[HTML][HTML] Recent advances in green synthesized nanoparticles: From production to application
With the increasing concern over the environmental impact of conventional chemical
methods, environmentally friendly processes, commonly known as green chemistry, for the …
methods, environmentally friendly processes, commonly known as green chemistry, for the …
Can we predict T cell specificity with digital biology and machine learning?
Recent advances in machine learning and experimental biology have offered breakthrough
solutions to problems such as protein structure prediction that were long thought to be …
solutions to problems such as protein structure prediction that were long thought to be …
UCSF ChimeraX: Tools for structure building and analysis
EC Meng, TD Goddard, EF Pettersen… - Protein …, 2023 - Wiley Online Library
Advances in computational tools for atomic model building are leading to accurate models of
large molecular assemblies seen in electron microscopy, often at challenging resolutions of …
large molecular assemblies seen in electron microscopy, often at challenging resolutions of …
Robust deep learning–based protein sequence design using ProteinMPNN
Although deep learning has revolutionized protein structure prediction, almost all
experimentally characterized de novo protein designs have been generated using …
experimentally characterized de novo protein designs have been generated using …
Modeling conformational states of proteins with AlphaFold
Many proteins exert their function by switching among different structures. Knowing the
conformational ensembles affiliated with these states is critical to elucidate key mechanistic …
conformational ensembles affiliated with these states is critical to elucidate key mechanistic …
Protein design: From the aspect of water solubility and stability
Water solubility and structural stability are key merits for proteins defined by the primary
sequence and 3D-conformation. Their manipulation represents important aspects of the …
sequence and 3D-conformation. Their manipulation represents important aspects of the …
Cross-linking mass spectrometry for investigating protein conformations and protein–protein interactions─ a method for all seasons
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this
review, the contributions of chemical cross-linking combined with mass spectrometry (XL …
review, the contributions of chemical cross-linking combined with mass spectrometry (XL …
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants
High‐resolution experimental structural determination of protein–protein interactions has led
to valuable mechanistic insights, yet due to the massive number of interactions and …
to valuable mechanistic insights, yet due to the massive number of interactions and …
AbDiffuser: full-atom generation of in-vitro functioning antibodies
We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint
generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new …
generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new …
[HTML][HTML] Machine learning in protein structure prediction
M AlQuraishi - Current opinion in chemical biology, 2021 - Elsevier
Prediction of protein structure from sequence has been intensely studied for many decades,
owing to the problem's importance and its uniquely well-defined physical and computational …
owing to the problem's importance and its uniquely well-defined physical and computational …