Recent advances in de novo protein design: Principles, methods, and applications
X Pan, T Kortemme - Journal of Biological Chemistry, 2021 - ASBMB
The computational de novo protein design is increasingly applied to address a number of
key challenges in biomedicine and biological engineering. Successes in expanding …
key challenges in biomedicine and biological engineering. Successes in expanding …
Alignment-free sequence comparison: benefits, applications, and tools
Alignment-free sequence analyses have been applied to problems ranging from whole-
genome phylogeny to the classification of protein families, identification of horizontally …
genome phylogeny to the classification of protein families, identification of horizontally …
High-resolution de novo structure prediction from primary sequence
Recent breakthroughs have used deep learning to exploit evolutionary information in
multiple sequence alignments (MSAs) to accurately predict protein structures. However …
multiple sequence alignments (MSAs) to accurately predict protein structures. However …
Sensitive protein alignments at tree-of-life scale using DIAMOND
B Buchfink, K Reuter, HG Drost - Nature methods, 2021 - nature.com
We are at the beginning of a genomic revolution in which all known species are planned to
be sequenced. Accessing such data for comparative analyses is crucial in this new age of …
be sequenced. Accessing such data for comparative analyses is crucial in this new age of …
Single-sequence protein structure prediction using a language model and deep learning
R Chowdhury, N Bouatta, S Biswas, C Floristean… - Nature …, 2022 - nature.com
AlphaFold2 and related computational systems predict protein structure using deep learning
and co-evolutionary relationships encoded in multiple sequence alignments (MSAs) …
and co-evolutionary relationships encoded in multiple sequence alignments (MSAs) …
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes
Abstract Structure comparison and alignment are of fundamental importance in structural
biology studies. We developed the first universal platform, US-align, to uniformly align …
biology studies. We developed the first universal platform, US-align, to uniformly align …
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental …
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB
PDB), the US data center for the global PDB archive and a founding member of the …
PDB), the US data center for the global PDB archive and a founding member of the …
Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses
K Seong, KV Krasileva - Nature Microbiology, 2023 - nature.com
Elucidating the similarity and diversity of pathogen effectors is critical to understand their
evolution across fungal phytopathogens. However, rapid divergence that diminishes …
evolution across fungal phytopathogens. However, rapid divergence that diminishes …
Protein sequence analysis using the MPI bioinformatics toolkit
Abstract The MPI Bioinformatics Toolkit (https://toolkit. tuebingen. mpg. de) provides
interactive access to a wide range of the best‐performing bioinformatics tools and …
interactive access to a wide range of the best‐performing bioinformatics tools and …
Learning the protein language: Evolution, structure, and function
Language models have recently emerged as a powerful machine-learning approach for
distilling information from massive protein sequence databases. From readily available …
distilling information from massive protein sequence databases. From readily available …