Protein sequence design with deep generative models

Z Wu, KE Johnston, FH Arnold, KK Yang - Current opinion in chemical …, 2021‏ - Elsevier
Protein engineering seeks to identify protein sequences with optimized properties. When
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

SD Fried, K Fujishima, M Makarov… - Journal of the …, 2022‏ - royalsocietypublishing.org
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 …

Structural biology in the clouds: the WeNMR-EOSC ecosystem

RV Honorato, PI Koukos, B Jiménez-García… - Frontiers in molecular …, 2021‏ - frontiersin.org
Structural biology aims at characterizing the structural and dynamic properties of biological
macromolecules at atomic details. Gaining insight into three dimensional structures of …

MetalPDB in 2018: a database of metal sites in biological macromolecular structures

V Putignano, A Rosato, L Banci… - Nucleic acids …, 2018‏ - academic.oup.com
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 …

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server

H Zheng, MD Chordia, DR Cooper, M Chruszcz… - Nature protocols, 2014‏ - nature.com
Metals have vital roles in both the mechanism and architecture of biological
macromolecules. Yet structures of metal-containing macromolecules in which metals are …

Design of metalloproteins and novel protein folds using variational autoencoders

JG Greener, L Moffat, DT Jones - Scientific reports, 2018‏ - nature.com
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 …

Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking

DA Capdevila, JJ Rondón, KA Edmonds… - Chemical …, 2024‏ - ACS Publications
Transition metals function as structural and catalytic cofactors for a large diversity of proteins
and enzymes that collectively comprise the metalloproteome. Metallostasis considers all …

Soft and dispersed interface-rich aqueous systems that promote and guide chemical reactions

S Serrano-Luginbühl, K Ruiz-Mirazo… - Nature reviews …, 2018‏ - nature.com
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 …

ZincBind—the database of zinc binding sites

SM Ireland, ACR Martin - Database, 2019‏ - academic.oup.com
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 …

Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection

H Zheng, IG Shabalin, KB Handing… - Nucleic acids …, 2015‏ - academic.oup.com
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 …