Sequence modeling and design from molecular to genome scale …
2024年11月14日 · The genome is a sequence that encodes the DNA, RNA, and proteins that orchestrate an organism’s function. We present Evo, a long-context genomic foundation model with a frontier architecture traine...
Evo: DNA foundation modeling from molecular to genome scale
2024年2月27日 · Evo is a long-context biological foundation model that generalizes across the fundamental languages of biology: DNA, RNA, and proteins. It is capable of both prediction tasks and generative design, from molecular to whole genome scale (over 650k tokens in length).
Multi-purpose RNA language modelling with motif-aware …
2024年5月13日 · Our method, RNAErnie, outperforms existing advanced techniques across seven RNA sequence datasets encompassing over 17,000 major RNA motifs, 20 RNA classes/types and 50,000 RNA sequences.
Evo: DNA foundation modeling from molecular to genome scale
2024年2月27日 · Evo: DNA foundation modeling from molecular to genome scale. Evo is a biological foundation model capable of long-context modeling and design. Evo uses the StripedHyena architecture to enable modeling of sequences at a single-nucleotide, byte-level resolution with near-linear scaling of compute and memory relative to context length.
Evo: DNA Foundation Model - Arc Institute
Evo is a genomic foundation model capable of generalist prediction and design tasks across DNA, RNA, and proteins. It uses a frontier deep learning architecture to enable modeling of biological sequences at single-nucleotide resolution with near-linear scaling of compute and memory relative to context length.
Automated detection and de novo structure modeling of nucleic …
2024年10月30日 · EM2NA builds the full-atom DNA/RNA structure from the map by integrating several modeling steps: segmenting the DNA/RNA density regions from raw cryo-EM maps, predicting the backbone atom ...
Coarse-grained modeling of DNA–RNA hybrids - AIP Publishing
2024年3月18日 · THE MODEL. Here, we provide a brief overview of the previously developed models for DNA and RNA as well as the introduction of new inter-strand interactions that enable the simulation of hybrids. We then describe in detail how …
Multiple sequence alignment-based RNA language model and its ...
2023年11月6日 · Here, we have developed an unsupervised multiple sequence alignment-based RNA language model (RNA-MSM) by utilizing homologous sequences from an automatic pipeline, RNAcmap, as it can provide significantly more homologous sequences than …
Molecular Modeling and Simulations of DNA and RNA: DNAzyme as a Model ...
2022年2月28日 · This is particularly true for DNAzymes, where DNA and RNA backbones can come as close as 2.4 Å with their charged phosphate groups during the catalytic cycle. Here, we present tools to simulate the structural dynamics of a DNAzyme, with a focus on detailed instructions for the Amber suite of programs.
Design and simulation of DNA, RNA and hybrid protein–nucleic …
2022年6月6日 · Here we present oxView, a design tool for visualization, design, editing and analysis of simulations of DNA, RNA and nucleic acid–protein nanostructures. oxView provides an accessible software...