10 papers · ranked by Valyu relevance
Authors not listed
Sequence is the critical determinant of macromolecular function, yet current polymer design approaches often optimize monomer composition and ratios while ignoring sequence. This creates poorly defined design spaces for active learning that miss the vast combinatorial landscape of sequence possibilities. We introduce…
Nicholas Tjahjono, Evgeni Penev, Boris Yakobson
Programmable self-assembly provides a promising avenue to improve upon traditional synthesis and create multi-component materials with emergent properties and arbitrary nanoscale complexity. However, its most successful realizations utilizing DNA often use complicated arduous procedures that result in low yields. Here…
Jeff Guo, Vendy Fialková, Juan Diego Arango, Christian Margreitter + 4 more
Reinforcement learning (RL) is a powerful paradigm that has gained popularity across multiple domains. However, applying RL may come at a cost of multiple interactions between the agent and the environment. This cost can be especially pronounced when the single feedback from the environment is slow or computationally…
Adrian Krzyzanowski, Axel Pahl, Michael Grigalunas, Herbert Waldmann
The fraction of sp3 hybridised carbons (Fsp3) and the fraction of stereogenic carbons (FCstereo) are two widely employed scores of molecular complexity with a strong link to biologically relevant features such as frequency, potency and selectivity of protein binding. However, due to their simplistic nature, they do not…
Authors not listed
Cyclic peptides become attractive therapeutic candidates due to their diverse biological activities. However, existing deep learning-based sequence design models, such as ProteinMPNN, are primarily optimized using cross-entropy loss and often overlook the unique topological constraints of cyclic peptides. This limits…
Authors not listed
This paper presents a simplified model of iterative compound optimization in drug/agrochemical discovery. Compounds are represented as binary strings, with project evolution simulated through random bit changes. The model reproduces key statistical features of real projects, including activity distributions and…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
Qi Zhang, Chang Liu, Stephen Wu, Ryo Yoshida
In the last few years, de novo molecular design using machine learning has made great technical progress but its practical deployment has not been as successful. This is mostly owing to the cost and technical difficulty of synthesizing such computationally designed molecules. To overcome such barriers, various methods…
Babu Bassa
In this communication the author describes a software tool named "ChameleonSort". The software program, developed by the present author is useful in the sorting of biological sequence variants like those accumulating mutations while diverging from the common ancestors. Examples include viral protein variants, protein…
Authors not listed
Terminally labeled DNA oligonucleotides have wide applications in modern biology and biotechnological applications. It has been observed that the fluorescent intensity of light released from these fluorescent labels is heavily influenced by the terminal sequence of nucleotides. Recent studies have assayed and published…