Frank DiMaio

Accurate prediction of protein structures and interactions using a three-track neural network

Deep learning takes on protein folding In 1972, Anfinsen won a Nobel prize for demonstrating a connection between a protein’s amino acid sequence and its three-dimensional struc...

Structure prediction for CASP8 with all‐atom refinement using Rosetta

Abstract We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggre...

Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report EM...

Automatically Fixing Errors in Glycoprotein Structures with Rosetta

Recent advances in single-particle cryo-electron microscopy (cryoEM) have resulted in determination of an increasing number of protein structures with resolved glycans. However,...

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), whi...

Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA

Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom

Abstract Although AlphaFold2 (AF2) and RoseTTAFold (RF) have transformed structural biology by enabling high-accuracy protein structure modeling, they are unable to model covale...