相关论文: Complete RNA inverse folding: computational design…
Protein generative models have shown remarkable promise in protein design, yet their success rates remain constrained by reliance on curated sequence-structure datasets and by misalignment between supervised objectives and real design…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design,…
We introduce a generative model for protein backbone design utilizing geometric products and higher order message passing. In particular, we propose Clifford Frame Attention (CFA), an extension of the invariant point attention (IPA)…
Optimizing molecular design and discovering novel chemical structures to meet certain objectives, such as quantitative estimates of the drug-likeness score (QEDs), is NP-hard due to the vast combinatorial design space of discrete molecular…
Zigzag edges of the honeycomb structure of graphene exhibit magnetic polarization making them attractive as building blocks for spintronic devices. Here, we show that devices with zigzag edged triangular antidots perform essential…
Designing complex physical systems, including photonic structures, is typically a tedious trial-and-error process that requires extensive simulations with iterative sweeps in multi-dimensional parameter space. To circumvent this…
The emerging field of hybrid DNA - protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with versatility of protein interactions. However, the design and…
Retrosynthesis is the process of determining the set of reactant molecules that can react to form a desired product. Semi-template-based retrosynthesis methods, which imitate the reverse logic of synthesis reactions, first predict the…
The AlphaFold computer program predicted protein structures for the whole human genome, which has been considered as a remarkable breakthrough both in artificial intelligence (AI) application and structural biology. Despite the varying…
Small molecule drug design hinges on obtaining co-crystallized ligand-protein structures. Despite AlphaFold2's strides in protein native structure prediction, its focus on apo structures overlooks ligands and associated holo structures.…
Given the importance of non-coding RNAs to cellular regulatory functions and rapid growth of RNA transcripts, computational prediction of RNA tertiary structure remains highly demanded yet significantly challenging. Even for a short RNA…
As robots become smarter and more ubiquitous, optimizing the power consumption of intelligent compute becomes imperative towards ensuring the sustainability of technological advancements. Neuromorphic computing hardware makes use of…
High-density microfluidics is becoming an important experimental platform for studying complex biological systems such as synthetic gene regulatory networks, molecular biocomputating of engineered cells, distributing rapid point-of-care…
Together with the Kirchhoff-Institute for Physics(KIP) the Fraunhofer IZM has developed a full wafer redistribution and embedding technology as base for a large-scale neuromorphic hardware system. The paper will give an overview of the…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…
Embedding computation in molecular contexts incompatible with traditional electronics is expected to have wide ranging impact in synthetic biology, medicine, nanofabrication and other fields. A key remaining challenge lies in developing…
While RNA technologies hold immense therapeutic potential in a range of applications from vaccination to gene editing, the broad implementation of these technologies is hindered by the challenge of delivering these agents effectively. Lipid…
Identifying protein targets for small molecules, or reverse screening, is essential for understanding drug action, guiding compound repurposing, predicting off-target effects, and elucidating the molecular mechanisms of bioactive compounds.…