Protein design aims to build novel proteins customized for specific purposes, thereby
holding the potential to tackle many environmental and biomedical problems. Recent …

We are now entering a new era in protein sequence and structure annotation, with hundreds
of millions of predicted protein structures made available through the AlphaFold database …

Highlights•In-depth sequence analysis reveals that the protein fold universe is more
evolutionarily connected than previously assumed.•Short ancestral fragments are observed …

Background: Calculation of ligand-binding affinity is an open problem in computational
medicinal chemistry. The ability to computationally predict affinities has a beneficial impact …

The design of structurally diverse enzymes is constrained by long-range interactions that are
necessary for accurate folding. We introduce an atomistic and machine learning strategy for …

Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the
structure, function, and motion of proteins for students, faculty, and researchers at all levels …

We surveyed the “dark” proteome–that is, regions of proteins never observed by
experimental structure determination and inaccessible to homology modeling. For 546,000 …

This article is dedicated to the memory of Michael G. Rossmann. Dating back to the last
universal common ancestor, P-loop NTPases and Rossmanns comprise the most ubiquitous …

Recent advances in protein structure prediction have generated accurate structures of
previously uncharacterized human proteins. Identifying domains in these predicted …

In mammalian cells, much of signal transduction is mediated by weak protein–protein
interactions between globular peptide-binding domains (PBDs) and unstructured peptidic …