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Protein sequence design with deep generative models
Protein engineering seeks to identify protein sequences with optimized properties. When
guided by machine learning, protein sequence generation methods can draw on prior …
guided by machine learning, protein sequence generation methods can draw on prior …
Peptides before and during the nucleotide world: An origins story emphasizing cooperation between proteins and nucleic acids
Recent developments in Origins of Life research have focused on substantiating the
narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular …
narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular …
Structural biology in the clouds: the WeNMR-EOSC ecosystem
Structural biology aims at characterizing the structural and dynamic properties of biological
macromolecules at atomic details. Gaining insight into three dimensional structures of …
macromolecules at atomic details. Gaining insight into three dimensional structures of …
MetalPDB in 2018: a database of metal sites in biological macromolecular structures
Abstract MetalPDB (http://metalweb. cerm. unifi. it/) is a database providing information on
metal-binding sites detected in the three-dimensional (3D) structures of biological …
metal-binding sites detected in the three-dimensional (3D) structures of biological …
Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server
Metals have vital roles in both the mechanism and architecture of biological
macromolecules. Yet structures of metal-containing macromolecules in which metals are …
macromolecules. Yet structures of metal-containing macromolecules in which metals are …
Design of metalloproteins and novel protein folds using variational autoencoders
The design of novel proteins has many applications but remains an attritional process with
success in isolated cases. Meanwhile, deep learning technologies have exploded in …
success in isolated cases. Meanwhile, deep learning technologies have exploded in …
Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking
Transition metals function as structural and catalytic cofactors for a large diversity of proteins
and enzymes that collectively comprise the metalloproteome. Metallostasis considers all …
and enzymes that collectively comprise the metalloproteome. Metallostasis considers all …
Soft and dispersed interface-rich aqueous systems that promote and guide chemical reactions
Although aqueous solutions are considered to be sustainable, environmentally friendly
reaction media, their use is often limited by poor reactant solubility. This limitation can be …
reaction media, their use is often limited by poor reactant solubility. This limitation can be …
ZincBind—the database of zinc binding sites
Zinc is one of the most important biologically active metals. Ten per cent of the human
genome is thought to encode a zinc binding protein and its uses encompass catalysis …
genome is thought to encode a zinc binding protein and its uses encompass catalysis …
Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection
The ubiquitous presence of magnesium ions in RNA has long been recognized as a key
factor governing RNA folding, and is crucial for many diverse functions of RNA molecules. In …
factor governing RNA folding, and is crucial for many diverse functions of RNA molecules. In …