Diffusion models: A comprehensive survey of methods and applications
Diffusion models have emerged as a powerful new family of deep generative models with
record-breaking performance in many applications, including image synthesis, video …
record-breaking performance in many applications, including image synthesis, video …
I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction
Most proteins in cells are composed of multiple folding units (or domains) to perform
complex functions in a cooperative manner. Relative to the rapid progress in single-domain …
complex functions in a cooperative manner. Relative to the rapid progress in single-domain …
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest
D Szklarczyk, R Kirsch, M Koutrouli… - Nucleic acids …, 2023 - academic.oup.com
Much of the complexity within cells arises from functional and regulatory interactions among
proteins. The core of these interactions is increasingly known, but novel interactions …
proteins. The core of these interactions is increasingly known, but novel interactions …
De novo design of protein structure and function with RFdiffusion
There has been considerable recent progress in designing new proteins using deep-
learning methods,,,,,,,–. Despite this progress, a general deep-learning framework for protein …
learning methods,,,,,,,–. Despite this progress, a general deep-learning framework for protein …
Accurate structure prediction of biomolecular interactions with AlphaFold 3
The introduction of AlphaFold 21 has spurred a revolution in modelling the structure of
proteins and their interactions, enabling a huge range of applications in protein modelling …
proteins and their interactions, enabling a huge range of applications in protein modelling …
RCSB Protein Data Bank (RCSB. org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from …
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB
PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center …
PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center …
An atlas of substrate specificities for the human serine/threonine kinome
Protein phosphorylation is one of the most widespread post-translational modifications in
biology,. With advances in mass-spectrometry-based phosphoproteomics, 90,000 sites of …
biology,. With advances in mass-spectrometry-based phosphoproteomics, 90,000 sites of …
Illuminating protein space with a programmable generative model
Three billion years of evolution has produced a tremendous diversity of protein molecules,
but the full potential of proteins is likely to be much greater. Accessing this potential has …
but the full potential of proteins is likely to be much greater. Accessing this potential has …
CB-Dock2: Improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting
Y Liu, X Yang, J Gan, S Chen, ZX Xiao… - Nucleic acids …, 2022 - academic.oup.com
Protein-ligand blind docking is a powerful method for exploring the binding sites of receptors
and the corresponding binding poses of ligands. It has seen wide applications in …
and the corresponding binding poses of ligands. It has seen wide applications in …
DALI shines a light on remote homologs: One hundred discoveries
Structural comparison reveals remote homology that often fails to be detected by sequence
comparison. The DALI web server (http://ekhidna2. biocenter. helsinki. fi/dali) is a platform …
comparison. The DALI web server (http://ekhidna2. biocenter. helsinki. fi/dali) is a platform …