A theoretical framework for proteome-scale single-molecule protein identification using multi-affinity protein binding reagents

JD Egertson, D DiPasquo, A Killeen, V Lobanov… - BioRxiv, 2021 - biorxiv.org
… However, no current method achieves both extremely high throughput and single-…
affinity reagent binding affinity. Proteome coverage was assessed as described in Calculation

Predicting protein function and orientation on a gold nanoparticle surface using a residue-based affinity scale

JX Xu, MS Alom, R Yadav, NC Fitzkee - Nature Communications, 2022 - nature.com
… The model developed here enables high-throughput predictions … for the binding affinity of a
residue, calculated by multiplying the … To visualize regions of high binding affinity, a protein is …

High-throughput virtual screening of small molecule inhibitors for SARS-CoV-2 protein targets with deep fusion models

GA Stevenson, D Jones, H Kim, WFD Bennett… - Proceedings of the …, 2021 - dl.acm.org
Binding affinity data in this study is measured as an inhibitory … as equivalent labels in our
calculations. Late Fusion takes … distributed architecture for faulttolerant scoring at scale. Using …

Fast, accurate, and reliable protocols for routine calculations of protein–ligand binding affinities in drug design projects using AMBER GPU-TI with ff14SB/GAFF

X He, S Liu, TS Lee, B Ji, VH Man, DM York… - ACS omega, 2020 - ACS Publications
… of the protein–ligand binding affinities becomes a primary task … to be suitable for high-throughput
screening of potentially … kcal/mol after a large-scale validation of 8 proteins and 200 …

Computational studies of protein–drug binding affinity changes upon mutations in the drug target

R Friedman - Wiley Interdisciplinary Reviews: Computational …, 2022 - Wiley Online Library
… DSF can be used for high-throughput screening, but the use of complementary … ) calculations
generally scale as N 3 where N is the number of basis functions that are used, MP2 scales

Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction

S Wan, AP Bhati, SJ Zasada… - Interface …, 2020 - royalsocietypublishing.org
… (MD) and the associated extreme sensitivity of trajectories to … binding affinity predictions need
to be made on time scales … them up for high-throughput free energy calculations, while pmx …

How to measure and evaluate binding affinities

I Jarmoskaite, I AlSadhan, PP Vaidyanathan… - Elife, 2020 - elifesciences.org
… Given the advances in high-throughput technologies and the … intuition for the time scales of
binding processes and we then … apparent affinity (determined by fitting the data to Equation 4b…

Expanding the boundaries of ligand–target modeling by exascale calculations

V Bolnykh, G Rossetti, U Rothlisberger… - Wiley Interdisciplinary …, 2021 - Wiley Online Library
… as a full-scale experimental High Throughput Screening (HTS). … heterogeneous system
with extreme possible hardware … such as binding affinities can be calculated and proper …

Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning

HT Rube, C Rastogi, S Feng, JF Kribelbauer, A Li… - Nature …, 2022 - nature.com
… are increasingly profiled at high throughput using affinity selection and … effects to determine
the absolute affinity scale. For Dll, the K D … equation under the assumption [P] F = [P] T , giving …

Drugsniffer: an open source workflow for virtually screening billions of molecules for binding affinity to protein targets

V Venkatraman, TH Colligan, GT Lesica… - Frontiers in …, 2022 - frontiersin.org
… While classical high-throughput screening methods may … designed to support distributed
computation on cluster and cloud … The AMIDE software carries out large-scale chemical ligand …