A practical guide to large-scale docking

BJ Bender, S Gahbauer, A Luttens, J Lyu, CM Webb… - Nature protocols, 2021 - nature.com
Abstract Structure-based docking screens of large compound libraries have become
common in early drug and probe discovery. As computer efficiency has improved and …

Protein design: From the aspect of water solubility and stability

R Qing, S Hao, E Smorodina, D **, A Zalevsky… - Chemical …, 2022 - ACS Publications
Water solubility and structural stability are key merits for proteins defined by the primary
sequence and 3D-conformation. Their manipulation represents important aspects of the …

De novo design of protein structure and function with RFdiffusion

JL Watson, D Juergens, NR Bennett, BL Trippe, J Yim… - Nature, 2023 - nature.com
There has been considerable recent progress in designing new proteins using deep-
learning methods,,,,,,,–. Despite this progress, a general deep-learning framework for protein …

Design of protein-binding proteins from the target structure alone

L Cao, B Coventry, I Goreshnik, B Huang, W Sheffler… - Nature, 2022 - nature.com
The design of proteins that bind to a specific site on the surface of a target protein using no
information other than the three-dimensional structure of the target remains a challenge …

[HTML][HTML] Progen2: exploring the boundaries of protein language models

E Nijkamp, JA Ruffolo, EN Weinstein, N Naik, A Madani - Cell systems, 2023 - cell.com
Attention-based models trained on protein sequences have demonstrated incredible
success at classification and generation tasks relevant for artificial-intelligence-driven …

Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models

JL Watson, D Juergens, NR Bennett, BL Trippe, J Yim… - BioRxiv, 2022 - biorxiv.org
There has been considerable recent progress in designing new proteins using deep
learning methods–. Despite this progress, a general deep learning framework for protein …

Improving de novo protein binder design with deep learning

NR Bennett, B Coventry, I Goreshnik, B Huang… - Nature …, 2023 - nature.com
Recently it has become possible to de novo design high affinity protein binding proteins from
target structural information alone. There is, however, considerable room for improvement as …

[HTML][HTML] Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations

F Muecksch, Y Weisblum, CO Barnes, F Schmidt… - Immunity, 2021 - cell.com
Antibodies elicited by infection accumulate somatic mutations in germinal centers that can
increase affinity for cognate antigens. We analyzed 6 independent groups of clonally related …

Learning the protein language: Evolution, structure, and function

T Bepler, B Berger - Cell systems, 2021 - cell.com
Language models have recently emerged as a powerful machine-learning approach for
distilling information from massive protein sequence databases. From readily available …

An engineered T7 RNA polymerase that produces mRNA free of immunostimulatory byproducts

A Dousis, K Ravichandran, EM Hobert, MJ Moore… - Nature …, 2023 - nature.com
In vitro transcription (IVT) is a DNA-templated process for synthesizing long RNA transcripts,
including messenger RNA (mRNA). For many research and commercial applications, IVT of …