We investigate the use of confidence scores to evaluate the accuracy of a given AlphaFold
(AF2) protein model for drug discovery. Prediction of accuracy is improved by not …

The assembly of individual proteins into functional complexes is fundamental to nearly all
biological processes. In recent decades, many thousands of homomeric and heteromeric …

Deep-learning (DL) methods like DeepMind's AlphaFold2 (AF2) have led to substantial
improvements in protein structure prediction. We analyse confident AF2 models from 21 …

The protein-protein docking problem is one of the focal points of activity in computational
biophysics and structural biology. The three-dimensional structure of a protein-protein …

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 …

Proteins interact with a variety of molecules including proteins and nucleic acids. We review
a comprehensive collection of over 50 studies that analyze and/or predict these interactions …

Topologically knotted proteins have entangled structural elements within their native
structures that cannot be disentangled simply by pulling from the N-and C-termini …

Introduction: Macromolecular X-ray crystallography has been the primary methodology for
determining the three-dimensional structures of proteins, nucleic acids and viruses …

With the success of an expanding array of genome sequencing projects, the number of
known protein sequences has been increasing exponentially. However, the sequences on …