which favor non-radiative decay, including overlap-forbidden states such as (n,π*) and CT states, spin-forbidden triplet states, which commonly exist in heteroatom-containing molecules.


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