A roadmap for metagenomic enzyme discovery
SL Robinson, J Piel, S Sunagawa - Natural Product Reports, 2021 - pubs.rsc.org
Covering: up to 2021 Metagenomics has yielded massive amounts of sequencing data
offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While …
offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While …
Toward the solution of the protein structure prediction problem
Since Anfinsen demonstrated that the information encoded in a protein's amino acid
sequence determines its structure in 1973, solving the protein structure prediction problem …
sequence determines its structure in 1973, solving the protein structure prediction problem …
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data
Leveraging iterative alignment search through genomic and metagenome sequence
databases, we report the DeepMSA2 pipeline for uniform protein single-and multichain …
databases, we report the DeepMSA2 pipeline for uniform protein single-and multichain …
DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins
Motivation The success of genome sequencing techniques has resulted in rapid explosion
of protein sequences. Collections of multiple homologous sequences can provide critical …
of protein sequences. Collections of multiple homologous sequences can provide critical …
Integrating deep learning, threading alignments, and a multi‐MSA strategy for high‐quality protein monomer and complex structure prediction in CASP15
We report the results of the “UM‐TBM” and “Zheng” groups in CASP15 for protein monomer
and complex structure prediction. These prediction sets were obtained using the D‐I …
and complex structure prediction. These prediction sets were obtained using the D‐I …
The origin and structural evolution of de novo genes in Drosophila
Recent studies reveal that de novo gene origination from previously non-genic sequences is
a common mechanism for gene innovation. These young genes provide an opportunity to …
a common mechanism for gene innovation. These young genes provide an opportunity to …
[HTML][HTML] rMSA: a sequence search and alignment algorithm to improve RNA structure modeling
The multiple sequence alignment (MSA) is the entry point of many RNA structure modeling
tasks, such as prediction of RNA secondary structure (rSS) and contacts. However, there are …
tasks, such as prediction of RNA secondary structure (rSS) and contacts. However, there are …
Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction
Information derived from metagenome sequences through deep-learning techniques has
significantly improved the accuracy of template free protein structure modeling. However …
significantly improved the accuracy of template free protein structure modeling. However …
[HTML][HTML] Petascale homology search for structure prediction
The recent CASP15 competition highlighted the critical role of multiple sequence alignments
(MSAs) in protein structure prediction, as demonstrated by the success of the top AlphaFold2 …
(MSAs) in protein structure prediction, as demonstrated by the success of the top AlphaFold2 …
Precision enzyme discovery through targeted mining of metagenomic data
S Ariaeenejad, J Gharechahi… - Natural Products and …, 2024 - Springer
Metagenomics has opened new avenues for exploring the genetic potential of uncultured
microorganisms, which may serve as promising sources of enzymes and natural products for …
microorganisms, which may serve as promising sources of enzymes and natural products for …